diff --git a/FCLp-subsc-FCLa-INSULA_left/name17-43-58_232/.hydra/config.yaml b/FCLp-subsc-FCLa-INSULA_left/name17-43-58_232/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..548593432922d73e328b9a30c55e1950383f9af2 --- /dev/null +++ b/FCLp-subsc-FCLa-INSULA_left/name17-43-58_232/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + FCLp-subsc-FCLa-INSULA_left: + dataset_name: FCLp-subsc-FCLa-INSULA_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lmask.npy + flip_dataset: false + input_size: (1, 35, 52, 51) diff --git a/FCLp-subsc-FCLa-INSULA_left/name17-43-58_232/logs/best_model_weights.pt b/FCLp-subsc-FCLa-INSULA_left/name17-43-58_232/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..0437a240f41e138a6fbe1edf59afffbf9079ad07 --- /dev/null +++ b/FCLp-subsc-FCLa-INSULA_left/name17-43-58_232/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a4993f3340b399fe74e20a60f2f9cc1216d600e68c6807ea0b16bdc30031ff0c +size 12332322 diff --git a/FCLp-subsc-FCLa-INSULA_left/name17-43-58_232/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/FCLp-subsc-FCLa-INSULA_left/name17-43-58_232/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..a11f391d3ce713c2a55920bfc49cf378a68aec09 --- /dev/null +++ b/FCLp-subsc-FCLa-INSULA_left/name17-43-58_232/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a8835ad6b440fe507f5c564adcb6f345359b9adeb71f70bac01ded14d8543d78 +size 36962920 diff --git a/FCLp-subsc-FCLa-INSULA_right/name17-47-16_166/.hydra/config.yaml b/FCLp-subsc-FCLa-INSULA_right/name17-47-16_166/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ebc5f60dc6e36bfb09e14338a094e772fcb9afa9 --- /dev/null +++ b/FCLp-subsc-FCLa-INSULA_right/name17-47-16_166/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + FCLp-subsc-FCLa-INSULA_right: + dataset_name: FCLp-subsc-FCLa-INSULA_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rmask.npy + flip_dataset: false + input_size: (1, 37, 44, 51) diff --git a/FCLp-subsc-FCLa-INSULA_right/name17-47-16_166/logs/best_model_weights.pt b/FCLp-subsc-FCLa-INSULA_right/name17-47-16_166/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..babe23b35328a714f3507628817d39a7d8285a53 --- /dev/null +++ b/FCLp-subsc-FCLa-INSULA_right/name17-47-16_166/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fcb9db07315e7659b61237313351c621bd23e83b89b3f1aa2046c0ffa2f2c55d +size 11758882 diff --git a/FCLp-subsc-FCLa-INSULA_right/name17-47-16_166/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/FCLp-subsc-FCLa-INSULA_right/name17-47-16_166/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..1d5cb4c325a8a7474262cd8937e03c12e604f230 --- /dev/null +++ b/FCLp-subsc-FCLa-INSULA_right/name17-47-16_166/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a6dc34eaa88b21df9917ad4b403d1e4392afa94497a8e725f3dec6d6be5a7ecf +size 35242600 diff --git a/FCMpost-SpC_left/name06-21-10_231/.hydra/config.yaml b/FCMpost-SpC_left/name06-21-10_231/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..fe535fef6493e7465e419104f4b30c2d0d16128a --- /dev/null +++ b/FCMpost-SpC_left/name06-21-10_231/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + FCMpost-SpC_left: + dataset_name: FCMpost-SpC_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lmask.npy + flip_dataset: false + input_size: (1, 16, 45, 31) diff --git a/FCMpost-SpC_left/name06-21-10_231/logs/best_model_weights.pt b/FCMpost-SpC_left/name06-21-10_231/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..ab0a827ff6cc1a18ad8dcbf7136ec4d9ebed2f94 --- /dev/null +++ b/FCMpost-SpC_left/name06-21-10_231/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2c75ba8c647b28edcd9cbf3f8e23a518ad0f2f4612046f01df8c62a6dbf456fb +size 9104674 diff --git a/FCMpost-SpC_left/name06-21-10_231/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/FCMpost-SpC_left/name06-21-10_231/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..2be7998d0b5e6047087e9937df0163c13a80318a --- /dev/null +++ b/FCMpost-SpC_left/name06-21-10_231/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:37f8dae021bd3a958f44fc8c31cf73afc25bca3b59210cf798e56c04a0db76e3 +size 27279976 diff --git a/FCMpost-SpC_right/name06-34-24_229/.hydra/config.yaml b/FCMpost-SpC_right/name06-34-24_229/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..bb913946f53431451585d5b820f52e3985dda4ee --- /dev/null +++ b/FCMpost-SpC_right/name06-34-24_229/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + FCMpost-SpC_right: + dataset_name: FCMpost-SpC_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rmask.npy + flip_dataset: false + input_size: (1, 17, 47, 31) diff --git a/FCMpost-SpC_right/name06-34-24_229/logs/best_model_weights.pt b/FCMpost-SpC_right/name06-34-24_229/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..52235d62cdb55f2198cbd3658f254894f43a19b0 --- /dev/null +++ b/FCMpost-SpC_right/name06-34-24_229/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bfd7ff536f3ea8176a9925c7dbf5f5ce3f6e1492505584c81af2501ca11ff4bc +size 9497890 diff --git a/FCMpost-SpC_right/name06-34-24_229/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/FCMpost-SpC_right/name06-34-24_229/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..8647605cc7ae434d28a6c7a4fe03e1316e91ac43 --- /dev/null +++ b/FCMpost-SpC_right/name06-34-24_229/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0d864e97dc055a4b0e0e0e75f3aeec7c4565ff5b7fceda88781d019798e8bfbd +size 28459624 diff --git a/FColl-SRh_left/name06-43-43_210/.hydra/config.yaml b/FColl-SRh_left/name06-43-43_210/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..e67a2360ea6dea242d13f18c005649559dc33d3a --- /dev/null +++ b/FColl-SRh_left/name06-43-43_210/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + FColl-SRh_left: + dataset_name: FColl-SRh_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lmask.npy + flip_dataset: false + input_size: (1, 29, 62, 36) diff --git a/FColl-SRh_left/name06-43-43_210/logs/best_model_weights.pt b/FColl-SRh_left/name06-43-43_210/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..cbf640258d7c9c13454d9ff59c62f1c740ae1e96 --- /dev/null +++ b/FColl-SRh_left/name06-43-43_210/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:102b4d79e165a3a8a75fc6fc0e3647fbb6ed4fb29cf507ca5656ffa86bef2b59 +size 10939682 diff --git a/FColl-SRh_left/name06-43-43_210/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/FColl-SRh_left/name06-43-43_210/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..dcb75d7674bca0ffd5ebabf1064a51eafb5f8814 --- /dev/null +++ b/FColl-SRh_left/name06-43-43_210/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:25fa018e8a5a155a8266f9c2b3ef62828af2dd3010056e70249d2f4cdd94b3a5 +size 32785000 diff --git a/FColl-SRh_right/name06-56-15_113/.hydra/config.yaml b/FColl-SRh_right/name06-56-15_113/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..f627b879b9fd7432404edb2ff35aaf628225db4f --- /dev/null +++ b/FColl-SRh_right/name06-56-15_113/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + FColl-SRh_right: + dataset_name: FColl-SRh_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rmask.npy + flip_dataset: false + input_size: (1, 34, 62, 41) diff --git a/FColl-SRh_right/name06-56-15_113/logs/best_model_weights.pt b/FColl-SRh_right/name06-56-15_113/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..2479a4a7bd361dff522bf95b9ca1e00d8c30aef6 --- /dev/null +++ b/FColl-SRh_right/name06-56-15_113/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d34085a787a1434b2f3284652f0bdca5291f26c04555c14ce3e0a12c4b56e434 +size 12250402 diff --git a/FColl-SRh_right/name06-56-15_113/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/FColl-SRh_right/name06-56-15_113/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..fda00dde8b8cd5bfd36816069175933b08f9c001 --- /dev/null +++ b/FColl-SRh_right/name06-56-15_113/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1d6949adfbd1d3cc6609149d35ea43228e01a87663af1c3e8e22670caae0817b +size 36717160 diff --git a/FIP-FIPPoCinf_left/name13-52-34_154/.hydra/config.yaml b/FIP-FIPPoCinf_left/name13-52-34_154/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..54c1c22113a9ce74fd28dc566074519ee4a0b12a --- /dev/null +++ b/FIP-FIPPoCinf_left/name13-52-34_154/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 40 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Input +dataset: + FIP-FIPPoCinf_left: + dataset_name: FIP-FIPPoCinf_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lmask.npy + flip_dataset: false + input_size: (1, 41, 53, 44) diff --git a/FIP-FIPPoCinf_left/name13-52-34_154/logs/best_model_weights.pt b/FIP-FIPPoCinf_left/name13-52-34_154/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..3becd3c569b35afade3ae2fc7371916b04705113 --- /dev/null +++ b/FIP-FIPPoCinf_left/name13-52-34_154/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:906a4b197b3bedd5dd2350ac937569c8a85283d538e952c110bf641e4aff8d9d +size 12447010 diff --git a/FIP-FIPPoCinf_left/name13-52-34_154/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/FIP-FIPPoCinf_left/name13-52-34_154/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..2d2a8ec07e4506fe344e37682aa533605af9c227 --- /dev/null +++ b/FIP-FIPPoCinf_left/name13-52-34_154/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5d1a5598da9d9c248aac80f4db93e8a8a1f0a3205778d6b1b92e4a798577ee7f +size 37306984 diff --git a/FIP-FIPPoCinf_right/name13-52-34_184/.hydra/config.yaml b/FIP-FIPPoCinf_right/name13-52-34_184/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..5336a6bdc795f609952ccac0f3dfab84e794f2f0 --- /dev/null +++ b/FIP-FIPPoCinf_right/name13-52-34_184/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 40 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Input +dataset: + FIP-FIPPoCinf_right: + dataset_name: FIP-FIPPoCinf_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rmask.npy + flip_dataset: false + input_size: (1, 39, 54, 45) diff --git a/FIP-FIPPoCinf_right/name13-52-34_184/logs/best_model_weights.pt b/FIP-FIPPoCinf_right/name13-52-34_184/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..41aa07d329e6f9534db92e8daab8d21a8cff932b --- /dev/null +++ b/FIP-FIPPoCinf_right/name13-52-34_184/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7a437af430af84fb7f1338e39214821410e39cd705ac78034c131ae5157eaf80 +size 11758882 diff --git a/FIP-FIPPoCinf_right/name13-52-34_184/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/FIP-FIPPoCinf_right/name13-52-34_184/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..07c4bf246481d850878b944ad0eaf5c5929cf55b --- /dev/null +++ b/FIP-FIPPoCinf_right/name13-52-34_184/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:77123a0bcccd705d1b413d9704bb99d004604c2301415202bf6b2d121a4ea4f1 +size 35242600 diff --git a/FPO-SCu-ScCal_left/name07-13-21_118/.hydra/config.yaml b/FPO-SCu-ScCal_left/name07-13-21_118/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..84779442377719be70a36520362881df21589d39 --- /dev/null +++ b/FPO-SCu-ScCal_left/name07-13-21_118/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + FPO-SCu-ScCal_left: + dataset_name: FPO-SCu-ScCal_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lmask.npy + flip_dataset: false + input_size: (1, 25, 42, 54) diff --git a/FPO-SCu-ScCal_left/name07-13-21_118/logs/best_model_weights.pt b/FPO-SCu-ScCal_left/name07-13-21_118/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..8aaca06009f1b35cf72c516a3f08cf9279325bbf --- /dev/null +++ b/FPO-SCu-ScCal_left/name07-13-21_118/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6b71415873128c6a3dfc95efa4bcc09c0409dcf4fe520842748e2ed0bca90bae +size 11070754 diff --git a/FPO-SCu-ScCal_left/name07-13-21_118/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/FPO-SCu-ScCal_left/name07-13-21_118/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..9b1b1d64cc8f932875658256e71ca6d80b607194 --- /dev/null +++ b/FPO-SCu-ScCal_left/name07-13-21_118/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c071e9088347b5fd534a1b5c8e91c893e8a33689740e571ae1669781d25d0396 +size 33178216 diff --git a/FPO-SCu-ScCal_right/name07-15-26_174/.hydra/config.yaml b/FPO-SCu-ScCal_right/name07-15-26_174/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..c92229eee15df2c8843fab398b484c0a9afbda36 --- /dev/null +++ b/FPO-SCu-ScCal_right/name07-15-26_174/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + FPO-SCu-ScCal_right: + dataset_name: FPO-SCu-ScCal_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rmask.npy + flip_dataset: false + input_size: (1, 26, 42, 55) diff --git a/FPO-SCu-ScCal_right/name07-15-26_174/logs/best_model_weights.pt b/FPO-SCu-ScCal_right/name07-15-26_174/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..a33a551f1e3567bc30a734cd016a24308c199bc2 --- /dev/null +++ b/FPO-SCu-ScCal_right/name07-15-26_174/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b85f175c304779a37aefc60c6caff60a042baa6d0e005b3b455b38fd6567be60 +size 11070754 diff --git a/FPO-SCu-ScCal_right/name07-15-26_174/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/FPO-SCu-ScCal_right/name07-15-26_174/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..85f212be96084224d35e1d3aa9125b1c500db14f --- /dev/null +++ b/FPO-SCu-ScCal_right/name07-15-26_174/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2356123f4fc8e312fb0cabb2052785a2765fddd1021cce09d5264cfcb06a8c44 +size 33178216 diff --git a/Lobule_parietal_sup_left/name07-23-04_36/.hydra/config.yaml b/Lobule_parietal_sup_left/name07-23-04_36/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..a54ecd512e8656e16bd016e6e85b491435fd536d --- /dev/null +++ b/Lobule_parietal_sup_left/name07-23-04_36/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + Lobule_parietal_sup_left: + dataset_name: Lobule_parietal_sup_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lmask.npy + flip_dataset: false + input_size: (1, 40, 47, 46) diff --git a/Lobule_parietal_sup_left/name07-23-04_36/logs/best_model_weights.pt b/Lobule_parietal_sup_left/name07-23-04_36/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..ba79dbda030eec914d190e16b8c86f0735c7939f --- /dev/null +++ b/Lobule_parietal_sup_left/name07-23-04_36/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:82908e349a4b72a4b09fb198d3edb1fd461dd7d7e6dc450771dcb742c39bffa1 +size 11267362 diff --git a/Lobule_parietal_sup_left/name07-23-04_36/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/Lobule_parietal_sup_left/name07-23-04_36/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..be39159cd938bb375e64054c2cf69cce847b170a --- /dev/null +++ b/Lobule_parietal_sup_left/name07-23-04_36/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e00f3b8ee453f4020ceb658663c70a285cbfd0b7e6a03b1cd93d65201d3ac163 +size 33768040 diff --git a/Lobule_parietal_sup_right/name07-24-01_193/.hydra/config.yaml b/Lobule_parietal_sup_right/name07-24-01_193/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..13e7ef97f659ccce9c71a965160a97c13ac1a437 --- /dev/null +++ b/Lobule_parietal_sup_right/name07-24-01_193/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + Lobule_parietal_sup_right: + dataset_name: Lobule_parietal_sup_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rmask.npy + flip_dataset: false + input_size: (1, 41, 45, 48) diff --git a/Lobule_parietal_sup_right/name07-24-01_193/logs/best_model_weights.pt b/Lobule_parietal_sup_right/name07-24-01_193/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..121c098addf157c15726a54f19c4e697bab34a91 --- /dev/null +++ b/Lobule_parietal_sup_right/name07-24-01_193/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9971cd017ab723102cdc613a6eb5ca83dc59cf1429adeeccb934ae7fdcd85e36 +size 11857186 diff --git a/Lobule_parietal_sup_right/name07-24-01_193/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/Lobule_parietal_sup_right/name07-24-01_193/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..1d9279e8d04f8ed404cfab635beecf0d958e35af --- /dev/null +++ b/Lobule_parietal_sup_right/name07-24-01_193/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:28457007c58a10401b67ddd55d1f3e51388b24089c3721f1579d279a1d7ad265 +size 35537512 diff --git a/OCCIPITAL_left/name07-34-40_229/.hydra/config.yaml b/OCCIPITAL_left/name07-34-40_229/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..7676507e7c993966f43dbc2e36ab374ca8b69139 --- /dev/null +++ b/OCCIPITAL_left/name07-34-40_229/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + OCCIPITAL_left: + dataset_name: OCCIPITAL_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lmask.npy + flip_dataset: false + input_size: (1, 35, 28, 42) diff --git a/OCCIPITAL_left/name07-34-40_229/logs/best_model_weights.pt b/OCCIPITAL_left/name07-34-40_229/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..a8c3c45d939023f4bfa514fc25656bf3b80119fe --- /dev/null +++ b/OCCIPITAL_left/name07-34-40_229/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e16b6c7b41b5096c01ff7498f8c51e58102e325bc22942bc7479d3e4308fa772 +size 10284322 diff --git a/OCCIPITAL_left/name07-34-40_229/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/OCCIPITAL_left/name07-34-40_229/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..4a6992ed98ae61e896607b3924fb3792a4011572 --- /dev/null +++ b/OCCIPITAL_left/name07-34-40_229/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f6989fc5e4bb61bff64d2a38bee88a07aff4cb553b992d5ea6da73760e9c78df +size 30818920 diff --git a/OCCIPITAL_right/name07-38-28_182/.hydra/config.yaml b/OCCIPITAL_right/name07-38-28_182/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..11bb93cd10f5897af771557317f8db293c5cd449 --- /dev/null +++ b/OCCIPITAL_right/name07-38-28_182/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + OCCIPITAL_right: + dataset_name: OCCIPITAL_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rmask.npy + flip_dataset: false + input_size: (1, 35, 30, 46) diff --git a/OCCIPITAL_right/name07-38-28_182/logs/best_model_weights.pt b/OCCIPITAL_right/name07-38-28_182/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..4b88e16b1823add89cbc5ae6e2407b099eacd404 --- /dev/null +++ b/OCCIPITAL_right/name07-38-28_182/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:76a45d0bcafe85c2307f17bf34b456104b91d19fe421bd62db287c3a08e3912c +size 10284322 diff --git a/OCCIPITAL_right/name07-38-28_182/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/OCCIPITAL_right/name07-38-28_182/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..06d1f551095c1bbcfe3227bc011a38d00b5ebcb0 --- /dev/null +++ b/OCCIPITAL_right/name07-38-28_182/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f20fd7533568b37e7118940a5662b24ab62ac312de13c564af1470d49a637187 +size 30818920 diff --git a/SC-SPeC_left/name22-16-47_177/.hydra/config.yaml b/SC-SPeC_left/name22-16-47_177/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..42945838e3a045680f093c9b1f284bdea4d044f7 --- /dev/null +++ b/SC-SPeC_left/name22-16-47_177/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 40 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SC-SPeC_left: + dataset_name: SC-SPeC_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lmask.npy + flip_dataset: false + input_size: (1, 38, 49, 52) diff --git a/SC-SPeC_left/name22-16-47_177/logs/best_model_weights.pt b/SC-SPeC_left/name22-16-47_177/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..32a9f5159d56528667a40c9d4d1cc8a16924a0da --- /dev/null +++ b/SC-SPeC_left/name22-16-47_177/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6a9613c82cddff650dafbc6314ab838d6320a133af930c7dd3baa3120694d25d +size 12332322 diff --git a/SC-SPeC_left/name22-16-47_177/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt 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+binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 40 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SC-SPeC_right: + dataset_name: SC-SPeC_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rmask.npy + flip_dataset: false + input_size: (1, 42, 47, 51) diff --git a/SC-SPeC_right/name06-17-00_24/logs/best_model_weights.pt b/SC-SPeC_right/name06-17-00_24/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..c03852a32c46d2320d04a7a16608ea0ed7dbbf90 --- /dev/null +++ b/SC-SPeC_right/name06-17-00_24/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ba5a2fabd8bcbc8c1142835e66c3afcead4f32c1b96cd5d7ff0671b3861a5bbe +size 12447010 diff --git a/SC-SPeC_right/name06-17-00_24/logs/lightning_logs/version_0/checkpoints/epoch=79-step=104960.ckpt b/SC-SPeC_right/name06-17-00_24/logs/lightning_logs/version_0/checkpoints/epoch=79-step=104960.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..56fef863fdb86b01649fbf038e3f2c9a4f0991e3 --- /dev/null +++ b/SC-SPeC_right/name06-17-00_24/logs/lightning_logs/version_0/checkpoints/epoch=79-step=104960.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:62a2bff176b48719620d6ce73e3689a03c404bd1d9a93ee039edd12d5cb8218f +size 37306984 diff --git a/SC-SPoC_left/name07-57-18_53/.hydra/config.yaml b/SC-SPoC_left/name07-57-18_53/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..3bee38f16a30347152249853bbbb5a644ee345b2 --- /dev/null +++ b/SC-SPoC_left/name07-57-18_53/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SC-SPoC_left: + dataset_name: SC-SPoC_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lmask.npy + flip_dataset: false + input_size: (1, 40, 44, 49) diff --git a/SC-SPoC_left/name07-57-18_53/logs/best_model_weights.pt b/SC-SPoC_left/name07-57-18_53/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..43d2c9544d64ad536552657454ba1133c6783065 --- /dev/null +++ b/SC-SPoC_left/name07-57-18_53/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:50d11fa3454e7600bc399ab5c76a7527010a3463d9257c5a46ffd31a5343be8a +size 11758882 diff --git a/SC-SPoC_left/name07-57-18_53/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SC-SPoC_left/name07-57-18_53/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..f69b80359d7071f9594ed3e82e444056ee710901 --- /dev/null +++ b/SC-SPoC_left/name07-57-18_53/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7f8a5f3c13ed62593de46ceb3e1e08de215d25f30e50f02a9eb0e0330e8f8b47 +size 35242600 diff --git a/SC-SPoC_right/name07-58-03_243/.hydra/config.yaml b/SC-SPoC_right/name07-58-03_243/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..444a5ba96626a62c34565f9c94e509a155d72460 --- /dev/null +++ b/SC-SPoC_right/name07-58-03_243/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SC-SPoC_right: + dataset_name: SC-SPoC_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Rmask.npy + flip_dataset: false + input_size: (1, 42, 43, 49) diff --git a/SC-SPoC_right/name07-58-03_243/logs/best_model_weights.pt b/SC-SPoC_right/name07-58-03_243/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..b6855c1d1c467eab3688b34cbb32b79cb29ba8ea --- /dev/null +++ b/SC-SPoC_right/name07-58-03_243/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version 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b/SC-sylv_left/name07-58-00_111/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SC-sylv_left: + dataset_name: SC-sylv_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Lmask.npy + flip_dataset: false + input_size: (1, 38, 36, 49) diff --git a/SC-sylv_left/name07-58-00_111/logs/best_model_weights.pt b/SC-sylv_left/name07-58-00_111/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..fac7e7130ef481b663a1e9c24603b20bccd1ef41 --- /dev/null +++ b/SC-sylv_left/name07-58-00_111/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8342fdc2d2bbfe3549b320324e364291a138ad034a51d93f345f8f7192a43526 +size 11185442 diff --git a/SC-sylv_left/name07-58-00_111/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SC-sylv_left/name07-58-00_111/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..4aee2af2b57c8493b9823bd11970dc4f9c3eb1e6 --- /dev/null +++ b/SC-sylv_left/name07-58-00_111/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:59dd7fa1090028d0e16cffda67f0f84138007e4011f6b5afdaec2bdc7efe5318 +size 33522280 diff --git a/SC-sylv_right/name06-17-02_84/.hydra/config.yaml b/SC-sylv_right/name06-17-02_84/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..a79c9b0e9484ae4981de542b28567c747c6f3905 --- /dev/null +++ b/SC-sylv_right/name06-17-02_84/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 40 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SC-sylv_right: + dataset_name: SC-sylv_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-sylv./mask/Rmask.npy + flip_dataset: false + input_size: (1, 42, 34, 49) diff --git a/SC-sylv_right/name06-17-02_84/logs/best_model_weights.pt b/SC-sylv_right/name06-17-02_84/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..ca080bae77b3adfa1b0edf3a54477dbe7f20fc6d --- /dev/null +++ b/SC-sylv_right/name06-17-02_84/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1955f24f22c84b0024b2998ecc2246eca95749e170ef0b5c5d82f94db454c94f +size 11758882 diff --git a/SC-sylv_right/name06-17-02_84/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SC-sylv_right/name06-17-02_84/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..cfe8e1b231adf6800ff0639fee4f8232dbd6529d --- /dev/null +++ b/SC-sylv_right/name06-17-02_84/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c174def06af630f8596b9033b9ecd2484bf0ae4ded201f87965fab4e2d873ca6 +size 35242600 diff --git a/SCall-SsP-SintraCing_left/name10-52-10_210/.hydra/config.yaml b/SCall-SsP-SintraCing_left/name10-52-10_210/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..0ba0c6b903cc63018fc100f0e8511b68449fbbb9 --- /dev/null +++ b/SCall-SsP-SintraCing_left/name10-52-10_210/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Input +dataset: + SCall-SsP-SintraCing_left: + dataset_name: SCall-SsP-SintraCing_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Lmask.npy + flip_dataset: false + input_size: (1, 18, 80, 46) diff --git a/SCall-SsP-SintraCing_left/name10-52-10_210/logs/best_model_weights.pt b/SCall-SsP-SintraCing_left/name10-52-10_210/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..f72d64145ea6d084d9099b1a60e6dc58a03fd6c1 --- /dev/null +++ b/SCall-SsP-SintraCing_left/name10-52-10_210/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:39eb2daf4adbdf1b19b66832f348301e3f2184546d114ffc6c23f82ed15a92c7 +size 11267362 diff --git a/SCall-SsP-SintraCing_left/name10-52-10_210/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SCall-SsP-SintraCing_left/name10-52-10_210/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..ec391850e0c4899f536266a99b2a381e2569cf38 --- /dev/null +++ b/SCall-SsP-SintraCing_left/name10-52-10_210/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1162a653d31f40b554296fad9e70867df672af80c3b3474bf9d5a7dad3914d68 +size 33768040 diff --git a/SCall-SsP-SintraCing_right/name18-49-13_26/.hydra/config.yaml b/SCall-SsP-SintraCing_right/name18-49-13_26/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..bc7c745800644f76e9c4874b911cd94a5b65e7ac --- /dev/null +++ b/SCall-SsP-SintraCing_right/name18-49-13_26/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 10 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Input +dataset: + SCall-SsP-SintraCing_right: + dataset_name: SCall-SsP-SintraCing_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call.-S.s.P.-S.intraCing./mask/Rmask.npy + flip_dataset: false + input_size: (1, 15, 63, 45) diff --git a/SCall-SsP-SintraCing_right/name18-49-13_26/logs/best_model_weights.pt b/SCall-SsP-SintraCing_right/name18-49-13_26/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..aaa445c992269e5785c6b8cc630bb5a1f6176431 --- /dev/null +++ b/SCall-SsP-SintraCing_right/name18-49-13_26/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c6e83cb5e583bb4d40456f6ad3acac6b5370ef9188a69b8a4e56ac494548b1eb +size 9891106 diff --git a/SCall-SsP-SintraCing_right/name18-49-13_26/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SCall-SsP-SintraCing_right/name18-49-13_26/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..74f6f9ba940caeb295af2d35520cd392ad4afa14 --- /dev/null +++ b/SCall-SsP-SintraCing_right/name18-49-13_26/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:94a6f03a54d4c9873ec95a1df1a6b5969554ff1b5752052af0b8ff658fb6c2f6 +size 29639272 diff --git a/SCall_left/name19-33-54_73/.hydra/config.yaml b/SCall_left/name19-33-54_73/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ca1a7189250304347501ac23f37e0f67c1e2277d --- /dev/null +++ b/SCall_left/name19-33-54_73/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: ../../../Output +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 10 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset: + SCall_left: + dataset_name: SCall_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Lmask.npy + flip_dataset: false + input_size: (1, 18, 52, 32) +dataset_folder: /neurospin/dico/data/deep_folding/current/datasets diff --git a/SCall_left/name19-33-54_73/logs/best_model_weights.pt b/SCall_left/name19-33-54_73/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..8eaa0cd3cab5a06d28fba270e6a10e3a2324881d --- /dev/null +++ b/SCall_left/name19-33-54_73/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:06965966cca3b06647a6e2506dd1d92d06fa72c2a69f3cbad5e71042fefd4f19 +size 9694498 diff --git a/SCall_left/name19-33-54_73/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SCall_left/name19-33-54_73/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..4925a7b3e33375ed1cb2c38319bdce97ca3f6590 --- /dev/null +++ b/SCall_left/name19-33-54_73/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0cb93c2c27eb33b8e18ecf1f516138f6abd661999798f5c7f634644a15d562bc +size 29049894 diff --git a/SCall_right/name09-24-24_37/.hydra/config.yaml b/SCall_right/name09-24-24_37/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..0320657b57b057ec16eb7deda4535c6aef96b5a8 --- /dev/null +++ b/SCall_right/name09-24-24_37/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: ../../../Output +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 10 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset: + SCall_right: + dataset_name: SCall_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.Call./mask/Rmask.npy + flip_dataset: false + input_size: (1, 15, 52, 34) +dataset_folder: /neurospin/dico/data/deep_folding/current/datasets diff --git a/SCall_right/name09-24-24_37/logs/best_model_weights.pt b/SCall_right/name09-24-24_37/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..f188d7849d0eae7d70774894dbd85e3e1dbc6eb9 --- /dev/null +++ b/SCall_right/name09-24-24_37/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e319ac29e86ccde7d836b5dfa19114a5622266b3da430ddecb5abd0c3b6a21d5 +size 9465122 diff --git a/SCall_right/name09-24-24_37/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SCall_right/name09-24-24_37/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..89f2b99539b632e828c56965dbbed64f23c8c4dd --- /dev/null +++ b/SCall_right/name09-24-24_37/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:749cf228a40e601889215c1f6f2d8884643eb19a8fdf2f9e1b91be5a1634599f +size 28361766 diff --git a/SFinf-BROCA-SPeCinf_left/name08-00-45_128/.hydra/config.yaml b/SFinf-BROCA-SPeCinf_left/name08-00-45_128/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..3cbc7071d0d6dec1859ec840635131a83727536c --- /dev/null +++ b/SFinf-BROCA-SPeCinf_left/name08-00-45_128/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SFinf-BROCA-SPeCinf_left: + dataset_name: SFinf-BROCA-SPeCinf_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Lmask.npy + flip_dataset: false + input_size: (1, 25, 41, 44) diff --git a/SFinf-BROCA-SPeCinf_left/name08-00-45_128/logs/best_model_weights.pt b/SFinf-BROCA-SPeCinf_left/name08-00-45_128/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..dabe63259ec5923accb31279846bb0ec77368de4 --- /dev/null +++ b/SFinf-BROCA-SPeCinf_left/name08-00-45_128/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2ce914f9ea24a1e85517334279bb2736592a57c64758862b13bdefac42dd1be5 +size 10677538 diff --git a/SFinf-BROCA-SPeCinf_left/name08-00-45_128/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SFinf-BROCA-SPeCinf_left/name08-00-45_128/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..163b629bc0e7e6df37a9f9e1bd29e36115032f27 --- /dev/null +++ b/SFinf-BROCA-SPeCinf_left/name08-00-45_128/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f10a66c929dd1444eb2410a50138229b95f94b2a452280afa2ec4c770e6782f7 +size 31998568 diff --git a/SFinf-BROCA-SPeCinf_right/name08-00-44_234/.hydra/config.yaml b/SFinf-BROCA-SPeCinf_right/name08-00-44_234/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..e1541c3881c18a79c125cbaa215785a03facd516 --- /dev/null +++ b/SFinf-BROCA-SPeCinf_right/name08-00-44_234/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SFinf-BROCA-SPeCinf_right: + dataset_name: SFinf-BROCA-SPeCinf_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inf.-BROCA-S.Pe.C.inf./mask/Rmask.npy + flip_dataset: false + input_size: (1, 26, 40, 43) diff --git a/SFinf-BROCA-SPeCinf_right/name08-00-44_234/logs/best_model_weights.pt b/SFinf-BROCA-SPeCinf_right/name08-00-44_234/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..158009f66748b3d8b08754695be21f0f3de35db0 --- /dev/null +++ b/SFinf-BROCA-SPeCinf_right/name08-00-44_234/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:585bf1d98605e3fa7fa755b54121b5a5bbce437bdd0a824084d5608feb4116e6 +size 10284322 diff --git a/SFinf-BROCA-SPeCinf_right/name08-00-44_234/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SFinf-BROCA-SPeCinf_right/name08-00-44_234/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..ae5fdd35c715bfcef8dbded129677abd0a25dac3 --- /dev/null +++ b/SFinf-BROCA-SPeCinf_right/name08-00-44_234/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:386586fdc8213704ef68a0eae3b15f8cbd2262aca6433119903993604ee21374 +size 30818920 diff --git a/SFint-FCMant_left/name08-09-20_81/.hydra/config.yaml b/SFint-FCMant_left/name08-09-20_81/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..03a90099235b084b6e2585b4830a3a8174b5621e --- /dev/null +++ b/SFint-FCMant_left/name08-09-20_81/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SFint-FCMant_left: + dataset_name: SFint-FCMant_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Lmask.npy + flip_dataset: false + input_size: (1, 16, 55, 52) diff --git a/SFint-FCMant_left/name08-09-20_81/logs/best_model_weights.pt b/SFint-FCMant_left/name08-09-20_81/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..7f45876885688ca2b2bd4e82a34d4fa6120081fc --- /dev/null +++ b/SFint-FCMant_left/name08-09-20_81/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6fc2b55ee96ff0c37f9b51267548f0f6a421966919640d2f798b6fa1c2c31c55 +size 9923874 diff --git a/SFint-FCMant_left/name08-09-20_81/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SFint-FCMant_left/name08-09-20_81/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..f4ab6417617225b7d8d87560c4df421fa8c5b52d --- /dev/null +++ b/SFint-FCMant_left/name08-09-20_81/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c501c18e0859c81daa7b3de9995ab50c342cc194276024f2a777dd36d737b5f9 +size 29737576 diff --git a/SFint-FCMant_right/name08-10-30_253/.hydra/config.yaml b/SFint-FCMant_right/name08-10-30_253/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..15d37d8d4a34208df96a8fe7d70d15d75ddf5ed5 --- /dev/null +++ b/SFint-FCMant_right/name08-10-30_253/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SFint-FCMant_right: + dataset_name: SFint-FCMant_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-F.C.M.ant./mask/Rmask.npy + flip_dataset: false + input_size: (1, 17, 57, 54) diff --git a/SFint-FCMant_right/name08-10-30_253/logs/best_model_weights.pt b/SFint-FCMant_right/name08-10-30_253/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..4474a5121920a55ec220053762fa7f0c0d0a7b54 --- /dev/null +++ b/SFint-FCMant_right/name08-10-30_253/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9f8cb1fcb5bb829a2662de8e766b237832746a46628d4c120397e8b190dd422f +size 11070754 diff --git a/SFint-FCMant_right/name08-10-30_253/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SFint-FCMant_right/name08-10-30_253/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..3d1c2fe986a9d89d862d270ee5b6fff8792b06af --- /dev/null +++ b/SFint-FCMant_right/name08-10-30_253/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1ffd3a1a3a08de1e6c9148c3b6f3cb3d120b97cec0d69cb9373ea0243f89897b +size 33178216 diff --git a/SFint-SR_left/name08-11-23_65/.hydra/config.yaml b/SFint-SR_left/name08-11-23_65/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..5a51c428dae4190bc05e088f2e884a2b26a06ebd --- /dev/null +++ b/SFint-SR_left/name08-11-23_65/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SFint-SR_left: + dataset_name: SFint-SR_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Lmask.npy + flip_dataset: false + input_size: (1, 16, 55, 58) diff --git a/SFint-SR_left/name08-11-23_65/logs/best_model_weights.pt b/SFint-SR_left/name08-11-23_65/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..86df2409c9d89093d43ab855e976592acfbdb50e --- /dev/null +++ b/SFint-SR_left/name08-11-23_65/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3cff00a41904fff424cefb4513bf7851decf850856b3c95d09998e3eedf9e90c +size 10153250 diff --git a/SFint-SR_left/name08-11-23_65/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SFint-SR_left/name08-11-23_65/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..053bbe2b6ad6ecd3bd2783f3a5ba108ff4d85905 --- /dev/null +++ b/SFint-SR_left/name08-11-23_65/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a6fac0af90750405dfb1cc7043ab54ff25e4a11abcacb5f41ae9b11cffe77102 +size 30425704 diff --git a/SFint-SR_right/name08-12-43_252/.hydra/config.yaml b/SFint-SR_right/name08-12-43_252/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2beca2ca5004b538d62517d9e53063da71d92d1b --- /dev/null +++ b/SFint-SR_right/name08-12-43_252/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SFint-SR_right: + dataset_name: SFint-SR_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.int.-S.R./mask/Rmask.npy + flip_dataset: false + input_size: (1, 17, 57, 59) diff --git a/SFint-SR_right/name08-12-43_252/logs/best_model_weights.pt b/SFint-SR_right/name08-12-43_252/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..31df0ab112f642aec9251ed54a6f5a0ec1861118 --- /dev/null +++ b/SFint-SR_right/name08-12-43_252/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2b8e18f488c4546467f1dc95e6e352385f54dce9d6cd110fa2d6243ab0175283 +size 11463970 diff --git a/SFint-SR_right/name08-12-43_252/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SFint-SR_right/name08-12-43_252/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..ea96e58ccded55011336a54b8b77e9337991f8fb --- /dev/null +++ b/SFint-SR_right/name08-12-43_252/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f1f5afe3bdea136a75e8e07b31d2033aad63a9bc37bdbfb114e219e7916bcf99 +size 34357864 diff --git a/SFinter-SFsup_left/name08-06-01_220/.hydra/config.yaml b/SFinter-SFsup_left/name08-06-01_220/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..66bdc50dc3f8a910b7e64cb9b157a05df360194b --- /dev/null +++ b/SFinter-SFsup_left/name08-06-01_220/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SFinter-SFsup_left: + dataset_name: SFinter-SFsup_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Lmask.npy + flip_dataset: false + input_size: (1, 30, 51, 50) diff --git a/SFinter-SFsup_left/name08-06-01_220/logs/best_model_weights.pt b/SFinter-SFsup_left/name08-06-01_220/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..857d8eebfc529e720dcb2b843f87d4766cb998d4 --- /dev/null +++ b/SFinter-SFsup_left/name08-06-01_220/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8a690b79aacb2c5e4a41d401356dd5a99dc4e4c1f097637c435357b2eda711bf +size 11529506 diff --git a/SFinter-SFsup_left/name08-06-01_220/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SFinter-SFsup_left/name08-06-01_220/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..e2c477ab15497479e529ff604b3b9a0603e01724 --- /dev/null +++ b/SFinter-SFsup_left/name08-06-01_220/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:599ee0a0bb2ae7e8e8b8005ce26bc75ede7a917b620c24b2797f3834109777d4 +size 34554472 diff --git a/SFinter-SFsup_right/name08-08-42_126/.hydra/config.yaml b/SFinter-SFsup_right/name08-08-42_126/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..09926a5543a27d160767bd555d0ea3aa659da307 --- /dev/null +++ b/SFinter-SFsup_right/name08-08-42_126/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SFinter-SFsup_right: + dataset_name: SFinter-SFsup_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.inter.-S.F.sup./mask/Rmask.npy + flip_dataset: false + input_size: (1, 31, 50, 53) diff --git a/SFinter-SFsup_right/name08-08-42_126/logs/best_model_weights.pt b/SFinter-SFsup_right/name08-08-42_126/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..98d0b03bf2514f9218974bbcf65bccca91e3c6d3 --- /dev/null +++ b/SFinter-SFsup_right/name08-08-42_126/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:edecfad2b0e03a0bcd414c0846eb68cb36837cc62e76e815272032acabf8c6e5 +size 11529506 diff --git a/SFinter-SFsup_right/name08-08-42_126/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SFinter-SFsup_right/name08-08-42_126/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..d7c946a9ff0ff12e84d2fd20e4e763b9b5446580 --- /dev/null +++ b/SFinter-SFsup_right/name08-08-42_126/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:309e155aea8dc8d5b72a3b6cdf3e5a40509a8693b3cee1efc26a7474c09c96f0 +size 34554472 diff --git a/SFmarginal-SFinfant_left/name08-15-17_25/.hydra/config.yaml b/SFmarginal-SFinfant_left/name08-15-17_25/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..92ee8f01441eed9a98f24b937ddd62c68d077854 --- /dev/null +++ b/SFmarginal-SFinfant_left/name08-15-17_25/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SFmarginal-SFinfant_left: + dataset_name: SFmarginal-SFinfant_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Lmask.npy + flip_dataset: false + input_size: (1, 34, 32, 39) diff --git a/SFmarginal-SFinfant_left/name08-15-17_25/logs/best_model_weights.pt b/SFmarginal-SFinfant_left/name08-15-17_25/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..eed4cd7dd0874f40642585b0c72879a9cf8a3e74 --- /dev/null +++ b/SFmarginal-SFinfant_left/name08-15-17_25/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d34121dd79dfa1fb8186c3e541c460d05ceede2f72f7b2440165fcf92bfdaf3b +size 9956642 diff --git a/SFmarginal-SFinfant_left/name08-15-17_25/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SFmarginal-SFinfant_left/name08-15-17_25/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..0b36eca4b5a3a2e4989526bf1ad3e16b8dcd0d1e --- /dev/null +++ b/SFmarginal-SFinfant_left/name08-15-17_25/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8a8e9c0f584058ab5126bb1b751eadaee04b4628cf6488340ca5889c5bad3456 +size 29835880 diff --git a/SFmarginal-SFinfant_right/name08-17-15_135/.hydra/config.yaml b/SFmarginal-SFinfant_right/name08-17-15_135/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..f489b106798129c6f07a37d331825118a9416d2b --- /dev/null +++ b/SFmarginal-SFinfant_right/name08-17-15_135/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SFmarginal-SFinfant_right: + dataset_name: SFmarginal-SFinfant_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.marginal-S.F.inf.ant./mask/Rmask.npy + flip_dataset: false + input_size: (1, 36, 32, 39) diff --git a/SFmarginal-SFinfant_right/name08-17-15_135/logs/best_model_weights.pt b/SFmarginal-SFinfant_right/name08-17-15_135/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..0cb62b26a393f6a00470269977f66dc5236a839f --- /dev/null +++ b/SFmarginal-SFinfant_right/name08-17-15_135/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6f6b28b262f5a5d7dca34426f4801415a6573d029de3ca73da9224bead320966 +size 9956642 diff --git a/SFmarginal-SFinfant_right/name08-17-15_135/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SFmarginal-SFinfant_right/name08-17-15_135/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..414eab755dfec1f30c3966f4e87a3ba72123832c --- /dev/null +++ b/SFmarginal-SFinfant_right/name08-17-15_135/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:41bbcac8039fbef8e680bc1d5b23ee8a9cc2513632036917ca97b3417c4dc4d3 +size 29835880 diff --git a/SFmedian-SFpoltr-SFsup_left/name06-17-02_114/.hydra/config.yaml b/SFmedian-SFpoltr-SFsup_left/name06-17-02_114/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..00ba771e75921c73b2fe054af1d668767f3ad21a --- /dev/null +++ b/SFmedian-SFpoltr-SFsup_left/name06-17-02_114/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 40 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SFmedian-SFpoltr-SFsup_left: + dataset_name: SFmedian-SFpoltr-SFsup_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Lmask.npy + flip_dataset: false + input_size: (1, 31, 54, 58) diff --git a/SFmedian-SFpoltr-SFsup_left/name06-17-02_114/logs/best_model_weights.pt b/SFmedian-SFpoltr-SFsup_left/name06-17-02_114/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..17d0a7555ffdd8d01d602e61fe090a160b739886 --- /dev/null +++ b/SFmedian-SFpoltr-SFsup_left/name06-17-02_114/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:55f8d897011653d2794838fceea58e23c659b68c4dffa116d0439cb1cf32871a +size 11988258 diff --git a/SFmedian-SFpoltr-SFsup_left/name06-17-02_114/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SFmedian-SFpoltr-SFsup_left/name06-17-02_114/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..de498072fc05fc67c39cd58b481ddf24f4766568 --- /dev/null +++ b/SFmedian-SFpoltr-SFsup_left/name06-17-02_114/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8c8abc329a1f972b11383683c1816129dcee5e1177729b2e3bfa56c34e09833e +size 35930728 diff --git a/SFmedian-SFpoltr-SFsup_right/name08-19-50_180/.hydra/config.yaml b/SFmedian-SFpoltr-SFsup_right/name08-19-50_180/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2e88fbbea90b60171116b725362bed8c2071c32e --- /dev/null +++ b/SFmedian-SFpoltr-SFsup_right/name08-19-50_180/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SFmedian-SFpoltr-SFsup_right: + dataset_name: SFmedian-SFpoltr-SFsup_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.F.median-S.F.pol.tr.-S.F.sup./mask/Rmask.npy + flip_dataset: false + input_size: (1, 30, 52, 55) diff --git a/SFmedian-SFpoltr-SFsup_right/name08-19-50_180/logs/best_model_weights.pt b/SFmedian-SFpoltr-SFsup_right/name08-19-50_180/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..7f846aee0c63941ea1deafb300e7679b21164cd2 --- /dev/null +++ b/SFmedian-SFpoltr-SFsup_right/name08-19-50_180/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9b1427fb7bb7bbfb734d2e76cf820be02500844f5f77da371a7ba3b6f27b18cd +size 11529506 diff --git a/SFmedian-SFpoltr-SFsup_right/name08-19-50_180/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SFmedian-SFpoltr-SFsup_right/name08-19-50_180/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..4cfbc6cac2395e4fbc75d88948096e52dcb59b43 --- /dev/null +++ b/SFmedian-SFpoltr-SFsup_right/name08-19-50_180/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:05d68ae5762d73fad7f58c68235baf344d3eb53ea04e2d7ec29249f46bf7fa44 +size 34554472 diff --git a/SOr-SOlf_left/name08-22-26_235/.hydra/config.yaml b/SOr-SOlf_left/name08-22-26_235/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ec150113160c92130f137a63f4bc494dde9e52ac --- /dev/null +++ b/SOr-SOlf_left/name08-22-26_235/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SOr-SOlf_left: + dataset_name: SOr-SOlf_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Lmask.npy + flip_dataset: false + input_size: (1, 31, 41, 23) diff --git a/SOr-SOlf_left/name08-22-26_235/logs/best_model_weights.pt b/SOr-SOlf_left/name08-22-26_235/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..9f2f478f92fef1c676b666b46391bbee3d6b8802 --- /dev/null +++ b/SOr-SOlf_left/name08-22-26_235/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f5fc9851e707d166f2c32ebcdcb922bec1b2e3912728e90cf743fc38e6f0eeee +size 9497890 diff --git a/SOr-SOlf_left/name08-22-26_235/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SOr-SOlf_left/name08-22-26_235/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..80f5655e9478a439653b8948fb6d1f2de47ca72a --- /dev/null +++ b/SOr-SOlf_left/name08-22-26_235/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:74ba79b54cb34e1b072bb94446feb63567fc2bb3298ec0af7ca927df2e175aac +size 28459624 diff --git a/SOr-SOlf_right/name08-22-27_80/.hydra/config.yaml b/SOr-SOlf_right/name08-22-27_80/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..29a4cd10def88df26c5fe9eba43d1c0292055590 --- /dev/null +++ b/SOr-SOlf_right/name08-22-27_80/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SOr-SOlf_right: + dataset_name: SOr-SOlf_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or.-S.Olf./mask/Rmask.npy + flip_dataset: false + input_size: (1, 31, 38, 24) diff --git a/SOr-SOlf_right/name08-22-27_80/logs/best_model_weights.pt b/SOr-SOlf_right/name08-22-27_80/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..f0f5926aa7fec5c4bd2b5bb61cdf76d5f5d3030c --- /dev/null +++ b/SOr-SOlf_right/name08-22-27_80/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:41d3ae08fbf60a0e8041efb2680af66c1d07b41719d1e4e7594544ef07e6a97e +size 9301282 diff --git a/SOr-SOlf_right/name08-22-27_80/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SOr-SOlf_right/name08-22-27_80/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..3eb21e7b00f9e4d22c3cba99a42a4688558cc011 --- /dev/null +++ b/SOr-SOlf_right/name08-22-27_80/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0c8387478e32d667da1dba4dd7c03ee588672bd23d6488a6aefbfc3f4d649ecc +size 27869800 diff --git a/SOr_left/name14-12-56_162/.hydra/config.yaml b/SOr_left/name14-12-56_162/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2759e7bd7d4b4205c44e9f09bb86397c4df37feb --- /dev/null +++ b/SOr_left/name14-12-56_162/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 40 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SOr_left: + dataset_name: SOr_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Lmask.npy + flip_dataset: false + input_size: (1, 30, 38, 22) diff --git a/SOr_left/name14-12-56_162/logs/best_model_weights.pt b/SOr_left/name14-12-56_162/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..93f3b0951db2bafb4a94f99716aca74998827a44 --- /dev/null +++ b/SOr_left/name14-12-56_162/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:960c83b8b32c993695141c6bb7015218d478f15f3743618d873d01b69a9e01d8 +size 9301282 diff --git a/SOr_left/name14-12-56_162/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SOr_left/name14-12-56_162/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..951fc7310d3f59ae24bca0f46215a2300594dc03 --- /dev/null +++ b/SOr_left/name14-12-56_162/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7333363696720a156debf145cafb7e8f4d2447b49a8202d4f67b8ef02565ae5f +size 27869800 diff --git a/SOr_right/name14-12-56_58/.hydra/config.yaml b/SOr_right/name14-12-56_58/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..c62ddae38891a380a22597f5cf8d40a3f643b86b --- /dev/null +++ b/SOr_right/name14-12-56_58/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 40 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SOr_right: + dataset_name: SOr_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.Or./mask/Rmask.npy + flip_dataset: false + input_size: (1, 26, 34, 23) diff --git a/SOr_right/name14-12-56_58/logs/best_model_weights.pt b/SOr_right/name14-12-56_58/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..c2a996321808cbec668db439f6e6205372b963f1 --- /dev/null +++ b/SOr_right/name14-12-56_58/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4e4005303fd53ca41bdc036627bf4464c0bb91f378bfb81b2f161c5c15815afd +size 9301282 diff --git a/SOr_right/name14-12-56_58/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SOr_right/name14-12-56_58/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..2c0e7f21df2156d12f2889d4f025cea7d36fc140 --- /dev/null +++ b/SOr_right/name14-12-56_58/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fbcf4a7bcadc2e7c9f5d8cd6e5839c4e50b9945ba5724ec8677b98c53b288750 +size 27869800 diff --git a/SPeC_left/name08-24-23_109/.hydra/config.yaml b/SPeC_left/name08-24-23_109/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..16693dd5c66c4317b045d50d4185cf745badc960 --- /dev/null +++ b/SPeC_left/name08-24-23_109/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SPeC_left: + dataset_name: SPeC_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Lmask.npy + flip_dataset: false + input_size: (1, 38, 41, 51) diff --git a/SPeC_left/name08-24-23_109/logs/best_model_weights.pt b/SPeC_left/name08-24-23_109/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..16ec7e763e4b87e35db1a0f8c08ba97e08ec2685 --- /dev/null +++ b/SPeC_left/name08-24-23_109/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:db9f33bcac12c4f0548ebdf6eedb6fab7f544dc187f51dd76594f48c67baa6f9 +size 11758882 diff --git a/SPeC_left/name08-24-23_109/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SPeC_left/name08-24-23_109/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..dfc07bb1b5e24cb57f29ec760a477da5de4f1ef3 --- /dev/null +++ b/SPeC_left/name08-24-23_109/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d44ed50a55d7da4f2bb95f18ba6984ccb03d267ea91faf653b6ffc9e6e73c324 +size 35242600 diff --git a/SPeC_right/name08-24-57_227/.hydra/config.yaml b/SPeC_right/name08-24-57_227/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..af8f48a85b27656907079e547db5e71497668c95 --- /dev/null +++ b/SPeC_right/name08-24-57_227/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SPeC_right: + dataset_name: SPeC_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.Pe.C./mask/Rmask.npy + flip_dataset: false + input_size: (1, 38, 40, 50) diff --git a/SPeC_right/name08-24-57_227/logs/best_model_weights.pt b/SPeC_right/name08-24-57_227/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..333b18a26f984354d74a386bea6c6f6cb644f130 --- /dev/null +++ b/SPeC_right/name08-24-57_227/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b4963d911e82a58df4b51f2816a5beda5bba5717d3e3a07f9fcb4ce09b8c300f +size 11185442 diff --git a/SPeC_right/name08-24-57_227/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SPeC_right/name08-24-57_227/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..26d328284ff5406ff1daca747b5a875c9fba0610 --- /dev/null +++ b/SPeC_right/name08-24-57_227/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a62509e4c95489fde245b675c3fd011cdf5d45df19a76c5f8b6641c7cc5729b8 +size 33522280 diff --git a/SPoC_left/name08-26-18_11/.hydra/config.yaml b/SPoC_left/name08-26-18_11/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..b85c7955d426a3eb6cd5cfb03509ae243a9aff89 --- /dev/null +++ b/SPoC_left/name08-26-18_11/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SPoC_left: + dataset_name: SPoC_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Lmask.npy + flip_dataset: false + input_size: (1, 40, 35, 43) diff --git a/SPoC_left/name08-26-18_11/logs/best_model_weights.pt b/SPoC_left/name08-26-18_11/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..c74e71823b7cec8c70dcadde1aba2cea6aa722be --- /dev/null +++ b/SPoC_left/name08-26-18_11/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7fe62182fef59a8846efd08c7629d0fc1592178c86fca76a03d9d031c8f5b2c4 +size 10775842 diff --git a/SPoC_left/name08-26-18_11/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SPoC_left/name08-26-18_11/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..da75abe135c6f1b0fbb7cb517a4b679f9e77f61f --- /dev/null +++ b/SPoC_left/name08-26-18_11/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c8c23b66af9ea755b93e203b443b933e7d561dcaf59097525855c99bb7d869d3 +size 32293480 diff --git a/SPoC_right/name08-28-01_155/.hydra/config.yaml b/SPoC_right/name08-28-01_155/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..188d05be4a1d295b0f4ed3d62e6608f3350a9242 --- /dev/null +++ b/SPoC_right/name08-28-01_155/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SPoC_right: + dataset_name: SPoC_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.Po.C./mask/Rmask.npy + flip_dataset: false + input_size: (1, 37, 37, 42) diff --git a/SPoC_right/name08-28-01_155/logs/best_model_weights.pt b/SPoC_right/name08-28-01_155/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..f230a0120de447a6fc54d1544b535d0f5607d03b --- /dev/null +++ b/SPoC_right/name08-28-01_155/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2af38dcce177f61b6835061073f58aed1dcadc4e4a3952dad4784f9d51cca0eb +size 10775842 diff --git a/SPoC_right/name08-28-01_155/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SPoC_right/name08-28-01_155/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..932947b4783a695a8086c01428be74fe7954dfeb --- /dev/null +++ b/SPoC_right/name08-28-01_155/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4a9956a80d17368e77b576b45d19caf48ec7e413d9b081c85aa5a9660c968bf2 +size 32293480 diff --git a/STi-SOTlat_left/name06-17-04_76/.hydra/config.yaml b/STi-SOTlat_left/name06-17-04_76/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..0282b59c0cb39cd93e2a679ef6f015fbbf8cd299 --- /dev/null +++ b/STi-SOTlat_left/name06-17-04_76/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 40 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + STi-SOTlat_left: + dataset_name: STi-SOTlat_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Lmask.npy + flip_dataset: false + input_size: (1, 34, 64, 53) diff --git a/STi-SOTlat_left/name06-17-04_76/logs/best_model_weights.pt b/STi-SOTlat_left/name06-17-04_76/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..bee663b220b937bc34f21fac9c9bd549d03e030c --- /dev/null +++ b/STi-SOTlat_left/name06-17-04_76/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:65439a62917d3694f26722ec213e2e1cf83b73d48c58395215c1c3a0c6c0a664 +size 12905762 diff --git a/STi-SOTlat_left/name06-17-04_76/logs/lightning_logs/version_0/checkpoints/epoch=71-step=94464.ckpt b/STi-SOTlat_left/name06-17-04_76/logs/lightning_logs/version_0/checkpoints/epoch=71-step=94464.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..f9f8faf87d1ca160296bb504de32ca1b0849bcd4 --- /dev/null +++ b/STi-SOTlat_left/name06-17-04_76/logs/lightning_logs/version_0/checkpoints/epoch=71-step=94464.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:865fde70b6cf26cd48f1deb08cd0f8e218770305f5660ab3df54ee2e7eb04186 +size 38683240 diff --git a/STi-SOTlat_right/name06-17-38_74/.hydra/config.yaml b/STi-SOTlat_right/name06-17-38_74/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..b08bc45be6a36f35dfecc156962751751e7813bb --- /dev/null +++ b/STi-SOTlat_right/name06-17-38_74/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 40 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + STi-SOTlat_right: + dataset_name: STi-SOTlat_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.O.T.lat./mask/Rmask.npy + flip_dataset: false + input_size: (1, 36, 59, 52) diff --git a/STi-SOTlat_right/name06-17-38_74/logs/best_model_weights.pt b/STi-SOTlat_right/name06-17-38_74/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..9212dd24a4d65d3afb8f38fb1827262492a250d5 --- /dev/null +++ b/STi-SOTlat_right/name06-17-38_74/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:54128e6c8dcaff68b941eb307f13206910170893c450b44e967678d2c20fdb0b +size 12905762 diff --git a/STi-SOTlat_right/name06-17-38_74/logs/lightning_logs/version_0/checkpoints/epoch=73-step=97088.ckpt b/STi-SOTlat_right/name06-17-38_74/logs/lightning_logs/version_0/checkpoints/epoch=73-step=97088.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..cbc964e5bd75f728f46ad0f754170942d89ae88f --- /dev/null +++ b/STi-SOTlat_right/name06-17-38_74/logs/lightning_logs/version_0/checkpoints/epoch=73-step=97088.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ca87f5ca46d88e2bb29062b45821b5661a3f7106f2524fcdf4806fa236ed9d8d +size 38683240 diff --git a/STi-STs-STpol_left/name06-17-41_148/.hydra/config.yaml b/STi-STs-STpol_left/name06-17-41_148/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..e6b62f671c02dfccdef3d6e8e3fb31b6211a8577 --- /dev/null +++ b/STi-STs-STpol_left/name06-17-41_148/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 40 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + STi-STs-STpol_left: + dataset_name: STi-STs-STpol_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Lmask.npy + flip_dataset: false + input_size: (1, 34, 67, 57) diff --git a/STi-STs-STpol_left/name06-17-41_148/logs/best_model_weights.pt b/STi-STs-STpol_left/name06-17-41_148/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..455c399156bc898e8168150ba60ed446b5702e71 --- /dev/null +++ b/STi-STs-STpol_left/name06-17-41_148/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fe5b3018d56510e32faba1cc576835ecd5c6f3dd3c973fa757d1a7ab9906c2aa +size 14216482 diff --git a/STi-STs-STpol_left/name06-17-41_148/logs/lightning_logs/version_0/checkpoints/epoch=61-step=81344.ckpt b/STi-STs-STpol_left/name06-17-41_148/logs/lightning_logs/version_0/checkpoints/epoch=61-step=81344.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..74d29579d000e232c238ffae56ba15fc8c3c9894 --- /dev/null +++ b/STi-STs-STpol_left/name06-17-41_148/logs/lightning_logs/version_0/checkpoints/epoch=61-step=81344.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1c21614eee6d034ec9af2a61b2791f0c2d1d66803508d1e67397d18b7f8aaa1c +size 42615400 diff --git a/STi-STs-STpol_right/name16-06-03_189/.hydra/config.yaml b/STi-STs-STpol_right/name16-06-03_189/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..7dbc683a3560d13f04626cf50a1618d96b9f7392 --- /dev/null +++ b/STi-STs-STpol_right/name16-06-03_189/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 40 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + STi-STs-STpol_right: + dataset_name: STi-STs-STpol_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.i.-S.T.s.-S.T.pol./mask/Rmask.npy + flip_dataset: false + input_size: (1, 33, 63, 56) diff --git a/STi-STs-STpol_right/name16-06-03_189/logs/best_model_weights.pt b/STi-STs-STpol_right/name16-06-03_189/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..d8e17dc64c9f9cf8383272810a24bb358cc7774f --- /dev/null +++ b/STi-STs-STpol_right/name16-06-03_189/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bf5ca4c14b0b1d9f774b08221d1dac5db69bc008121d926fd1151b683579c16c +size 12905762 diff --git a/STi-STs-STpol_right/name16-06-03_189/logs/lightning_logs/version_0/checkpoints/epoch=68-step=90528.ckpt b/STi-STs-STpol_right/name16-06-03_189/logs/lightning_logs/version_0/checkpoints/epoch=68-step=90528.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..20e50415cd642e2a30627f876654ab0f091b5002 --- /dev/null +++ b/STi-STs-STpol_right/name16-06-03_189/logs/lightning_logs/version_0/checkpoints/epoch=68-step=90528.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8900ddeda1ec5cd0158bc51467d3d2c4af2d2c02ab959d339214e85e9ba47fb0 +size 38683240 diff --git a/STs_left/name08-32-58_223/.hydra/config.yaml b/STs_left/name08-32-58_223/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..687e6a6db2e5ed9d784915a5156d92dbcb2c8ee1 --- /dev/null +++ b/STs_left/name08-32-58_223/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + STs_left: + dataset_name: STs_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Lmask.npy + flip_dataset: false + input_size: (1, 25, 55, 50) diff --git a/STs_left/name08-32-58_223/logs/best_model_weights.pt b/STs_left/name08-32-58_223/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..32adcda3064a87c1a59651f9e9afffcc4239b36e --- /dev/null +++ b/STs_left/name08-32-58_223/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d29dcc8e0156b4778309ca86db294578fb3a5f6ea0520036107e57e37596b4a6 +size 11529506 diff --git a/STs_left/name08-32-58_223/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/STs_left/name08-32-58_223/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..37b96fbad06db79a783eff129c5c498dd29759bf --- /dev/null +++ b/STs_left/name08-32-58_223/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cec81c37d589af94bd08a2dc673e3203f0b5768bff3235881012ecd4a877eb27 +size 34554472 diff --git a/STs_right/name08-32-58_52/.hydra/config.yaml b/STs_right/name08-32-58_52/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a6ee7cba4e0e2ed60f9eaa1d3b3299bd148bb4f --- /dev/null +++ b/STs_right/name08-32-58_52/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + STs_right: + dataset_name: STs_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s./mask/Rmask.npy + flip_dataset: false + input_size: (1, 24, 52, 51) diff --git a/STs_right/name08-32-58_52/logs/best_model_weights.pt b/STs_right/name08-32-58_52/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..7f1a90b90037d4a134d03a44a5519487b3509f22 --- /dev/null +++ b/STs_right/name08-32-58_52/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:40d594ae78027ed63748cbc042918a65a6c089385ec5a426155cd8451c8909b2 +size 10726690 diff --git a/STs_right/name08-32-58_52/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/STs_right/name08-32-58_52/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..e5abcc2fcc9bc876f597ec4b33ebb19b9c4fdb2b --- /dev/null +++ b/STs_right/name08-32-58_52/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a13ed33268f1db72c4281f0e7d64626f2dfe5ce23df5267591459ed0b4ffe32a +size 32146024 diff --git a/STsbr_left/name08-31-32_170/.hydra/config.yaml b/STsbr_left/name08-31-32_170/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..de9145e0f7337f681434a2777be8318d8dcb9e65 --- /dev/null +++ b/STsbr_left/name08-31-32_170/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + STsbr_left: + dataset_name: STsbr_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Lmask.npy + flip_dataset: false + input_size: (1, 29, 40, 41) diff --git a/STsbr_left/name08-31-32_170/logs/best_model_weights.pt b/STsbr_left/name08-31-32_170/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..e609bfe7f95066576471041577d33ae42c64a8ca --- /dev/null +++ b/STsbr_left/name08-31-32_170/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8c036aa752e25b18bcc0e0df2aa15e40f2e6d886f706bf8928b7093058246f6d +size 10284322 diff --git a/STsbr_left/name08-31-32_170/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/STsbr_left/name08-31-32_170/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..128d6b66d580325c9c14a18f86d0373127db253b --- /dev/null +++ b/STsbr_left/name08-31-32_170/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e06c906c8d9d799561656240a74c0b331614722f6a8a6fac9fa0ffff4ad1f9f6 +size 30818920 diff --git a/STsbr_right/name08-32-57_200/.hydra/config.yaml b/STsbr_right/name08-32-57_200/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..4048d320a0cf4afb4170745abeed7321009fac4e --- /dev/null +++ b/STsbr_right/name08-32-57_200/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + STsbr_right: + dataset_name: STsbr_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.T.s.br./mask/Rmask.npy + flip_dataset: false + input_size: (1, 28, 38, 42) diff --git a/STsbr_right/name08-32-57_200/logs/best_model_weights.pt b/STsbr_right/name08-32-57_200/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..c36365dc4fd5fe1942492d0c4353d9a3ad668599 --- /dev/null +++ b/STsbr_right/name08-32-57_200/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d0c8fd05fe8391185f8997faaf1508465ce04ca48c87c1b40e3a7367666151f0 +size 10284322 diff --git a/STsbr_right/name08-32-57_200/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/STsbr_right/name08-32-57_200/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..8dba2c6eff30838785a2b5db24e0ea4abf4ff516 --- /dev/null +++ b/STsbr_right/name08-32-57_200/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f125bd82ba0ade73354964f1f577ba4c389359d082352f76c2b293739599bd01 +size 30818920 diff --git a/ScCal-SLi_left/name07-41-43_180/.hydra/config.yaml b/ScCal-SLi_left/name07-41-43_180/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..47f254d5502705260c322a91360916702a18ff28 --- /dev/null +++ b/ScCal-SLi_left/name07-41-43_180/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + ScCal-SLi_left: + dataset_name: ScCal-SLi_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Lmask.npy + flip_dataset: false + input_size: (1, 25, 42, 36) diff --git a/ScCal-SLi_left/name07-41-43_180/logs/best_model_weights.pt b/ScCal-SLi_left/name07-41-43_180/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..a67fbed94b72b2ede21a4c7e86d6910223bc21e2 --- /dev/null +++ b/ScCal-SLi_left/name07-41-43_180/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ce4534c84f732b670b3a6448b5e154783dd7591f5d1f3e080a57e2ec59a3faad +size 10284322 diff --git a/ScCal-SLi_left/name07-41-43_180/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/ScCal-SLi_left/name07-41-43_180/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..192acb7639b6c4d72d31f2ee712d9e35f702a725 --- /dev/null +++ b/ScCal-SLi_left/name07-41-43_180/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:743c131cbdf162df05d5316da586c75d4ae0e0a9707b25941bda3f2d4b0bdc9d +size 30818920 diff --git a/ScCal-SLi_right/name07-54-42_78/.hydra/config.yaml b/ScCal-SLi_right/name07-54-42_78/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..9f5c126b854524ab901652343c72707375d180f7 --- /dev/null +++ b/ScCal-SLi_right/name07-54-42_78/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + ScCal-SLi_right: + dataset_name: ScCal-SLi_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/Sc.Cal.-S.Li./mask/Rmask.npy + flip_dataset: false + input_size: (1, 26, 42, 44) diff --git a/ScCal-SLi_right/name07-54-42_78/logs/best_model_weights.pt b/ScCal-SLi_right/name07-54-42_78/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..b7926086814952cd19a237dc93d76ca5dddc56d9 --- /dev/null +++ b/ScCal-SLi_right/name07-54-42_78/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:38c8a7a7d2a4f35d35c8088f28796eae4a03b32c59e4285757bb705e8d7b9624 +size 10677538 diff --git a/ScCal-SLi_right/name07-54-42_78/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/ScCal-SLi_right/name07-54-42_78/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..ef71ecd66eb6edc823e15631c1bb220a1dbe8445 --- /dev/null +++ b/ScCal-SLi_right/name07-54-42_78/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:638932d6f4b54e01e3526f7dbeced3485696b9e5bbbce45aa277256c774145df +size 31998568 diff --git a/SsP-SPaint_left/name08-28-13_26/.hydra/config.yaml b/SsP-SPaint_left/name08-28-13_26/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..58e4e128746a693d209e40bea54eb4c49b171f31 --- /dev/null +++ b/SsP-SPaint_left/name08-28-13_26/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SsP-SPaint_left: + dataset_name: SsP-SPaint_left + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Lskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Lskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Lskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Lcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Llabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Llabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Llabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Ldistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Ldistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Lextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Lextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Lextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Ldistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Lskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Lmask.npy + flip_dataset: false + input_size: (1, 27, 43, 56) diff --git a/SsP-SPaint_left/name08-28-13_26/logs/best_model_weights.pt b/SsP-SPaint_left/name08-28-13_26/logs/best_model_weights.pt new file mode 100644 index 0000000000000000000000000000000000000000..bde84aaee97f37dc1cf52af99b3b9d3bab8b2db8 --- /dev/null +++ b/SsP-SPaint_left/name08-28-13_26/logs/best_model_weights.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:69074260b15d98267b0450c24fe52bf1e50a3f416c10ac44899a2dfc6b6b7a43 +size 11070754 diff --git a/SsP-SPaint_left/name08-28-13_26/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt b/SsP-SPaint_left/name08-28-13_26/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt new file mode 100644 index 0000000000000000000000000000000000000000..0de384bebc0718016ad8ac2a6a1686da04e9f05e --- /dev/null +++ b/SsP-SPaint_left/name08-28-13_26/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:18d522fa1f8570e6c17c44798dfea45978ef6147d60f7ef62182f571adf686de +size 33178216 diff --git a/SsP-SPaint_right/name08-29-38_71/.hydra/config.yaml b/SsP-SPaint_right/name08-29-38_71/.hydra/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2340086b0009adf12551ae9c813ceacc32869cc4 --- /dev/null +++ b/SsP-SPaint_right/name08-29-38_71/.hydra/config.yaml @@ -0,0 +1,182 @@ +data: ${oc.dict.values:dataset} +datakey: ${oc.dict.keys:dataset} +apply_augmentations: true +random_choice: false +mixed: true +foldlabel: false +trimdepth: false +uniform_trim: false +binary_trim: true +binary_proba_trim: 0.5 +max_distance: 100 +trimdepth_delta: 141 +proba_trimedges: 0.5 +proba_pepper_trimedges: 0.5 +proba_pepper_trimdepth: 1.0 +ball_radius: 2 +fill_value: 0 +max_translation: 1 +proba_translation: 1 +keep_extremity: bottom +keep_extremity_trimdepth: top +patch_size_cutout: +- 5 +- 30 +patch_size_cutin: +- 20 +- 90 +keep_proba_per_branch_cutout: 0.5 +keep_proba_global_cutout: 1.0 +keep_proba_per_branch_cutin: 0.5 +keep_proba_global_cutin: 1.0 +mask_constraint: true +offset_proba_no_augm: 0.0 +proba_trimdepth: 0.0 +proba_trimextremities: 0.0 +proba_cutout: 0.4 +proba_cutin: 0.4 +redefine_bottom: true +proba_contour: 0.0 +proba_rotation: 1 +max_angle: 18 +backbone_name: convnet +encoder_depth: 3 +filters: +- 32 +- 64 +- 128 +initial_kernel_size: 7 +initial_stride: 1 +max_pool: false +block_depth: 4 +backbone_output_size: 32 +adaptive_pooling: null +projection_head_hidden_layers: null +classifier_name: svm +training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv +results_save_path: null +labels_of_interest: null +class_max_epochs: 1000 +n_repeat: 5 +classifier_seed: 24 +classifier_test_size: 0.2 +model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1 +embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings +pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy +pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy +n_pca: 10 +output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1 +sweep_day: ${now:%Y-%m-%d} +suffix_dir: '' +sweep_dir: ${output_dir}/${sweep_day}${suffix_dir} +run_time: ${now:%H-%M-%S} +checkpoint_dir: output_dir +label_names: +- Left_OFC +label_type: multiclass +nb_classes: 4 +test: false +mode: encoder +contrastive_model: BarlowTwins +BT_correlation: cross +with_labels: false +proportion_pure_contrastive: 1.0 +temperature_initial: 0.1 +temperature: 0.1 +temperature_supervised: 0.3 +lambda_BT: 2.56 +lambda_VR: 2.56 +epsilon_VR: 0.001 +model: SimCLR_fusion +sigma_labels: 2.0 +sigma: 5 +drop_rate: 0.05 +pretrained_model_path: null +load_encoder_only: false +load_convolutions_only: false +freeze_loaded_layers: false +freeze_bias: false +freeze_encoders: false +fusioned_latent_space_size: -1 +converter_activation: relu +device: cuda +num_cpu_workers: 20 +environment: not_brainvisa +projection_head_name: relu +proj_layers_shapes: +- 32 +- 128 +- 128 +- 128 +length_projection_head: 3 +ph_drop_rate: 0.0 +batch_size: 32 +pin_mem: true +lr: 0.0004 +weight_decay: 5.0e-05 +max_epochs: 81 +nb_epochs_per_saving: 1 +nb_epochs_per_tSNE: -1 +nb_epochs_per_matrix_plot: 10 +nb_epochs_per_weight_save: 10 +nb_steps_per_flush_logs: 1 +log_every_n_steps: 2 +early_stopping_patience: 30 +diff_auc_threshold: 0.4 +start_epoch: 0 +checkpoint_path: null +analysis_path: null +verbose: 1 +checking: false +seed: 1 +partition: +- 0.99 +- 0.01 +nb_subjects: -1 +random: false +random_state: 25 +scheduler: false +step_size: 10 +gamma: 1.0 +threshold_plateau: 0.1 +factor: 0.33 +class_weights: +- 1.0 +- 1.0 +accumulate_grad_batches: 1 +multiregion_single_encoder: false +multiple_projection_heads: false +linear_in_backbone: true +load_sparse: false +save_views: true +wandb: + grid_search: false + entity: aymeric-gaudin + project: 2023_brain_regions_grid_searches + lambda_gs_crit: 2 +dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input +dataset: + SsP-SPaint_right: + dataset_name: SsP-SPaint_right + pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Rskeleton.pkl + numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Rskeleton.npy + subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Rskeleton_subject.csv + crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Rcrops + foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Rlabels + foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Rlabel.npy + subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Rlabel_subject.csv + distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Rdistbottom + distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Rdistbottom.npy + extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Rextremities + extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Rextremities.npy + subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Rextremities_subject.csv + subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Rdistbottom_subject.csv + crop_file_suffix: _cropped_skeleton.nii.gz + pickle_benchmark: null + train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Rskeleton_subject.csv + subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv + subject_column_name: Subject + cutout_mask_path: null + cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.s.P.-S.Pa.int./mask/Rmask.npy + flip_dataset: false + input_size: (1, 23, 34, 43) diff --git 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