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- FCLp-subsc-FCLa-INSULA_left/name17-43-58_232/.hydra/config.yaml +182 -0
- FCLp-subsc-FCLa-INSULA_left/name17-43-58_232/logs/best_model_weights.pt +3 -0
- FCLp-subsc-FCLa-INSULA_left/name17-43-58_232/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt +3 -0
- FCLp-subsc-FCLa-INSULA_right/name17-47-16_166/.hydra/config.yaml +182 -0
- FCLp-subsc-FCLa-INSULA_right/name17-47-16_166/logs/best_model_weights.pt +3 -0
- FCLp-subsc-FCLa-INSULA_right/name17-47-16_166/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt +3 -0
- FCMpost-SpC_left/name06-21-10_231/.hydra/config.yaml +182 -0
- FCMpost-SpC_left/name06-21-10_231/logs/best_model_weights.pt +3 -0
- FCMpost-SpC_left/name06-21-10_231/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt +3 -0
- FCMpost-SpC_right/name06-34-24_229/.hydra/config.yaml +182 -0
- FCMpost-SpC_right/name06-34-24_229/logs/best_model_weights.pt +3 -0
- FCMpost-SpC_right/name06-34-24_229/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt +3 -0
- FColl-SRh_left/name06-43-43_210/.hydra/config.yaml +182 -0
- FColl-SRh_left/name06-43-43_210/logs/best_model_weights.pt +3 -0
- FColl-SRh_left/name06-43-43_210/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt +3 -0
- FColl-SRh_right/name06-56-15_113/.hydra/config.yaml +182 -0
- FColl-SRh_right/name06-56-15_113/logs/best_model_weights.pt +3 -0
- FColl-SRh_right/name06-56-15_113/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt +3 -0
- FIP-FIPPoCinf_left/name13-52-34_154/.hydra/config.yaml +182 -0
- FIP-FIPPoCinf_left/name13-52-34_154/logs/best_model_weights.pt +3 -0
- FIP-FIPPoCinf_left/name13-52-34_154/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt +3 -0
- FIP-FIPPoCinf_right/name13-52-34_184/.hydra/config.yaml +182 -0
- FIP-FIPPoCinf_right/name13-52-34_184/logs/best_model_weights.pt +3 -0
- FIP-FIPPoCinf_right/name13-52-34_184/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt +3 -0
- FPO-SCu-ScCal_left/name07-13-21_118/.hydra/config.yaml +182 -0
- FPO-SCu-ScCal_left/name07-13-21_118/logs/best_model_weights.pt +3 -0
- FPO-SCu-ScCal_left/name07-13-21_118/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt +3 -0
- FPO-SCu-ScCal_right/name07-15-26_174/.hydra/config.yaml +182 -0
- FPO-SCu-ScCal_right/name07-15-26_174/logs/best_model_weights.pt +3 -0
- FPO-SCu-ScCal_right/name07-15-26_174/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt +3 -0
- Lobule_parietal_sup_left/name07-23-04_36/.hydra/config.yaml +182 -0
- Lobule_parietal_sup_left/name07-23-04_36/logs/best_model_weights.pt +3 -0
- Lobule_parietal_sup_left/name07-23-04_36/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt +3 -0
- Lobule_parietal_sup_right/name07-24-01_193/.hydra/config.yaml +182 -0
- Lobule_parietal_sup_right/name07-24-01_193/logs/best_model_weights.pt +3 -0
- Lobule_parietal_sup_right/name07-24-01_193/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt +3 -0
- OCCIPITAL_left/name07-34-40_229/.hydra/config.yaml +182 -0
- OCCIPITAL_left/name07-34-40_229/logs/best_model_weights.pt +3 -0
- OCCIPITAL_left/name07-34-40_229/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt +3 -0
- OCCIPITAL_right/name07-38-28_182/.hydra/config.yaml +182 -0
- OCCIPITAL_right/name07-38-28_182/logs/best_model_weights.pt +3 -0
- OCCIPITAL_right/name07-38-28_182/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt +3 -0
- SC-SPeC_left/name22-16-47_177/.hydra/config.yaml +182 -0
- SC-SPeC_left/name22-16-47_177/logs/best_model_weights.pt +3 -0
- SC-SPeC_left/name22-16-47_177/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt +3 -0
- SC-SPeC_right/name06-17-00_24/.hydra/config.yaml +182 -0
- SC-SPeC_right/name06-17-00_24/logs/best_model_weights.pt +3 -0
- SC-SPeC_right/name06-17-00_24/logs/lightning_logs/version_0/checkpoints/epoch=79-step=104960.ckpt +3 -0
- SC-SPoC_left/name07-57-18_53/.hydra/config.yaml +182 -0
- SC-SPoC_left/name07-57-18_53/logs/best_model_weights.pt +3 -0
FCLp-subsc-FCLa-INSULA_left/name17-43-58_232/.hydra/config.yaml
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| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 20
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
+
- 128
|
| 111 |
+
length_projection_head: 3
|
| 112 |
+
ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
+
checking: false
|
| 131 |
+
seed: 1
|
| 132 |
+
partition:
|
| 133 |
+
- 0.99
|
| 134 |
+
- 0.01
|
| 135 |
+
nb_subjects: -1
|
| 136 |
+
random: false
|
| 137 |
+
random_state: 25
|
| 138 |
+
scheduler: false
|
| 139 |
+
step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
+
factor: 0.33
|
| 143 |
+
class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input
|
| 158 |
+
dataset:
|
| 159 |
+
FCLp-subsc-FCLa-INSULA_left:
|
| 160 |
+
dataset_name: FCLp-subsc-FCLa-INSULA_left
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Llabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Llabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Llabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Ldistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Ldistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Ldistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Lmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 35, 52, 51)
|
FCLp-subsc-FCLa-INSULA_left/name17-43-58_232/logs/best_model_weights.pt
ADDED
|
@@ -0,0 +1,3 @@
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|
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|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:a4993f3340b399fe74e20a60f2f9cc1216d600e68c6807ea0b16bdc30031ff0c
|
| 3 |
+
size 12332322
|
FCLp-subsc-FCLa-INSULA_left/name17-43-58_232/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:a8835ad6b440fe507f5c564adcb6f345359b9adeb71f70bac01ded14d8543d78
|
| 3 |
+
size 36962920
|
FCLp-subsc-FCLa-INSULA_right/name17-47-16_166/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 20
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
+
- 128
|
| 111 |
+
length_projection_head: 3
|
| 112 |
+
ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
+
checking: false
|
| 131 |
+
seed: 1
|
| 132 |
+
partition:
|
| 133 |
+
- 0.99
|
| 134 |
+
- 0.01
|
| 135 |
+
nb_subjects: -1
|
| 136 |
+
random: false
|
| 137 |
+
random_state: 25
|
| 138 |
+
scheduler: false
|
| 139 |
+
step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
+
factor: 0.33
|
| 143 |
+
class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input
|
| 158 |
+
dataset:
|
| 159 |
+
FCLp-subsc-FCLa-INSULA_right:
|
| 160 |
+
dataset_name: FCLp-subsc-FCLa-INSULA_right
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rlabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rlabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rlabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rdistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rdistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rdistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.L.p.-subsc.-F.C.L.a.-INSULA./mask/Rmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 37, 44, 51)
|
FCLp-subsc-FCLa-INSULA_right/name17-47-16_166/logs/best_model_weights.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:fcb9db07315e7659b61237313351c621bd23e83b89b3f1aa2046c0ffa2f2c55d
|
| 3 |
+
size 11758882
|
FCLp-subsc-FCLa-INSULA_right/name17-47-16_166/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:a6dc34eaa88b21df9917ad4b403d1e4392afa94497a8e725f3dec6d6be5a7ecf
|
| 3 |
+
size 35242600
|
FCMpost-SpC_left/name06-21-10_231/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
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|
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|
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|
|
|
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|
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|
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|
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|
|
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|
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|
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|
|
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|
|
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|
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|
|
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|
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|
|
|
|
|
|
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|
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|
|
|
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|
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|
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|
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|
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|
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|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 20
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
+
- 128
|
| 111 |
+
length_projection_head: 3
|
| 112 |
+
ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
+
checking: false
|
| 131 |
+
seed: 1
|
| 132 |
+
partition:
|
| 133 |
+
- 0.99
|
| 134 |
+
- 0.01
|
| 135 |
+
nb_subjects: -1
|
| 136 |
+
random: false
|
| 137 |
+
random_state: 25
|
| 138 |
+
scheduler: false
|
| 139 |
+
step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
+
factor: 0.33
|
| 143 |
+
class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input
|
| 158 |
+
dataset:
|
| 159 |
+
FCMpost-SpC_left:
|
| 160 |
+
dataset_name: FCMpost-SpC_left
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Llabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Llabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Llabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Ldistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Ldistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Ldistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Lmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 16, 45, 31)
|
FCMpost-SpC_left/name06-21-10_231/logs/best_model_weights.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:2c75ba8c647b28edcd9cbf3f8e23a518ad0f2f4612046f01df8c62a6dbf456fb
|
| 3 |
+
size 9104674
|
FCMpost-SpC_left/name06-21-10_231/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:37f8dae021bd3a958f44fc8c31cf73afc25bca3b59210cf798e56c04a0db76e3
|
| 3 |
+
size 27279976
|
FCMpost-SpC_right/name06-34-24_229/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
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|
| 51 |
+
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|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
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|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
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|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
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pretrained_model_path: null
|
| 95 |
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load_encoder_only: false
|
| 96 |
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load_convolutions_only: false
|
| 97 |
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freeze_loaded_layers: false
|
| 98 |
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freeze_bias: false
|
| 99 |
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freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
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converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 20
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
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proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
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- 128
|
| 110 |
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- 128
|
| 111 |
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length_projection_head: 3
|
| 112 |
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ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
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nb_epochs_per_weight_save: 10
|
| 122 |
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nb_steps_per_flush_logs: 1
|
| 123 |
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log_every_n_steps: 2
|
| 124 |
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early_stopping_patience: 30
|
| 125 |
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diff_auc_threshold: 0.4
|
| 126 |
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start_epoch: 0
|
| 127 |
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checkpoint_path: null
|
| 128 |
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analysis_path: null
|
| 129 |
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verbose: 1
|
| 130 |
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checking: false
|
| 131 |
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seed: 1
|
| 132 |
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partition:
|
| 133 |
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- 0.99
|
| 134 |
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- 0.01
|
| 135 |
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nb_subjects: -1
|
| 136 |
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random: false
|
| 137 |
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random_state: 25
|
| 138 |
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scheduler: false
|
| 139 |
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step_size: 10
|
| 140 |
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gamma: 1.0
|
| 141 |
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threshold_plateau: 0.1
|
| 142 |
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factor: 0.33
|
| 143 |
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class_weights:
|
| 144 |
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- 1.0
|
| 145 |
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- 1.0
|
| 146 |
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accumulate_grad_batches: 1
|
| 147 |
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multiregion_single_encoder: false
|
| 148 |
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multiple_projection_heads: false
|
| 149 |
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linear_in_backbone: true
|
| 150 |
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load_sparse: false
|
| 151 |
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save_views: true
|
| 152 |
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wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input
|
| 158 |
+
dataset:
|
| 159 |
+
FCMpost-SpC_right:
|
| 160 |
+
dataset_name: FCMpost-SpC_right
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rlabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rlabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rlabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rdistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rdistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rdistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.C.M.post.-S.p.C./mask/Rmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 17, 47, 31)
|
FCMpost-SpC_right/name06-34-24_229/logs/best_model_weights.pt
ADDED
|
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version https://git-lfs.github.com/spec/v1
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oid sha256:bfd7ff536f3ea8176a9925c7dbf5f5ce3f6e1492505584c81af2501ca11ff4bc
|
| 3 |
+
size 9497890
|
FCMpost-SpC_right/name06-34-24_229/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt
ADDED
|
@@ -0,0 +1,3 @@
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|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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|
| 3 |
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size 28459624
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FColl-SRh_left/name06-43-43_210/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
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foldlabel: false
|
| 7 |
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trimdepth: false
|
| 8 |
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uniform_trim: false
|
| 9 |
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binary_trim: true
|
| 10 |
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binary_proba_trim: 0.5
|
| 11 |
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max_distance: 100
|
| 12 |
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trimdepth_delta: 141
|
| 13 |
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proba_trimedges: 0.5
|
| 14 |
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proba_pepper_trimedges: 0.5
|
| 15 |
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proba_pepper_trimdepth: 1.0
|
| 16 |
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ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
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keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 20
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
+
- 128
|
| 111 |
+
length_projection_head: 3
|
| 112 |
+
ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
+
checking: false
|
| 131 |
+
seed: 1
|
| 132 |
+
partition:
|
| 133 |
+
- 0.99
|
| 134 |
+
- 0.01
|
| 135 |
+
nb_subjects: -1
|
| 136 |
+
random: false
|
| 137 |
+
random_state: 25
|
| 138 |
+
scheduler: false
|
| 139 |
+
step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
+
factor: 0.33
|
| 143 |
+
class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input
|
| 158 |
+
dataset:
|
| 159 |
+
FColl-SRh_left:
|
| 160 |
+
dataset_name: FColl-SRh_left
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Llabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Llabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Llabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Ldistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Ldistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Ldistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Lmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 29, 62, 36)
|
FColl-SRh_left/name06-43-43_210/logs/best_model_weights.pt
ADDED
|
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version https://git-lfs.github.com/spec/v1
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oid sha256:102b4d79e165a3a8a75fc6fc0e3647fbb6ed4fb29cf507ca5656ffa86bef2b59
|
| 3 |
+
size 10939682
|
FColl-SRh_left/name06-43-43_210/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt
ADDED
|
@@ -0,0 +1,3 @@
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|
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| 1 |
+
version https://git-lfs.github.com/spec/v1
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oid sha256:25fa018e8a5a155a8266f9c2b3ef62828af2dd3010056e70249d2f4cdd94b3a5
|
| 3 |
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size 32785000
|
FColl-SRh_right/name06-56-15_113/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 20
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
+
- 128
|
| 111 |
+
length_projection_head: 3
|
| 112 |
+
ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
+
checking: false
|
| 131 |
+
seed: 1
|
| 132 |
+
partition:
|
| 133 |
+
- 0.99
|
| 134 |
+
- 0.01
|
| 135 |
+
nb_subjects: -1
|
| 136 |
+
random: false
|
| 137 |
+
random_state: 25
|
| 138 |
+
scheduler: false
|
| 139 |
+
step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
+
factor: 0.33
|
| 143 |
+
class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input
|
| 158 |
+
dataset:
|
| 159 |
+
FColl-SRh_right:
|
| 160 |
+
dataset_name: FColl-SRh_right
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rlabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rlabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rlabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rdistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rdistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rdistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.Coll.-S.Rh./mask/Rmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 34, 62, 41)
|
FColl-SRh_right/name06-56-15_113/logs/best_model_weights.pt
ADDED
|
@@ -0,0 +1,3 @@
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|
|
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|
|
|
|
|
|
|
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|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:d34085a787a1434b2f3284652f0bdca5291f26c04555c14ce3e0a12c4b56e434
|
| 3 |
+
size 12250402
|
FColl-SRh_right/name06-56-15_113/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:1d6949adfbd1d3cc6609149d35ea43228e01a87663af1c3e8e22670caae0817b
|
| 3 |
+
size 36717160
|
FIP-FIPPoCinf_left/name13-52-34_154/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 40
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
+
- 128
|
| 111 |
+
length_projection_head: 3
|
| 112 |
+
ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
+
checking: false
|
| 131 |
+
seed: 1
|
| 132 |
+
partition:
|
| 133 |
+
- 0.99
|
| 134 |
+
- 0.01
|
| 135 |
+
nb_subjects: -1
|
| 136 |
+
random: false
|
| 137 |
+
random_state: 25
|
| 138 |
+
scheduler: false
|
| 139 |
+
step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
+
factor: 0.33
|
| 143 |
+
class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Input
|
| 158 |
+
dataset:
|
| 159 |
+
FIP-FIPPoCinf_left:
|
| 160 |
+
dataset_name: FIP-FIPPoCinf_left
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Llabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Llabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Llabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Ldistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Ldistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Ldistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Lmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 41, 53, 44)
|
FIP-FIPPoCinf_left/name13-52-34_154/logs/best_model_weights.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:906a4b197b3bedd5dd2350ac937569c8a85283d538e952c110bf641e4aff8d9d
|
| 3 |
+
size 12447010
|
FIP-FIPPoCinf_left/name13-52-34_154/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:5d1a5598da9d9c248aac80f4db93e8a8a1f0a3205778d6b1b92e4a798577ee7f
|
| 3 |
+
size 37306984
|
FIP-FIPPoCinf_right/name13-52-34_184/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
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|
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|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 40
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
+
- 128
|
| 111 |
+
length_projection_head: 3
|
| 112 |
+
ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
+
checking: false
|
| 131 |
+
seed: 1
|
| 132 |
+
partition:
|
| 133 |
+
- 0.99
|
| 134 |
+
- 0.01
|
| 135 |
+
nb_subjects: -1
|
| 136 |
+
random: false
|
| 137 |
+
random_state: 25
|
| 138 |
+
scheduler: false
|
| 139 |
+
step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
+
factor: 0.33
|
| 143 |
+
class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Input
|
| 158 |
+
dataset:
|
| 159 |
+
FIP-FIPPoCinf_right:
|
| 160 |
+
dataset_name: FIP-FIPPoCinf_right
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rlabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rlabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rlabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rdistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rdistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rdistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.I.P.-F.I.P.Po.C.inf./mask/Rmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 39, 54, 45)
|
FIP-FIPPoCinf_right/name13-52-34_184/logs/best_model_weights.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:7a437af430af84fb7f1338e39214821410e39cd705ac78034c131ae5157eaf80
|
| 3 |
+
size 11758882
|
FIP-FIPPoCinf_right/name13-52-34_184/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:77123a0bcccd705d1b413d9704bb99d004604c2301415202bf6b2d121a4ea4f1
|
| 3 |
+
size 35242600
|
FPO-SCu-ScCal_left/name07-13-21_118/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 20
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
+
- 128
|
| 111 |
+
length_projection_head: 3
|
| 112 |
+
ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
+
checking: false
|
| 131 |
+
seed: 1
|
| 132 |
+
partition:
|
| 133 |
+
- 0.99
|
| 134 |
+
- 0.01
|
| 135 |
+
nb_subjects: -1
|
| 136 |
+
random: false
|
| 137 |
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random_state: 25
|
| 138 |
+
scheduler: false
|
| 139 |
+
step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
+
factor: 0.33
|
| 143 |
+
class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input
|
| 158 |
+
dataset:
|
| 159 |
+
FPO-SCu-ScCal_left:
|
| 160 |
+
dataset_name: FPO-SCu-ScCal_left
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Llabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Llabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Llabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Ldistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Ldistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Ldistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Lmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 25, 42, 54)
|
FPO-SCu-ScCal_left/name07-13-21_118/logs/best_model_weights.pt
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:6b71415873128c6a3dfc95efa4bcc09c0409dcf4fe520842748e2ed0bca90bae
|
| 3 |
+
size 11070754
|
FPO-SCu-ScCal_left/name07-13-21_118/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:c071e9088347b5fd534a1b5c8e91c893e8a33689740e571ae1669781d25d0396
|
| 3 |
+
size 33178216
|
FPO-SCu-ScCal_right/name07-15-26_174/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 20
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
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- 128
|
| 111 |
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length_projection_head: 3
|
| 112 |
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ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
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checking: false
|
| 131 |
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seed: 1
|
| 132 |
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partition:
|
| 133 |
+
- 0.99
|
| 134 |
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- 0.01
|
| 135 |
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nb_subjects: -1
|
| 136 |
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random: false
|
| 137 |
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random_state: 25
|
| 138 |
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scheduler: false
|
| 139 |
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step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
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factor: 0.33
|
| 143 |
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class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input
|
| 158 |
+
dataset:
|
| 159 |
+
FPO-SCu-ScCal_right:
|
| 160 |
+
dataset_name: FPO-SCu-ScCal_right
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rlabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rlabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rlabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rdistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rdistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rdistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/F.P.O.-S.Cu.-Sc.Cal./mask/Rmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 26, 42, 55)
|
FPO-SCu-ScCal_right/name07-15-26_174/logs/best_model_weights.pt
ADDED
|
@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:b85f175c304779a37aefc60c6caff60a042baa6d0e005b3b455b38fd6567be60
|
| 3 |
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size 11070754
|
FPO-SCu-ScCal_right/name07-15-26_174/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt
ADDED
|
@@ -0,0 +1,3 @@
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|
|
|
|
|
|
|
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|
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|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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oid sha256:2356123f4fc8e312fb0cabb2052785a2765fddd1021cce09d5264cfcb06a8c44
|
| 3 |
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size 33178216
|
Lobule_parietal_sup_left/name07-23-04_36/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 20
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
+
- 128
|
| 111 |
+
length_projection_head: 3
|
| 112 |
+
ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
+
checking: false
|
| 131 |
+
seed: 1
|
| 132 |
+
partition:
|
| 133 |
+
- 0.99
|
| 134 |
+
- 0.01
|
| 135 |
+
nb_subjects: -1
|
| 136 |
+
random: false
|
| 137 |
+
random_state: 25
|
| 138 |
+
scheduler: false
|
| 139 |
+
step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
+
factor: 0.33
|
| 143 |
+
class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input
|
| 158 |
+
dataset:
|
| 159 |
+
Lobule_parietal_sup_left:
|
| 160 |
+
dataset_name: Lobule_parietal_sup_left
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Llabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Llabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Llabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Ldistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Ldistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Ldistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Lmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 40, 47, 46)
|
Lobule_parietal_sup_left/name07-23-04_36/logs/best_model_weights.pt
ADDED
|
@@ -0,0 +1,3 @@
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|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:82908e349a4b72a4b09fb198d3edb1fd461dd7d7e6dc450771dcb742c39bffa1
|
| 3 |
+
size 11267362
|
Lobule_parietal_sup_left/name07-23-04_36/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:e00f3b8ee453f4020ceb658663c70a285cbfd0b7e6a03b1cd93d65201d3ac163
|
| 3 |
+
size 33768040
|
Lobule_parietal_sup_right/name07-24-01_193/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
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|
|
|
|
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|
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|
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|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
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|
|
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|
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|
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|
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|
|
|
|
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|
|
|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
|
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|
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|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 20
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
+
- 128
|
| 111 |
+
length_projection_head: 3
|
| 112 |
+
ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
+
checking: false
|
| 131 |
+
seed: 1
|
| 132 |
+
partition:
|
| 133 |
+
- 0.99
|
| 134 |
+
- 0.01
|
| 135 |
+
nb_subjects: -1
|
| 136 |
+
random: false
|
| 137 |
+
random_state: 25
|
| 138 |
+
scheduler: false
|
| 139 |
+
step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
+
factor: 0.33
|
| 143 |
+
class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input
|
| 158 |
+
dataset:
|
| 159 |
+
Lobule_parietal_sup_right:
|
| 160 |
+
dataset_name: Lobule_parietal_sup_right
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rlabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rlabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rlabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rdistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rdistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rdistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/Lobule_parietal_sup./mask/Rmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 41, 45, 48)
|
Lobule_parietal_sup_right/name07-24-01_193/logs/best_model_weights.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:9971cd017ab723102cdc613a6eb5ca83dc59cf1429adeeccb934ae7fdcd85e36
|
| 3 |
+
size 11857186
|
Lobule_parietal_sup_right/name07-24-01_193/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:28457007c58a10401b67ddd55d1f3e51388b24089c3721f1579d279a1d7ad265
|
| 3 |
+
size 35537512
|
OCCIPITAL_left/name07-34-40_229/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
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|
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|
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|
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|
|
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|
|
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|
|
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|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 20
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
+
- 128
|
| 111 |
+
length_projection_head: 3
|
| 112 |
+
ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
+
checking: false
|
| 131 |
+
seed: 1
|
| 132 |
+
partition:
|
| 133 |
+
- 0.99
|
| 134 |
+
- 0.01
|
| 135 |
+
nb_subjects: -1
|
| 136 |
+
random: false
|
| 137 |
+
random_state: 25
|
| 138 |
+
scheduler: false
|
| 139 |
+
step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
+
factor: 0.33
|
| 143 |
+
class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input
|
| 158 |
+
dataset:
|
| 159 |
+
OCCIPITAL_left:
|
| 160 |
+
dataset_name: OCCIPITAL_left
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Llabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Llabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Llabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Ldistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Ldistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Ldistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Lmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 35, 28, 42)
|
OCCIPITAL_left/name07-34-40_229/logs/best_model_weights.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:e16b6c7b41b5096c01ff7498f8c51e58102e325bc22942bc7479d3e4308fa772
|
| 3 |
+
size 10284322
|
OCCIPITAL_left/name07-34-40_229/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:f6989fc5e4bb61bff64d2a38bee88a07aff4cb553b992d5ea6da73760e9c78df
|
| 3 |
+
size 30818920
|
OCCIPITAL_right/name07-38-28_182/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 20
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
+
- 128
|
| 111 |
+
length_projection_head: 3
|
| 112 |
+
ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
+
checking: false
|
| 131 |
+
seed: 1
|
| 132 |
+
partition:
|
| 133 |
+
- 0.99
|
| 134 |
+
- 0.01
|
| 135 |
+
nb_subjects: -1
|
| 136 |
+
random: false
|
| 137 |
+
random_state: 25
|
| 138 |
+
scheduler: false
|
| 139 |
+
step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
+
factor: 0.33
|
| 143 |
+
class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input
|
| 158 |
+
dataset:
|
| 159 |
+
OCCIPITAL_right:
|
| 160 |
+
dataset_name: OCCIPITAL_right
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rlabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rlabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rlabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rdistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rdistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rdistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/OCCIPITAL/mask/Rmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 35, 30, 46)
|
OCCIPITAL_right/name07-38-28_182/logs/best_model_weights.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:76a45d0bcafe85c2307f17bf34b456104b91d19fe421bd62db287c3a08e3912c
|
| 3 |
+
size 10284322
|
OCCIPITAL_right/name07-38-28_182/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:f20fd7533568b37e7118940a5662b24ab62ac312de13c564af1470d49a637187
|
| 3 |
+
size 30818920
|
SC-SPeC_left/name22-16-47_177/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 40
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
+
- 128
|
| 111 |
+
length_projection_head: 3
|
| 112 |
+
ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
+
checking: false
|
| 131 |
+
seed: 1
|
| 132 |
+
partition:
|
| 133 |
+
- 0.99
|
| 134 |
+
- 0.01
|
| 135 |
+
nb_subjects: -1
|
| 136 |
+
random: false
|
| 137 |
+
random_state: 25
|
| 138 |
+
scheduler: false
|
| 139 |
+
step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
+
factor: 0.33
|
| 143 |
+
class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input
|
| 158 |
+
dataset:
|
| 159 |
+
SC-SPeC_left:
|
| 160 |
+
dataset_name: SC-SPeC_left
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Llabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Llabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Llabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Ldistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Ldistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Ldistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Lmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 38, 49, 52)
|
SC-SPeC_left/name22-16-47_177/logs/best_model_weights.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:6a9613c82cddff650dafbc6314ab838d6320a133af930c7dd3baa3120694d25d
|
| 3 |
+
size 12332322
|
SC-SPeC_left/name22-16-47_177/logs/lightning_logs/version_0/checkpoints/epoch=80-step=106272.ckpt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:3ca4ced710672f035084c34022e7d5b8ffd1c6baba42e399ec8d9fe87c57f46e
|
| 3 |
+
size 36962920
|
SC-SPeC_right/name06-17-00_24/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 40
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
+
- 128
|
| 111 |
+
length_projection_head: 3
|
| 112 |
+
ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
+
checking: false
|
| 131 |
+
seed: 1
|
| 132 |
+
partition:
|
| 133 |
+
- 0.99
|
| 134 |
+
- 0.01
|
| 135 |
+
nb_subjects: -1
|
| 136 |
+
random: false
|
| 137 |
+
random_state: 25
|
| 138 |
+
scheduler: false
|
| 139 |
+
step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
+
factor: 0.33
|
| 143 |
+
class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input
|
| 158 |
+
dataset:
|
| 159 |
+
SC-SPeC_right:
|
| 160 |
+
dataset_name: SC-SPeC_right
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rlabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rlabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rlabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rdistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rdistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rdistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Pe.C./mask/Rmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 42, 47, 51)
|
SC-SPeC_right/name06-17-00_24/logs/best_model_weights.pt
ADDED
|
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version https://git-lfs.github.com/spec/v1
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size 12447010
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SC-SPeC_right/name06-17-00_24/logs/lightning_logs/version_0/checkpoints/epoch=79-step=104960.ckpt
ADDED
|
@@ -0,0 +1,3 @@
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|
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|
| 1 |
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version https://git-lfs.github.com/spec/v1
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size 37306984
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SC-SPoC_left/name07-57-18_53/.hydra/config.yaml
ADDED
|
@@ -0,0 +1,182 @@
|
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|
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|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
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|
|
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|
|
|
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|
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|
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|
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|
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|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
|
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|
|
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|
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|
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|
|
|
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|
|
|
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|
|
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|
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|
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|
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|
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|
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|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
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|
|
|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
data: ${oc.dict.values:dataset}
|
| 2 |
+
datakey: ${oc.dict.keys:dataset}
|
| 3 |
+
apply_augmentations: true
|
| 4 |
+
random_choice: false
|
| 5 |
+
mixed: true
|
| 6 |
+
foldlabel: false
|
| 7 |
+
trimdepth: false
|
| 8 |
+
uniform_trim: false
|
| 9 |
+
binary_trim: true
|
| 10 |
+
binary_proba_trim: 0.5
|
| 11 |
+
max_distance: 100
|
| 12 |
+
trimdepth_delta: 141
|
| 13 |
+
proba_trimedges: 0.5
|
| 14 |
+
proba_pepper_trimedges: 0.5
|
| 15 |
+
proba_pepper_trimdepth: 1.0
|
| 16 |
+
ball_radius: 2
|
| 17 |
+
fill_value: 0
|
| 18 |
+
max_translation: 1
|
| 19 |
+
proba_translation: 1
|
| 20 |
+
keep_extremity: bottom
|
| 21 |
+
keep_extremity_trimdepth: top
|
| 22 |
+
patch_size_cutout:
|
| 23 |
+
- 5
|
| 24 |
+
- 30
|
| 25 |
+
patch_size_cutin:
|
| 26 |
+
- 20
|
| 27 |
+
- 90
|
| 28 |
+
keep_proba_per_branch_cutout: 0.5
|
| 29 |
+
keep_proba_global_cutout: 1.0
|
| 30 |
+
keep_proba_per_branch_cutin: 0.5
|
| 31 |
+
keep_proba_global_cutin: 1.0
|
| 32 |
+
mask_constraint: true
|
| 33 |
+
offset_proba_no_augm: 0.0
|
| 34 |
+
proba_trimdepth: 0.0
|
| 35 |
+
proba_trimextremities: 0.0
|
| 36 |
+
proba_cutout: 0.4
|
| 37 |
+
proba_cutin: 0.4
|
| 38 |
+
redefine_bottom: true
|
| 39 |
+
proba_contour: 0.0
|
| 40 |
+
proba_rotation: 1
|
| 41 |
+
max_angle: 18
|
| 42 |
+
backbone_name: convnet
|
| 43 |
+
encoder_depth: 3
|
| 44 |
+
filters:
|
| 45 |
+
- 32
|
| 46 |
+
- 64
|
| 47 |
+
- 128
|
| 48 |
+
initial_kernel_size: 7
|
| 49 |
+
initial_stride: 1
|
| 50 |
+
max_pool: false
|
| 51 |
+
block_depth: 4
|
| 52 |
+
backbone_output_size: 32
|
| 53 |
+
adaptive_pooling: null
|
| 54 |
+
projection_head_hidden_layers: null
|
| 55 |
+
classifier_name: svm
|
| 56 |
+
training_embeddings: /neurospin/dico/data/deep_folding/current/datasets/schiz/morphometry_statistics/F.C.M.ant/shape_embs.csv
|
| 57 |
+
results_save_path: null
|
| 58 |
+
labels_of_interest: null
|
| 59 |
+
class_max_epochs: 1000
|
| 60 |
+
n_repeat: 5
|
| 61 |
+
classifier_seed: 24
|
| 62 |
+
classifier_test_size: 0.2
|
| 63 |
+
model_path: /neurospin/dico/agaudin/Runs/04_pointnet/Output/2022-10-07/09-22-42_1
|
| 64 |
+
embeddings_save_path: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/embeddings
|
| 65 |
+
pca_Xfit: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/fit_Lskeleton.npy
|
| 66 |
+
pca_Xtransform: /neurospin/dico/data/deep_folding/current/datasets/schiz/crops/2mm/CINGULATE/mask/pca/transform_Lskeleton.npy
|
| 67 |
+
n_pca: 10
|
| 68 |
+
output_dir: /lustre/fswork/projects/rech/tgu/uic67me/Runs/Champollion/Output/all_regions/1_V1
|
| 69 |
+
sweep_day: ${now:%Y-%m-%d}
|
| 70 |
+
suffix_dir: ''
|
| 71 |
+
sweep_dir: ${output_dir}/${sweep_day}${suffix_dir}
|
| 72 |
+
run_time: ${now:%H-%M-%S}
|
| 73 |
+
checkpoint_dir: output_dir
|
| 74 |
+
label_names:
|
| 75 |
+
- Left_OFC
|
| 76 |
+
label_type: multiclass
|
| 77 |
+
nb_classes: 4
|
| 78 |
+
test: false
|
| 79 |
+
mode: encoder
|
| 80 |
+
contrastive_model: BarlowTwins
|
| 81 |
+
BT_correlation: cross
|
| 82 |
+
with_labels: false
|
| 83 |
+
proportion_pure_contrastive: 1.0
|
| 84 |
+
temperature_initial: 0.1
|
| 85 |
+
temperature: 0.1
|
| 86 |
+
temperature_supervised: 0.3
|
| 87 |
+
lambda_BT: 2.56
|
| 88 |
+
lambda_VR: 2.56
|
| 89 |
+
epsilon_VR: 0.001
|
| 90 |
+
model: SimCLR_fusion
|
| 91 |
+
sigma_labels: 2.0
|
| 92 |
+
sigma: 5
|
| 93 |
+
drop_rate: 0.05
|
| 94 |
+
pretrained_model_path: null
|
| 95 |
+
load_encoder_only: false
|
| 96 |
+
load_convolutions_only: false
|
| 97 |
+
freeze_loaded_layers: false
|
| 98 |
+
freeze_bias: false
|
| 99 |
+
freeze_encoders: false
|
| 100 |
+
fusioned_latent_space_size: -1
|
| 101 |
+
converter_activation: relu
|
| 102 |
+
device: cuda
|
| 103 |
+
num_cpu_workers: 20
|
| 104 |
+
environment: not_brainvisa
|
| 105 |
+
projection_head_name: relu
|
| 106 |
+
proj_layers_shapes:
|
| 107 |
+
- 32
|
| 108 |
+
- 128
|
| 109 |
+
- 128
|
| 110 |
+
- 128
|
| 111 |
+
length_projection_head: 3
|
| 112 |
+
ph_drop_rate: 0.0
|
| 113 |
+
batch_size: 32
|
| 114 |
+
pin_mem: true
|
| 115 |
+
lr: 0.0004
|
| 116 |
+
weight_decay: 5.0e-05
|
| 117 |
+
max_epochs: 81
|
| 118 |
+
nb_epochs_per_saving: 1
|
| 119 |
+
nb_epochs_per_tSNE: -1
|
| 120 |
+
nb_epochs_per_matrix_plot: 10
|
| 121 |
+
nb_epochs_per_weight_save: 10
|
| 122 |
+
nb_steps_per_flush_logs: 1
|
| 123 |
+
log_every_n_steps: 2
|
| 124 |
+
early_stopping_patience: 30
|
| 125 |
+
diff_auc_threshold: 0.4
|
| 126 |
+
start_epoch: 0
|
| 127 |
+
checkpoint_path: null
|
| 128 |
+
analysis_path: null
|
| 129 |
+
verbose: 1
|
| 130 |
+
checking: false
|
| 131 |
+
seed: 1
|
| 132 |
+
partition:
|
| 133 |
+
- 0.99
|
| 134 |
+
- 0.01
|
| 135 |
+
nb_subjects: -1
|
| 136 |
+
random: false
|
| 137 |
+
random_state: 25
|
| 138 |
+
scheduler: false
|
| 139 |
+
step_size: 10
|
| 140 |
+
gamma: 1.0
|
| 141 |
+
threshold_plateau: 0.1
|
| 142 |
+
factor: 0.33
|
| 143 |
+
class_weights:
|
| 144 |
+
- 1.0
|
| 145 |
+
- 1.0
|
| 146 |
+
accumulate_grad_batches: 1
|
| 147 |
+
multiregion_single_encoder: false
|
| 148 |
+
multiple_projection_heads: false
|
| 149 |
+
linear_in_backbone: true
|
| 150 |
+
load_sparse: false
|
| 151 |
+
save_views: true
|
| 152 |
+
wandb:
|
| 153 |
+
grid_search: false
|
| 154 |
+
entity: aymeric-gaudin
|
| 155 |
+
project: 2023_brain_regions_grid_searches
|
| 156 |
+
lambda_gs_crit: 2
|
| 157 |
+
dataset_folder: /lustre/fswork/projects/rech/tgu/umy22uu/Runs/70_self-supervised_two-regions/Input
|
| 158 |
+
dataset:
|
| 159 |
+
SC-SPoC_left:
|
| 160 |
+
dataset_name: SC-SPoC_left
|
| 161 |
+
pickle_normal: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lskeleton.pkl
|
| 162 |
+
numpy_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lskeleton.npy
|
| 163 |
+
subjects_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lskeleton_subject.csv
|
| 164 |
+
crop_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lcrops
|
| 165 |
+
foldlabel_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Llabels
|
| 166 |
+
foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Llabel.npy
|
| 167 |
+
subjects_foldlabel_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Llabel_subject.csv
|
| 168 |
+
distbottom_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Ldistbottom
|
| 169 |
+
distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Ldistbottom.npy
|
| 170 |
+
extremity_dir: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lextremities
|
| 171 |
+
extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lextremities.npy
|
| 172 |
+
subjects_extremity_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lextremities_subject.csv
|
| 173 |
+
subjects_distbottom_all: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Ldistbottom_subject.csv
|
| 174 |
+
crop_file_suffix: _cropped_skeleton.nii.gz
|
| 175 |
+
pickle_benchmark: null
|
| 176 |
+
train_val_csv_file: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lskeleton_subject.csv
|
| 177 |
+
subject_labels_file: ${dataset_folder}/UkBioBank40/participants_sex_age.csv
|
| 178 |
+
subject_column_name: Subject
|
| 179 |
+
cutout_mask_path: null
|
| 180 |
+
cutin_mask_path: ${dataset_folder}/UkBioBank40/crops/2mm/S.C.-S.Po.C./mask/Lmask.npy
|
| 181 |
+
flip_dataset: false
|
| 182 |
+
input_size: (1, 40, 44, 49)
|
SC-SPoC_left/name07-57-18_53/logs/best_model_weights.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:50d11fa3454e7600bc399ab5c76a7527010a3463d9257c5a46ffd31a5343be8a
|
| 3 |
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size 11758882
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