cfgs/generator/default.yaml

device_generator:

data_root: /autofs/vast/lemon/data_curated/brain_mris_QCed


split: train # train or test
split_root: /autofs/vast/lemon/temp_stuff/peirong/train_test_split
train_txt: /autofs/vast/lemon/temp_stuff/peirong/train_test_split/train.txt
test_txt: /autofs/vast/lemon/temp_stuff/peirong/train_test_split/test.txt


dataset_names: ['ADNI'] # list of datasets
dataset_probs: # [1.] 
modality_probs: { # default
  'ADHD200': {'T1': 0.5, 'T2': 0., 'FLAIR': 0., 'CT': 0., 'synth': 1.},
  'HCP': {'T1': 0.3333, 'T2': 0.6667, 'FLAIR': 0., 'CT': 0., 'synth': 1.},
  'AIBL': {'T1': 0.25, 'T2': 0.5, 'FLAIR': 0.75, 'CT': 0., 'synth': 1.},
  'OASIS3': {'T1': 0.25, 'T2': 0.5, 'FLAIR': 0., 'CT': 0.75, 'synth': 1.},
  'ADNI': {'T1': 0.5, 'T2': 0., 'FLAIR': 0., 'CT': 0., 'synth': 1.},
  'ADNI3': {'T1': 0.3333, 'T2': 0., 'FLAIR': 0.6667, 'CT': 0., 'synth': 1.},
  'ATLAS': {'T1': 0.5, 'T2': 0., 'FLAIR': 0., 'CT': 0., 'synth': 1.},
  'ISLES': {'T1': 0., 'T2': 0., 'FLAIR': 0.5, 'CT': 0., 'synth': 1.},

  # TODO
  'ABIDE': {'T1': 0.5, 'T2': 0., 'FLAIR': 0., 'CT': 0., 'synth': 1.},
  'Buckner40': {'T1': 0.5, 'T2': 0., 'FLAIR': 0., 'CT': 0., 'synth': 1.},
  'COBRE': {'T1': 0.5, 'T2': 0., 'FLAIR': 0., 'CT': 0., 'synth': 1.},
  'Chinese-HCP': {'T1': 0.5, 'T2': 0., 'FLAIR': 0., 'CT': 0., 'synth': 1.},
  'ISBI2015': {'T1': 0.5, 'T2': 0., 'FLAIR': 0., 'CT': 0., 'synth': 1.},
  'MCIC': {'T1': 0.5, 'T2': 0., 'FLAIR': 0., 'CT': 0., 'synth': 1.}, 
} 
mix_synth_prob: 0. # mix synth with real images
dataset_option: default # or brain_id
segment_prefix: brainseg_with_extracerebral


# setups for training/testing tasks 
task:
  T1: True
  T2: True
  FLAIR: True
  CT: True
 
  segmentation: True
  distance: True 
  bias_field: True
  registration: True

  super_resolution: False 
  surface: False 
  pathology: False 

  contrastive: False


# setups for augmentation functions to apply
augmentation_steps: {'synth': ['gamma', 'bias_field', 'resample', 'noise'], 'real': ['gamma', 'bias_field', 'resample', 'noise']} 


# setups for generator
generator:

  size: [128, 128, 128]

  photo_prob: 0.2
  max_rotation: 15
  max_shear: 0.2
  max_scaling: 0.2
  nonlin_scale_min: 0.03
  nonlin_scale_max: 0.06
  nonlin_std_max: 4
  bag_prob: 0.5
  bag_scale_min: 0.02
  bag_scale_max: 0.08
  bf_scale_min: 0.02
  bf_scale_max: 0.04
  bf_std_min: 0.1
  bf_std_max: 0.6
  gamma_std: 0.1
  noise_std_min: 5
  noise_std_max: 15
  exvixo_prob: 0.25
  exvixo_prob_vs_photo: 0.66666666666666


  pv: True
  random_shift: False
  deform_one_hots: False
  
  produce_surfaces: False
  bspline_zooming: False  
  n_steps_svf_integration: 8
  nonlinear_transform: True 

  left_hemis_only: False
  low_res_only: False
  ct_prob: 0
  flip_prob: 0.5
  
  pathology_prob: 0. # pathology_prob when synth
  random_shape_prob: 0. # initialize pathol shape from random noise (instead of existing shapes)
  augment_pathology: False 


synth_image_generator:     
  noise_std_min: 5.
  noise_std_max: 15. 
real_image_generator:     
  noise_std_min: 0.
  noise_std_max: 0.02 


pathology_shape_generator:
  perlin_res: [2, 2, 2] # shape must be a multiple of res
  mask_percentile_min: 85
  mask_percentile_max: 99.9
  integ_method: dopri5 # choices=['dopri5', 'adams', 'rk4', 'euler'] 
  bc: neumann # choices=['neumann', 'cauchy', 'dirichlet', 'source_neumann', 'dirichlet_neumann'] 
  V_multiplier: 500
  dt: 0.1
  max_nt: 10 # >= 2
  pathol_thres: 0.5
  pathol_tol: 0.0000001 # if pathol mean < tol, skip


### some constants

max_surf_distance: 3. # clamp at plus / minus this number (both the ground truth and the prediction)

## NEW VAST synth 
label_list_segmentation_brainseg_with_extracerebral: [0, 11, 12, 13, 16, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46,
                                   1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 17, 47, 49, 51, 53, 55,
                                   18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 48, 50, 52, 54, 56] 
n_neutral_labels_brainseg_with_extracerebral: 20

## synth
label_list_segmentation_with_csf: [0,14,15,16,24,77,85,   2, 3, 4, 7, 8, 10,11,12,13,17,18,26,28,   41,42,43,46,47,49,50,51,52,53,54,58,60] # 33
n_neutral_labels_with_csf: 7
label_list_segmentation_without_csf: [0,14,15,16,77,85,   2, 3, 4, 7, 8, 10,11,12,13,17,18,26,28,   41,42,43,46,47,49,50,51,52,53,54,58,60]
n_neutral_labels_without_csf: 6


## synth_hemi
# without cerebellum and brainstem
label_list_segmentation: [0, 2, 3, 4, 10, 11, 12, 13, 17, 18, 26, 28, 77]
n_neutral_labels: 6

# with cerebellum and brainstem  
label_list_segmentation_with_cb: [0, 2, 3, 4, 7, 8, 10, 11, 12, 13, 16, 17, 18, 26, 28, 77]