cfgs/generator/train/brain_id_synth.yaml

device_generator: 

split: train # NOTE: train or test

dataset_names: [] # NOTE: None for all, 'ADHD200' for age estimation
dataset_probs:
modality_probs: { 
  '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: 0.2 # blend synth with real images
dataset_option: brain_id
segment_prefix: brainseg_with_extracerebral

# setups for training/testing tasks 
task:
  T1: True
  T2: True
  FLAIR: True
  CT: True  # NOTE: turn off for photo_hemis setup
 
  segmentation: False
  distance: False 
  bias_field: False 
  registration: False

  # downstream
  super_resolution: False  
  age: False

  surface: False 
  pathology: False  
  contrastive: False


# setups for generator
generator:

  size: [160, 160, 160] # [128, 128, 128], [160, 160, 160]

  left_hemis_only: False # UNDER TESTING
  low_res_only: False # UNDER TESTING

  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: 0.05
  noise_std_max: 1.
  exvixo_prob: 0.25
  exvixo_prob_vs_photo: 0.66666666666666

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

  ct_prob: 0
  flip_prob: 0.5
  

  # brain-id customized setups

  # mild-to-severe intra-subject aug params
  mild_samples: 0 # 2
  all_samples: 1 # 4
  all_contrasts: 1 # 4 # >= 1, <= all_samples
  num_deformations: 1



# brain-id customized setups

mild_generator:   
  bag_prob: 0.1
  bag_scale_min: 0.01
  bag_scale_max: 0.02
  bf_scale_min: 0.01
  bf_scale_max: 0.02
  bf_std_min: 0.
  bf_std_max: 0.02
  gamma_std: 0.01
  noise_std_min: 0.
  noise_std_max: 0.02 


severe_generator:   
  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: 0.05 # 0.05 # 5
  noise_std_max: 1. # 0.15 # 15