settings.ini

[DATA]
data_folder_name = "datasets"
use_data_file = False
data_directory = "/well/win-biobank/projects/imaging/data/data3/subjectsAll/"
data_file = "/well/win-biobank/projects/imaging/data/data3/subjectsAll/subj_22k.txt"
k_fold = None
data_split_flag = False
test_percentage = 5
subject_number = 600
train_list = "datasets/train.txt"
validation_list = "datasets/validation.txt"
test_list = "datasets/test.txt"
scaling_factors = "datasets/scaling_factors.pkl"
train_data_file = "dMRI/autoptx_preproc/tractsNormSummed.nii.gz"
train_output_targets = "fMRI/rfMRI_25.dr/dr_stage2.nii.gz"
validation_data_file = "dMRI/autoptx_preproc/tractsNormSummed.nii.gz"
validation_target_file = "fMRI/rfMRI_25.dr/dr_stage2.nii.gz"
brain_mask_path = "utils/MNI152_T1_2mm_brain_mask.nii.gz"
mean_mask_path = "utils/mean_dr_stage2.nii.gz"
mean_reduction = True

[TRAINING]
experiment_name = "CU3D17-3"
pre_trained_path = "saved_models/CU3D17-3.pth.tar"
final_model_output_file = "CU3D17-3.pth.tar"
training_batch_size = 3
validation_batch_size = 3
use_pre_trained = False
learning_rate = 1e-1
optimizer_beta = (0.9, 0.999)
optimizer_epsilon = 1e-8
optimizer_weigth_decay = 1e-5
number_of_epochs = 200
loss_log_period = 50
learning_rate_scheduler_step_size = 5
learning_rate_scheduler_gamma = 1e-1
use_last_checkpoint = False

[NETWORK]
kernel_heigth = 3
kernel_width = 3
kernel_depth = 3
; kernel_classification = 1
input_channels = 1
output_channels = 64
convolution_stride = 1
dropout = 0.2
; pool_kernel_size = 2
pool_stride = 2
up_mode = "upconv"
number_of_classes = 1
; ---> parameters for the ResNet CGAN
pool_kernel_size = 3
kernel_classification = 7


[MISC]
save_model_directory = "saved_models"
logs_directory = "logs"
checkpoint_directory = "checkpoints"
experiments_directory = "experiments"
device = 0

[EVALUATION]
trained_model_path = "saved_models/model.pth.tar"
data_directory = "/well/win-biobank/projects/imaging/data/data3/subjectsAll/"
data_file = "/dMRI/autoptx_preproc/tractsNormSummed.nii.gz"
output_targets = "/fMRI/rfMRI_25.dr/dr_stage2.nii.gz"
data_list = "test.txt"
orientation = "coronal"
saved_predictions_directory = "predictions"