settings.ini 2.15 KB
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[DATA]
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data_folder_name = "datasets"
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use_data_file = False
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data_directory = "/well/win-biobank/projects/imaging/data/data3/subjectsAll/"
data_file = "/well/win-biobank/projects/imaging/data/data3/subjectsAll/subj_22k.txt"
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k_fold = None
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data_split_flag = False
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test_percentage = 5
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subject_number = 12000
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train_list = "datasets/train.txt"
validation_list = "datasets/validation.txt"
test_list = "datasets/test.txt"
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scaling_factors = "datasets/scaling_factors.pkl"
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regression_weights = "datasets/regression_weights.pkl"
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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"
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brain_mask_path = "utils/MNI152_T1_2mm_brain_mask.nii.gz"
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rsfmri_mean_mask_path = "utils/mean_dr_stage2.nii.gz"
dmri_mean_mask_path = "utils/mean_tractsNormSummed_downsampled.nii.gz"
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mean_regression = False
mean_subtraction = True
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[TRAINING]
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experiment_name = "VA2-1"
pre_trained_path = "saved_models/VA2-1.pth.tar"
final_model_output_file = "VA2-1.pth.tar"
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training_batch_size = 5
validation_batch_size = 5
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use_pre_trained = False
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learning_rate = 1e-5
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optimizer_beta = (0.9, 0.999)
optimizer_epsilon = 1e-8
optimizer_weigth_decay = 1e-5
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number_of_epochs = 10
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loss_log_period = 50
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learning_rate_scheduler_step_size = 5
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learning_rate_scheduler_gamma = 1e-1
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use_last_checkpoint = False
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[NETWORK]
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kernel_heigth = 3
kernel_width = 3
kernel_depth = 3
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kernel_classification = 7
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input_channels = 1
output_channels = 64
convolution_stride = 1
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dropout = 0
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pool_kernel_size = 3
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pool_stride = 2
up_mode = "upconv"
number_of_classes = 1

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