Convert DICOM data to BIDS

.gitignore

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+.DS_Store

bids_conversion/config_file_ucd.txt

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+{
+    "descriptions": [
+        {
+            "dataType": "anat",
+            "modalityLabel": "T1w",
+            "criteria": {
+	        "SeriesDescription": "Sag T1 FLAIR",
+                "ProtocolName": "*PPCM*"
+            }
+        },
+        {
+            "dataType": "anat",
+            "modalityLabel": "T2w",
+            "criteria": {
+                "SeriesDescription": "Sag T2 frFSE",
+                "ProtocolName": "*PPCM*"
+            }
+        }
+    ]
+}

bids_conversion/curate_bids_ucd.py

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+###
+# Prerequirements:
+# dcm2bids
+# dcm2niix
+
+# How to use ?
+# python curate_bids_ucd.py -i PATH_TO_DATASET_TO_CONVERT -o OUTPUT_PATH -c PATH_TO_CONFIG_FILE
+
+import os
+import shutil
+import json
+import argparse
+
+
+def get_parameters():
+    parser = argparse.ArgumentParser(description='Convert dataset to BIDS format.')
+    parser.add_argument("-i", "--path-input",
+                        help="Path to folder containing the dataset to convert to BIDS",
+                        required=True)
+    parser.add_argument("-o", "--path-output",
+                        help="Path to the output BIDS folder",
+                        required=True,
+                        )
+    parser.add_argument("-c", "--path-config-file",
+                        help="Path to the config file for dcm2bids",
+                        required=True)
+    arguments = parser.parse_args()
+    return arguments
+
+
+def main(path_input, path_output, path_config_file):
+    if os.path.isdir(path_output):
+        shutil.rmtree(path_output)
+    os.makedirs(path_output, exist_ok=True)
+
+    for subject in os.listdir(path_input):
+        bids_subject_name = 'sub-' + subject
+        path_data_subject = os.path.join(path_input,subject)
+        command = 'dcm2bids -d ' + path_data_subject + ' -p ' + bids_subject_name + ' -c ' + path_config_file + ' -o ' + path_output
+        os.system(command)
+    shutil.rmtree(os.path.join(path_output,'tmp_dcm2bids'))
+    sub_list = os.listdir(path_output)
+    sub_list.sort()
+
+    import csv
+
+    participants = []
+    for subject in sub_list:
+        row_sub = []
+        row_sub.append(subject)
+        row_sub.append('n/a')
+        row_sub.append('n/a')
+        participants.append(row_sub)
+
+    print(participants)
+    with open(path_output + '/participants.tsv', 'w') as tsv_file:
+        tsv_writer = csv.writer(tsv_file, delimiter='\t', lineterminator='\n')
+        tsv_writer.writerow(["participant_id", "sex", "age"])
+        for item in participants:
+            tsv_writer.writerow(item)
+
+    # Create participants.json
+    data_json = {"participant_id": {
+        "Description": "Unique Participant ID",
+        "LongName": "Participant ID"
+        },
+        "sex": {
+            "Description": "M or F",
+            "LongName": "Participant sex"
+        },
+        "age": {
+            "Description": "yy",
+            "LongName": "Participant age"}
+    }
+
+    with open(path_output + '/participants.json', 'w') as json_file:
+        json.dump(data_json, json_file, indent=4)
+
+    # Create dataset_description.json
+    dataset_description = {"BIDSVersion": "BIDS 1.6.0",
+                           "Name": "sci-lesion-segmentation"
+                           }
+
+    with open(path_output + '/dataset_description.json', 'w') as json_file:
+        json.dump(dataset_description, json_file, indent=4)
+
+    # Create README
+    with open(path_output + '/README', 'w') as readme_file:
+        readme_file.write('Dataset for sct-pipeline/sci-lesion-segmentation.')
+
+
+if __name__ == "__main__":
+    args = get_parameters()
+    main(args.path_input, args.path_output, args.path_config_file)