package_for_correction.py - move to SCT?

preprocess/package_for_correction.py

@@ -61,6 +61,11 @@ def get_parser():
         help="Zip file that contains the packaged data, without the extension. Default: data_to_correct",
         default='data_to_correct'
     )
+    parser.add_argument(
+        '-suffix-files-seg',
+        help="FILES-SEG suffix. For example _seg or _label-SC_mask",
+        default='_seg'
+    )
     parser.add_argument(
         '-v', '--verbose',
         help="Full verbose (for debugging)",
@@ -116,7 +121,7 @@ def main():
     for task, files in dict_yml.items():
         for file in files:
             if task == 'FILES_SEG':
-                suffix_label = '_seg'
+                suffix_label = args.suffix_files_seg		# e.g., _seg or _label-SC_mask
             elif task == 'FILES_LABEL':
                 suffix_label = None
             elif task == 'FILES_PMJ':

preprocess/utils.py

@@ -12,22 +12,30 @@
 from pathlib import Path
 from enum import Enum
 
+
 # BIDS utility tool
 def get_subject(file):
     """
     Get subject from BIDS file name
-    :param file:
-    :return: subject
+    :param file: input nifti filename (e.g., sub-001_ses-01_T1w.nii.gz) or file path
+    (e.g., /home/user/MRI/bids/derivatives/labels/sub-001/ses-01/anat/sub-001_ses-01_T1w.nii.gz
+    :return: subject_id: subject ID (e.g., sub-001)
     """
-    return file.split('_')[0]
+    subject = re.search('sub-(.*?)[_/]', file)                # [_/] slash or underscore
+    subject_id = subject.group(0)[:-1] if subject else ""    # [:-1] removes the last underscore or slash
+    return subject_id
+
 
 def get_ses(file):
     """
     Get session from BIDS file name
-    :param file:
-    :return: ses
+    :param file: input nifti filename (e.g., sub-001_ses-01_T1w.nii.gz) or file path
+    (e.g., /home/user/MRI/bids/derivatives/labels/sub-001/ses-01/anat/sub-001_ses-01_T1w.nii.gz
+    :return: sessionID: session ID (e.g., ses-01)
     """
-    return file.split('_')[1]
+    session = re.findall(r'ses-..', file)                   # .. - any two characters (e.g., ses-01 or ses-M0)
+    sessionID = session[0] if session else ""             # Return None if there is no session
+    return sessionID
 
 
 def get_contrast(file):