Added script to convert dataset to BIDS

bids_conversion.py

@@ -0,0 +1,64 @@
+import os
+import shutil
+
+path_in = '/Users/julien/code/rf-shimming-7t/RF_shimming_project_cleanupload/SubA'
+path_out = '/Users/julien/Desktop/rf_shimming_spinalcord/sub-02'
+
+# Get subject name from path_out
+subject = os.path.basename(path_out)
+
+# Convert MPRAGE data
+# Get the absolute file name of the MPRAGE file that has the string "noRFshim" in it
+mprage_file = [os.path.join(path_in, f) for f in os.listdir(path_in) if 'noRFshim' in f][0]
+# Copy the file to the output directory with the correct file name: sub-01_acq-CP_T1w.nii.gz
+shutil.copy2(mprage_file, os.path.join(path_out, f'{subject}_acq-CP_T1w.nii.gz'))
+
+
+
+
+
+def process_tfl_b1map(files):
+    sorted_files = sorted([f for f in files if 'tfl_b1map' in f])
+    processed_files = []
+    if len(sorted_files) >= 3:
+        # Append _part-mag before the file extension for the first file
+        name, ext = os.path.splitext(sorted_files[0])
+        processed_files.append(name + '_part-mag' + ext)
+        # Include the third file as is
+        processed_files.append(sorted_files[2])
+    return processed_files
+
+def process_gre2d(files):
+    sorted_files = sorted([f for f in files if 'gre2d' in f])
+    return sorted_files[:-1] if len(sorted_files) > 1 else sorted_files
+
+def create_bids_structure(base_dir, bids_dir):
+    for root, dirs, files in os.walk(base_dir):
+        # Filter out system files like .DS_Store
+        files = [f for f in files if not f.startswith('.')]
+
+        tfl_b1map_files = process_tfl_b1map(files)
+        gre2d_files = process_gre2d(files)
+
+        processed_files = tfl_b1map_files + gre2d_files + [f for f in files if 'tfl_b1map' not in f and 'gre2d' not in f]
+
+        for file in processed_files:
+            subject_id = '01'  # Modify this as per your dataset
+            category = 'fmap' if 'b1map' in file else 'anat'
+
+            new_file_name = f'sub-{subject_id}_{file}'
+            new_file_path = os.path.join(bids_dir, category, new_file_name)
+
+            os.makedirs(os.path.dirname(new_file_path), exist_ok=True)
+
+            original_file_path = os.path.join(root, file)
+            if os.path.exists(original_file_path):
+                shutil.copy2(original_file_path, new_file_path)
+                print(f'File {file} moved to {new_file_path}')
+            else:
+                print(f'Warning: File {original_file_path} not found. Skipping.')
+
+if __name__ == "__main__":
+    original_dir = '/Users/julien/code/rf-shimming-7t/RF_shimming_project_cleanupload/SubA'
+    bids_dir = '/Users/julien/Desktop/rf_shimming_spinalcord/sub-01bis'
+    create_bids_structure(original_dir, bids_dir)