Working MPRAGE conversion

bids_conversion.py

@@ -4,61 +4,25 @@
 path_in = '/Users/julien/code/rf-shimming-7t/RF_shimming_project_cleanupload/SubA'
 path_out = '/Users/julien/Desktop/rf_shimming_spinalcord/sub-02'
 
+# Create dictionary for shim type output
+shimtype_dict = {'noRFshim': 'CP', 'CVred': 'CVred'}
+
 # 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
+# Create output directory
+os.makedirs(path_out, exist_ok=True)
+os.makedirs(os.path.join(path_out, 'anat'), exist_ok=True)
+os.makedirs(os.path.join(path_out, 'fmap'), exist_ok=True)
 
-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)
+# Convert MPRAGE data
+# Get the absolute file name of the NIfTI and JSON files under the MPRAGE subfolder, that has the string "noRFshim" in it
+for shimtype in ['noRFshim', 'CVred']:
+    for ext in ['nii.gz', 'json']:
+        mprage_file = [os.path.join(path_in, 'MPRAGE', f) for f in os.listdir(os.path.join(path_in, 'MPRAGE')) if shimtype in f and f.endswith(ext)][0]
+        shutil.copy2(mprage_file, os.path.join(path_out, f'anat/sub-{subject}_acq-{shimtype_dict[shimtype]}_T1w.{ext}'))
 
-            os.makedirs(os.path.dirname(new_file_path), exist_ok=True)
+# Convert RF map data
 
-            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)
+