Merge pull request #8 from sct-pipeline/jv/fix_folder_creation

Fix folder creation

file_loader.py

@@ -340,6 +340,14 @@ def write_participants_tsv(bids_folder, participant_id, session_id, source_id, a
         ])
         logging.info(f"Info: Added entry for {participant_id}/{session_id} to participants.tsv")
 
+def print_script_finished():
+    """
+    Print a message that the script has finished successfully.
+    """
+    logging.info(100 * "-")
+    logging.info(f'{os.path.abspath(__file__)} finished successfully.')
+    logging.info(100 * "-")
+
 
 def main():
     """
@@ -403,6 +411,7 @@ def main():
                 break
             elif user_input in ['n', 'no']:
                 logging.info("Skipping the DICOM to NIfTI conversion.")
+                print_script_finished()
                 return False
             else:
                 logging.info("Warning: Invalid input. Please enter 'yes' or 'no'.")
@@ -458,9 +467,7 @@ def main():
     source_id = os.path.basename(os.path.normpath(dicom_folder))
     write_participants_tsv(bids_folder, participant_id, session_id, source_id, args.age, args.sex)
 
-    logging.info(100 * "-")
-    logging.info(f'{os.path.abspath(__file__)} finished successfully.')
-    logging.info(100 * "-")
+    print_script_finished()
 
 
 if __name__ == "__main__":

process_data.sh

@@ -154,7 +154,10 @@ create_results_folder_and_copy_images()
     # Go to folder where data will be copied and processed
     cd "$results_folder"
     # Copy source images
-    cp -r "$bids_folder"/"$participant_id"/"$session_id" .
+    mkdir -p "$participant_id"
+    cp -r "$bids_folder/$participant_id/$session_id" "$participant_id/"
+    # Note: We need to create "$participant_id" first, to preserve the directory structure (e.g., sub-001/ses-01) when
+    # copying the files. Otherwise, only ses-01 folder would be copied to the results folder.
 }
 
 # Inspiration: https://github.com/spinalcordtoolbox/sct_tutorial_data/blob/master/multi_subject/process_data.sh#L66-L89