diff --git a/PyNutil/io/file_operations.py b/PyNutil/io/file_operations.py index b4be5b188d170d24525138ed57c0536528f4455a..5c0287437b27eaf67381b0de24cf597b411df70f 100644 --- a/PyNutil/io/file_operations.py +++ b/PyNutil/io/file_operations.py @@ -107,6 +107,28 @@ def save_analysis_output( "custom_region_path": custom_region_path, } + pixel_points, + centroids, + label_df, + per_section_df, + labeled_points, + labeled_points_centroids, + points_hemi_labels, + centroids_hemi_labels, + points_len, + centroids_len, + segmentation_filenames, + atlas_labels, + output_folder, + segmentation_folder=None, + alignment_json=None, + colour=None, + atlas_name=None, + custom_region_path=None, + atlas_path=None, + label_path=None, + settings_file=None, + prepend=None, # Add atlas information to settings if atlas_name: settings_dict["atlas_name"] = atlas_name @@ -118,7 +140,6 @@ def save_analysis_output( settings_dict["settings_file"] = settings_file if custom_region_path: settings_dict["custom_region_path"] = custom_region_path - if # Write settings to file settings_file_path = os.path.join(output_folder, "pynutil_settings.json") with open(settings_file_path, "w") as f: