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Update [FreeSurfer] : Make notebook create missing Girder output path folders + add default path inside girder dataset #58

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Merged
camarasu merged 1 commit into from
Jul 9, 2026
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Update [FreeSurfer] : Make notebook create missing Girder output path folders + add default path inside girder dataset #58

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38 changes: 35 additions & 3 deletions examples/freesurfer/freesurfer_longitudinal_processing/freesurfer_longitudinal.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -93,7 +93,34 @@
" parent = folder.parent\n",
" for f in folder.iterdir():\n",
" f.rename(parent / f.name)\n",
" shutil.rmtree(folder)\n"
" shutil.rmtree(folder)\n",
"\n",
"def ensure_girder_path(client, path):\n",
" \"\"\"\n",
" Create missing Girder folders in a path like:\n",
" /collection/name/folder/subfolder\n",
" \"\"\"\n",
" parts = path.strip(\"/\").split(\"/\")\n",
" current = \"/\" + \"/\".join(parts[:2])\n",
" resource = client.resourceLookup(current)\n",
" parent_id = resource[\"_id\"]\n",
" parent_type = resource[\"_modelType\"]\n",
" for part in parts[2:-1]:\n",
" next_path = current + \"/\" + part\n",
" try:\n",
" resource = client.resourceLookup(next_path)\n",
" except Exception:\n",
" resource = client.createFolder(\n",
" parent_id,\n",
" part,\n",
" parentType=parent_type\n",
" )\n",
"\n",
" parent_id = resource[\"_id\"]\n",
" parent_type = \"folder\"\n",
" current = next_path\n",
"\n",
" return resource"
],
"id": "18aa877afac9a865",
"outputs": [],
Expand Down Expand Up @@ -133,7 +160,7 @@
"# Girder\n",
"GIRDER_CLIENT = GirderClient(apiUrl='GIRDER_URL') # Your Girder API endpoint url (ex : https://srmnopt.creatis.insa-lyon.fr/warehouse/api/v1 or https://myriad.creatis.insa-lyon.fr/api/v1)\n",
"GIRDER_DATASET_PATH = '/collection/COLLECTION_NAME/FOLDER_NAME' # Your Girder path to the dataset, can be in collections or user folders\n",
"GIRDER_OUTPUT_PATH = '/user/USER_NAME/FOLDER_NAME' # Your Girder path to the final outputs folder (must already exist), can be in collections or user folders\n",
"GIRDER_OUTPUT_PATH = GIRDER_DATASET_PATH + '/derivatives/freesurfer' # Your Girder path to the final outputs folder, can be in collections or user folders. Defaults to `GIRDER_DATASET_PATH/derivatives/freesurfer` but can be changed to format '/user/USER_NAME/FOLDER_NAME' or '/collection/COLLECTION_NAME/FOLDER_NAME'. The girder folders will be created automatically if they do not exist, but the script cannot create collections.\n",
"\n",
"# Local\n",
"LOCAL_DATASET_PATH = Path('~/PATH').expanduser() # Your local dataset path, where the Girder dataset will be downloaded, must already exist and be empty. Do not add unrelated custom files in this directory and its subdirectories as it may break vip executions.\n",
Expand Down Expand Up @@ -716,8 +743,13 @@
" moved_files.append((license_path, temp_path))\n",
"\n",
"try :\n",
" output_folder = ensure_girder_path(\n",
" cfg.GIRDER_CLIENT,\n",
" cfg.GIRDER_OUTPUT_PATH\n",
" )\n",
"\n",
" # Upload full freesurfer dir (outputs) to Girder selected path GIRDER_OUTPUT_PATH\n",
" cfg.GIRDER_CLIENT.upload(str(FREESURFER_DIR), cfg.GIRDER_CLIENT.resourceLookup(cfg.GIRDER_OUTPUT_PATH)['_id'], leafFoldersAsItems=True, reuseExisting=True)\n",
" cfg.GIRDER_CLIENT.upload(str(FREESURFER_DIR), output_folder[\"_id\"], leafFoldersAsItems=True, reuseExisting=True)\n",
"finally:\n",
" restore_files(moved_files)\n",
" print(f\"✅ Done: uploaded FreeSurfer outputs to Girder path '{cfg.GIRDER_OUTPUT_PATH}'.\")"
Expand Down
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