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Merged
Albireo-B merged 2 commits into from
Jun 26, 2026
Merged

Fix/freesurfer #57

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e5a1dc3
Update [FreeSurfer] : remove windows-failing input()
Jun 26, 2026
38e820b
fix
Jun 26, 2026
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28 changes: 21 additions & 7 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 @@ -82,6 +82,8 @@
"# Built-ins\n",
"import tarfile\n",
"import shutil\n",
"import ipywidgets as widgets\n",
"from IPython.display import display, clear_output\n",
"from pathlib import Path\n",
"\n",
"# VIP\n",
Expand Down Expand Up @@ -134,17 +136,29 @@
"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",
"\n",
"# Local\n",
"LOCAL_DATASET_PATH = Path('~/PATH').expanduser() # Your local dataset path, where the Girder dataset will be downloaded, must already exist\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",
"LICENSE_PATH = Path('~/PATH/LICENSE_NAME.txt').expanduser() # Your pipeline license path, will be copied into VIP input_dirs automatically\n",
"\"\"\"\n",
"\n",
"if CONFIG_PATH.exists():\n",
" answer = input(\"The user_config.py file already exists. Overwrite config ? (y/N): \")\n",
" if answer != \"y\":\n",
" print(\"File not created, as user_config.py already exists.\")\n",
" else:\n",
" CONFIG_PATH.write_text(user_config)\n",
" print(\"User_config.py overwritten with default values.\")\n",
" print(\"The user_config.py file already exists. Overwrite config ?\")\n",
" out = widgets.Output()\n",
" yes_btn = widgets.Button(description=\"Yes\")\n",
" no_btn = widgets.Button(description=\"No\")\n",
" display(widgets.HBox([yes_btn, no_btn]), out)\n",
" def on_yes(_):\n",
" with out:\n",
" clear_output(wait=True)\n",
" CONFIG_PATH.write_text(user_config)\n",
" print(\"User_config.py overwritten with default values.\")\n",
"\n",
" def on_no(_):\n",
" with out:\n",
" clear_output(wait=True)\n",
" print(\"File not created, as user_config.py already exists.\")\n",
"\n",
" yes_btn.on_click(on_yes)\n",
" no_btn.on_click(on_no)\n",
"else:\n",
" CONFIG_PATH.write_text(user_config)\n",
" print(\"User_config.py created with default values.\")\n"
Expand Down
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