Unraveling Brainstem Deformations in Joubert Syndrome: A Statistical Shape Analysis of MRI-Derived Structures

Code repository under construction for the MICCAI 2025 paper: Unraveling Brainstem Deformation in Joubert Syndrome: A Statistical Shape Analysis of MRI-Derived Structures

🧑‍💻️ Installation and Requirements

Our project requires the creation of a virtual environment with python version 3.11.9. The pipeline requires the installation of pyFM , as specified in requirements.txt.

conda create -n SSA-brainstem python=3.11.9   # create conda virtual environment
conda activate SSA-brainstem
pip install -r requirements.txt  # install other necessary libraries via pip

📝 Dataset

Under folder 'data', data used in the project are available and divided in three subfolders:

• 'original': contains the raw .obj shapes of brainstem at original resolution as obtained by segmentation masks from MRI;
• 'remeshed': contains preprocessed .obj shapes at 3K resolution after cleaning and remeshing procedure via ReMatching
• 'bm': contains .mat files scaling back from low to high resolution shapes

For privacy reasons, all data are anonymized and provided with basic information in 'info_subjects.xlsx'.
After approval, data will also be available in Zenodo and BOARD

⚙️ Pipeline

🙏 Acknowledgement

🎓 Attribution

License 🚀 This project is licensed under the MIT License.