tract-clustering

Data-driven approach for identifying white matter tracts in quantitative histology of the spinal cord. This code was applied to the rat spinal cord, but it could equally be applied to other species.

Citation

Nami H, Perone CS and Cohen-Adad J (2022) Histology-informed automatic parcellation of white matter tracts in the rat spinal cord. Front. Neuroanat. 16:960475. doi: 10.3389/fnana.2022.960475

Dependency

• Python 3.7 (conda distribution)
• ANTs

Getting started

Data

Download the RatAtlas. For more information about how this dataset was generated, see Saliani et al. Neuroimage 2019.

Code

Download this repository:

git clone https://github.com/neuropoly/tract-clustering.git

Install package and dependencies:

cd tract-clustering
pip install -e .

Edit the script scripts/params.py and update variables according to your files location

Run registration:

python register_slicewise.py

Slice-wise clustering:

python clustering_slicewise.py

Region-wise clustering:

# Run clustering
python clustering_regionwise.py