A Marimo notebook for visualizing white matter fiber bundles from diffusion MRI tractography using NiiVue.
VOLUME_PATH=brain.nii.gz TRX_PATH=tracts.trx marimo run viewer.py
Where:
VOLUME_PATHis the path to a T1-weighted anatomical image (.nii.gz)TRX_PATHis the path to a TRX tractography file containing fiber bundles
pip install marimo
All other dependencies are installed automatically by marimo's sandbox.
This notebook reads a TRX tractography file and lets you interactively explore individual fiber bundles overlaid on a T1-weighted anatomical image. Select bundles using checkboxes to visualize one or more brain regions at a time.
Built with NiiVue by Chris Rorden and ipyniivue. Based on the NiiVue marimo notebooks.