Structural Connectivity Applied To Targeted Regions (SCATTR)

SCATTR is a BIDS App that performs tractography to identify connections between subcortical structures (i.e. map the subcortical connectome), making use of existing neuroimaging tools like prepdwi, Freesurfer, and Mrtrix3.

This workflow was used to process the data for the analysis from hcp_subcortical_repo.

Contributing

Clone the git repository. SCATTR dependencies are managed with Poetry (version 1.2.x), which you'll need installed on your machine. You can find instructions on the Poetry website.

Then, setup the development environment with the following commands:

poetry install
poetry run poe setup

SCATTR uses poethepoet as a task runner. You can see what commands are available by running:

poetry run poe

If you wish, you can also run poe [command] directly by installing poethepoet on your system. Follow the install instructions at the link above.

SCATTR uses pre-commit hooks (installed via the poe setup command above) to lint and format code (we use black, isort, flake8). By default, these hooks are run on every commit.

Please be sure they all pass before making a PR.

Notes

• Original workflow had worked on HCP data which had transforms readily available. Transforms need to be computed to standard spaces used (MNI2009b is sufficient).
• Current workflow assumes dwi data has been preprocessed and Freesurfer has already been run. Future implementation will include option to run missing steps.
• Original workflow was run using scripts similar to those in resources/example_scripts

Relevant Papers

• Kai, J., Khan, A.R., Haast, R.A.M., Lau, J.C. (2022). Mapping the subcortical connectome using in vivo diffusion MRI: feasibility and reliability. Terra incognita: diving into the human subcortex, special issue of NeuroImage. doi: 10.1016/j.neuroimage.2022.119553.