pydra-freesurfer

Pydra tasks for FreeSurfer.

Pydra is a dataflow engine which provides a set of lightweight abstractions for DAG construction, manipulation, and distributed execution.

FreeSurfer is a neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images.

This project exposes some of FreeSurfer's utilities as Pydra tasks to facilitate their integration into more advanced processing workflows.

Table of contents

• Installation
• Available interfaces
• Development
• Licensing

Installation

pip install pydra-freesurfer

Available interfaces

• gtmseg
• mri_convert
• mri_label2vol
• mri_surf2surf
• mri_vol2vol
• mris_anatomical_stats
• mris_ca_label
• mris_ca_train
• mris_expand
• mris_preproc
• recon-all
• tkregister2

Development

This project is managed with Hatch:

pipx install hatch

To run the test suite:

hatch run test:no-cov

To fix linting issues:

hatch run lint:fix

To check the documentation:

hatch run docs:serve --open-browser

Licensing

This project is released under the terms of the Apache License, Version 2.0.