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 incorporation into more advanced processing workflows.

Table of contents

• Installation
• Available interfaces
• Development
• Licensing

Installation

pip install pydra-freesurfer

Available interfaces

• gtmseg
• mri_convert
• 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 using Poetry.

To install, check and test the code:

make

To run the test suite when hacking:

make test

To format the code before review:

make format

To build the project's documentation:

make docs

Licensing

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