clinica-pydra-freesurfer

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Pydra tasks for FreeSurfer designed for Clinica.

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.

Available interfaces

Module	Interfaces
gtmseg	GTMSeg
mri	Aparc2Aseg, Binarize, Convert, Coreg, Label2Vol, RobustRegister, RobustTemplate, Surf2Surf, Vol2Vol
mris	AnatomicalStats, CALabel, CATrain, Expand, Preproc
recon_all	ReconAll, BaseReconAll, LongReconAll

Installation

pip install clinica-pydra-freesurfer

A separate installation of FreeSurfer is required to use this package. Please review the following instructions and licensing details.

Development

This project is managed with Hatch:

pipx install hatch

To run the test suite:

hatch run test

To fix linting issues:

hatch fmt

To check the documentation:

hatch run docs:serve --open-browser

Licensing

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