# clinica-pydra-freesurfer [![PyPI - Version][pypi-version]][pypi-project] [![PyPI - Python Version][pypi-pyversions]][pypi-project] ![][status-docs] ![][status-test] ---- Pydra tasks for FreeSurfer designed for Clinica. [Pydra][pydra] is a dataflow engine which provides a set of lightweight abstractions for DAG construction, manipulation, and distributed execution. [FreeSurfer][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 ```console pip install clinica-pydra-freesurfer ``` A separate installation of FreeSurfer is required to use this package. Please review the following [instructions][freesurfer-install] and [licensing details][freesurfer-license]. ## Development This project is managed with [Hatch][hatch]: ```console pipx install hatch ``` To run the test suite: ```console hatch run test ``` To fix linting issues: ```console hatch fmt ``` To check the documentation: ```console hatch run docs:serve --open-browser ``` ## Licensing This project is distributed under the terms of the [Apache License, Version 2.0][license]. [freesurfer]: https://surfer.nmr.mgh.harvard.edu [freesurfer-install]: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall [freesurfer-license]: https://surfer.nmr.mgh.harvard.edu/registration.html [hatch]: https://hatch.pypa.io [license]: https://opensource.org/licenses/Apache-2.0 [pydra]: https://nipype.github.io/pydra [pypi-project]: https://pypi.org/project/clinica-pydra-freesurfer [pypi-pyversions]: https://img.shields.io/pypi/pyversions/clinica-pydra-freesurfer.svg [pypi-version]: https://img.shields.io/pypi/v/clinica-pydra-freesurfer.svg [status-docs]: https://github.com/aramis-lab/clinica-pydra-freesurfer/actions/workflows/docs.yaml/badge.svg [status-test]: https://github.com/aramis-lab/clinica-pydra-freesurfer/actions/workflows/test.yaml/badge.svg