# 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
Raw data
{
"_id": null,
"home_page": null,
"name": "clinica-pydra-freesurfer",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.8",
"maintainer_email": null,
"keywords": "freesurfer, neuroimaging, pydra",
"author": null,
"author_email": "Ghislain Vaillant <ghislain.vaillant@inria.fr>",
"download_url": "https://files.pythonhosted.org/packages/43/ec/58270e46567bef92ea70f5bfb9d3edd8f05af2a01633b8a5a7da5d684e48/clinica_pydra_freesurfer-0.1.0.tar.gz",
"platform": null,
"description": "# clinica-pydra-freesurfer\n\n[![PyPI - Version][pypi-version]][pypi-project]\n[![PyPI - Python Version][pypi-pyversions]][pypi-project]\n![][status-docs]\n![][status-test]\n\n----\n\nPydra tasks for FreeSurfer designed for Clinica.\n\n[Pydra][pydra] is a dataflow engine\nwhich provides a set of lightweight abstractions\nfor DAG construction, manipulation, and distributed execution.\n\n[FreeSurfer][freesurfer] is a neuroimaging toolkit\nfor processing, analyzing, and visualizing human brain MR images.\n\nThis project exposes some of FreeSurfer's utilities as Pydra tasks\nto facilitate their integration into more advanced processing workflows.\n\n## Available interfaces\n\n| Module | Interfaces |\n|-----------|-----------------------------------------------------------------------------------------------------|\n| gtmseg | GTMSeg |\n| mri | Aparc2Aseg, Binarize, Convert, Coreg, Label2Vol, RobustRegister, RobustTemplate, Surf2Surf, Vol2Vol |\n| mris | AnatomicalStats, CALabel, CATrain, Expand, Preproc |\n| recon_all | ReconAll, BaseReconAll, LongReconAll |\n\n## Installation\n\n```console\npip install clinica-pydra-freesurfer\n```\n\nA separate installation of FreeSurfer is required to use this package.\nPlease review the following [instructions][freesurfer-install]\nand [licensing details][freesurfer-license].\n\n## Development\n\nThis project is managed with [Hatch][hatch]:\n\n```console\npipx install hatch\n```\n\nTo run the test suite:\n\n```console\nhatch run test\n```\n\nTo fix linting issues:\n\n```console\nhatch fmt\n```\n\nTo check the documentation:\n\n```console\nhatch run docs:serve --open-browser\n```\n\n## Licensing\n\nThis project is distributed under the terms of the [Apache License, Version 2.0][license].\n\n[freesurfer]: https://surfer.nmr.mgh.harvard.edu\n\n[freesurfer-install]: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall\n\n[freesurfer-license]: https://surfer.nmr.mgh.harvard.edu/registration.html\n\n[hatch]: https://hatch.pypa.io\n\n[license]: https://opensource.org/licenses/Apache-2.0\n\n[pydra]: https://nipype.github.io/pydra\n\n[pypi-project]: https://pypi.org/project/clinica-pydra-freesurfer\n\n[pypi-pyversions]: https://img.shields.io/pypi/pyversions/clinica-pydra-freesurfer.svg\n\n[pypi-version]: https://img.shields.io/pypi/v/clinica-pydra-freesurfer.svg\n\n[status-docs]: https://github.com/aramis-lab/clinica-pydra-freesurfer/actions/workflows/docs.yaml/badge.svg\n\n[status-test]: https://github.com/aramis-lab/clinica-pydra-freesurfer/actions/workflows/test.yaml/badge.svg\n",
"bugtrack_url": null,
"license": null,
"summary": "Pydra tasks for FreeSurfer designed for Clinica",
"version": "0.1.0",
"project_urls": {
"Documentation": "https://aramis-lab.github.io/clinica-pydra-freesurfer",
"Issues": "https://github.com/aramis-lab/clinica-pydra-freesurfer/issues",
"Repository": "https://github.com/aramis-lab/clinica-pydra-freesurfer"
},
"split_keywords": [
"freesurfer",
" neuroimaging",
" pydra"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "cd61d845a1ca8ebb526eed7a6af57f490f94c570406dea7d5f2e83813dc02e74",
"md5": "9576e89141291a21e7ce63bd11228888",
"sha256": "e63e4bd09ceefe96c58250908b556295e6ebf0ac5bd35b8106799f6513c7bbea"
},
"downloads": -1,
"filename": "clinica_pydra_freesurfer-0.1.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "9576e89141291a21e7ce63bd11228888",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.8",
"size": 33898,
"upload_time": "2024-04-30T13:23:46",
"upload_time_iso_8601": "2024-04-30T13:23:46.086629Z",
"url": "https://files.pythonhosted.org/packages/cd/61/d845a1ca8ebb526eed7a6af57f490f94c570406dea7d5f2e83813dc02e74/clinica_pydra_freesurfer-0.1.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "43ec58270e46567bef92ea70f5bfb9d3edd8f05af2a01633b8a5a7da5d684e48",
"md5": "3c83fa65b874eebaddd12f00b5b6c348",
"sha256": "9eb5142c009d9c016edc722d0771772a5d2d5d2787f4e49a22d6926974ad3116"
},
"downloads": -1,
"filename": "clinica_pydra_freesurfer-0.1.0.tar.gz",
"has_sig": false,
"md5_digest": "3c83fa65b874eebaddd12f00b5b6c348",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.8",
"size": 21871,
"upload_time": "2024-04-30T13:23:47",
"upload_time_iso_8601": "2024-04-30T13:23:47.880806Z",
"url": "https://files.pythonhosted.org/packages/43/ec/58270e46567bef92ea70f5bfb9d3edd8f05af2a01633b8a5a7da5d684e48/clinica_pydra_freesurfer-0.1.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-04-30 13:23:47",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "aramis-lab",
"github_project": "clinica-pydra-freesurfer",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "clinica-pydra-freesurfer"
}
JSON
