clinica-pydra-freesurfer
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.
3 maintainers
Metadata
3 maintainers
Release files for clinica-pydra-freesurfer 0.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| clinica_pydra_freesurfer-0.1.0.tar.gz | 21.9 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| clinica_pydra_freesurfer-0.1.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 55.8 kB
Release files / clinica_pydra_freesurfer-0.1.0.tar.gz
| Download URL | clinica_pydra_freesurfer-0.1.0.tar.gz |
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| Size | 21.9 kB |
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Release files / clinica_pydra_freesurfer-0.1.0-py3-none-any.whl
| Download URL | clinica_pydra_freesurfer-0.1.0-py3-none-any.whl |
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| Size | 33.9 kB |
| Tags | Python 3 |
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