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Pydra tasks for FSL designed for Clinica

Project description

pydra-fsl

PyPI - Version PyPI - Python Version


Pydra tasks for FSL designed for Clinica.

Pydra is a dataflow engine which provides a set of lightweight abstractions for DAG construction, manipulation, and distributed execution.

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

Available tasks

Module Tasks
bet BET, RobustFOV
eddy Eddy, ApplyTopup, Topup
fast FAST
flirt FLIRT, ApplyXFM, ConcatXFM, ConvertXFM, InvertXFM, FixScaleSkew, Img2ImgCoord, Img2StdCoord, Std2ImgCoord
fnirt FNIRT, FNIRTFileUtils, ApplyWarp, ConvertWarp, InvWarp
fugue FUGUE, PrepareFieldmap, Prelude, SigLoss
maths (experimental) Maths, Mul
susan SUSAN
utils ChFileType, FFT, Info, Interleave, Merge, Orient, Reorient2Std, ROI, SelectVols, Slice, SmoothFill, Split, SwapDim

Installation

pip install clinica-pydra-fsl

A separate installation of FSL is required to use this package. Please review the FSL installation 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

License

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

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