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Pydra tasks for FSL designed for Clinica

Home Page: https://aramis-lab.github.io/clinica-pydra-fsl/

License: Apache License 2.0

Python 100.00%

fsl neuroimaging pydra

clinica-pydra-fsl's Introduction

pydra-fsl

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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