Pydra tasks for FSL designed for Clinica
Project description
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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