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.
| 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 |
pip install clinica-pydra-fslA separate installation of FSL is required to use this package. Please review the FSL installation instructions and licensing details.
This project is managed with Hatch:
pipx install hatchTo run the test suite:
hatch run testTo fix linting issues:
hatch fmtThis project is distributed under the terms of the Apache License, Version 2.0.