childmindresearch / niwrap

NiWrap

NiWrap is an extensive collection of neuroimaging command line tool metadata used for generating modern, ideomatic Python wrappers.

Metadata is partly hand-written and partly extracted from the source code of the tools themselves. NiWrap is based on the Boutiques Descriptor Schema and powered by the Styx Boutiques-to-Python compiler.

Supported frameworks

Framework	Approach	Status	API Coverage
AFNI	Manual	In progress	561/621 (90.3%)
ANTs	Manual	In progress	9/120 (7.5%)
Connectome Workbench	Source extraction	Testing	202/202 (100% 🎉)
Convert3D	Manual	In progress	2/4 (50.0%)
FSL	Manual	In progress	221/376 (58.8%)
FreeSurfer	Manual	In progress	2/104 (1.9%)
MRTrix3	Source extraction	Testing	116/125 (92.8%)
NiftyReg	Manual	In progress	7/7 (100% 🎉)

Note

API Coverage is defined as the percentage of individual binaries for which a descriptor is available in NiWrap. This is not a measure of the completeness of the descriptors themselves nor is reaching 100% strictly necessary as e.g. FSL and AFNI contain many small utilities for which Python offers much easier standard library functions. One way to increase coverage is to mark known-irrelevant binaries as "status": "ignore" in frameworks/.

Repository structure

Directory	Description
/descriptors	Boutiques descriptors
/schemas	JSON schema for Boutiques descriptors
/python	Generated niwrap Python package
/extraction	Source metadata extraction
/frameworks	Framework-specific metadata

Python package

Install the niwrap Python package to use the generated Python wrappers.

See the niwrap Python package README for installation instructions and usage information.

Contributing

See the CONTRIBUTING.md file for information on how to contribute to NiWrap.

niwrap's Issues

c3: C3dAffineTool

Implement the c3 C3dAffineTool descriptor in descriptors/c3/c3d_affine_tool.json.

afni: Calc

Implement the afni Calc descriptor in descriptors/afni/calc.json.

afni: Detrend

Implement the afni Detrend descriptor in descriptors/afni/detrend.json.

fsl: BET

Implement the fsl BET descriptor in descriptors/fsl/bet.json.

ants: Registration

Implement the ants Registration descriptor in descriptors/ants/registration.json.

afni: TCorr1D

Implement the afni TCorr1D descriptor in descriptors/afni/tcorr1_d.json.

fsl: FLAMEO

Implement the fsl FLAMEO descriptor in descriptors/fsl/flameo.json.

freesurfer: ApplyVolTransform

Implement the freesurfer ApplyVolTransform descriptor in descriptors/freesurfer/apply_vol_transform.json.

afni: BlurToFWHM

Implement the afni BlurToFWHM descriptor in descriptors/afni/blur_to_fwhm.json.

afni: Automask

Implement the afni Automask descriptor in descriptors/afni/automask.json.

fsl: FAST

Implement the fsl FAST descriptor in descriptors/fsl/fast.json.

afni: TProject

Implement the afni TProject descriptor in descriptors/afni/tproject.json.

afni: SkullStrip

Implement the afni SkullStrip descriptor in descriptors/afni/skull_strip.json.

freesurfer: ReconAll

Implement the freesurfer ReconAll descriptor in descriptors/freesurfer/recon_all.json.

afni: TCat

Implement the afni TCat descriptor in descriptors/afni/tcat.json.

fsl: ApplyWarp

Implement the fsl ApplyWarp descriptor in descriptors/fsl/apply_warp.json.

afni: TStat

Implement the afni TStat descriptor in descriptors/afni/tstat.json.

freesurfer: Binarize

Implement the freesurfer Binarize descriptor in descriptors/freesurfer/binarize.json.

fsl: EpiReg

Implement the fsl EpiReg descriptor in descriptors/fsl/epi_reg.json.

fsl: ErodeImage

Implement the fsl ErodeImage descriptor in descriptors/fsl/erode_image.json.

fsl: BinaryMaths

Implement the fsl BinaryMaths descriptor in descriptors/fsl/binary_maths.json.

fsl: Cluster

Implement the fsl Cluster descriptor in descriptors/fsl/cluster.json.

afni: Refit

Implement the afni Refit descriptor in descriptors/afni/refit.json.

afni: DegreeCentrality

Implement the afni DegreeCentrality descriptor in descriptors/afni/degree_centrality.json.

afni: Bandpass

Implement the afni Bandpass descriptor in descriptors/afni/bandpass.json.

afni: Unifize

Implement the afni Unifize descriptor in descriptors/afni/unifize.json.

ants: Atropos

Implement the ants Atropos descriptor in descriptors/ants/atropos.json.

fsl: ExtractROI

Implement the fsl ExtractROI descriptor in descriptors/fsl/extract_roi.json.

fsl: ConvertXFM

Implement the fsl ConvertXFM descriptor in descriptors/fsl/convert_xfm.json.

afni: MaskTool

Implement the afni MaskTool descriptor in descriptors/afni/mask_tool.json.

fsl: DilateImage

Implement the fsl DilateImage descriptor in descriptors/fsl/dilate_image.json.

ants: ApplyTransforms

Implement the ants ApplyTransforms descriptor in descriptors/ants/apply_transforms.json.

afni: ROIStats

Implement the afni ROIStats descriptor in descriptors/afni/roistats.json.

[afni] Automask

Implement the afni Automask descriptor in descriptors/afni/automask.json.

afni: Resample

Implement the afni Resample descriptor in descriptors/afni/resample.json.

[afni] Automask

Implement the afni Automask descriptor in descriptors/afni/automask.json.

fsl: FNIRT

Implement the fsl FNIRT descriptor in descriptors/fsl/fnirt.json.

afni: TCorrelate

Implement the afni TCorrelate descriptor in descriptors/afni/tcorrelate.json.

afni: Despike

Implement the afni Despike descriptor in descriptors/afni/despike.json.

ants: MultiplyImages

Implement the ants MultiplyImages descriptor in descriptors/ants/multiply_images.json.

ants: DenoiseImage

Implement the ants DenoiseImage descriptor in descriptors/ants/denoise_image.json.

afni: ECM

Implement the afni ECM descriptor in descriptors/afni/ecm.json.

fsl: ConvertWarp

Implement the fsl ConvertWarp descriptor in descriptors/fsl/convert_warp.json.

afni: TShift

Implement the afni TShift descriptor in descriptors/afni/tshift.json.

afni: LFCD

Implement the afni LFCD descriptor in descriptors/afni/lfcd.json.

fsl: ApplyMask

Implement the fsl ApplyMask descriptor in descriptors/fsl/apply_mask.json.

fsl: FLIRT

Implement the fsl FLIRT descriptor in descriptors/fsl/flirt.json.

ants: N4BiasFieldCorrection

Implement the ants N4BiasFieldCorrection descriptor in descriptors/ants/n4_bias_field_correction.json.

afni: Maskave

Implement the afni Maskave descriptor in descriptors/afni/maskave.json.

afni: Volreg

Implement the afni Volreg descriptor in descriptors/afni/volreg.json.