├── .circleci ├── config.yml └── test_pytest.sh ├── .codespellrc ├── .coveragerc ├── .dockerignore ├── .et ├── .git-blame-ignore-revs ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE.md ├── PULL_REQUEST_TEMPLATE.md ├── dependabot.yml ├── release-drafter.yml └── workflows │ ├── codespell.yml │ ├── tests.yml │ └── tutorials.yml ├── .gitignore ├── .mailmap ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── .wci.yml ├── .zenodo.json ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── INSTALL ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.rst ├── THANKS.rst ├── Vagrantfile ├── codecov.yml ├── doc ├── .gitignore ├── Makefile ├── _static │ ├── nipy.css │ ├── nipype-banner-bg.png │ ├── nipype.css │ └── snakebrain-nipype.svg ├── _templates │ ├── gse.html │ ├── indexsidebar.html │ ├── layout.html │ ├── navbar.html │ └── sidebar_versions.html ├── about.rst ├── changelog │ ├── 0.X.X-changelog.rst │ └── 1.X.X-changelog.rst ├── changes.rst ├── conf.py ├── devel │ ├── architecture.rst │ ├── cmd_interface_devel.rst │ ├── filename_generation.rst │ ├── gitwash │ │ ├── branch_list.png │ │ ├── branch_list_compare.png │ │ ├── configure_git.rst │ │ ├── development_workflow.rst │ │ ├── following_latest.rst │ │ ├── forking_button.png │ │ ├── forking_hell.rst │ │ ├── git_development.rst │ │ ├── git_install.rst │ │ ├── git_intro.rst │ │ ├── git_links.inc │ │ ├── git_resources.rst │ │ ├── index.rst │ │ ├── known_projects.inc │ │ ├── links.inc │ │ ├── patching.rst │ │ ├── pull_button.png │ │ ├── set_up_fork.rst │ │ └── this_project.inc │ ├── index.rst │ ├── interface_specs.rst │ ├── matlab_example1.py │ ├── matlab_example2.py │ ├── matlab_interface_devel.rst │ ├── provenance.rst │ ├── python_interface_devel.rst │ ├── software_using_nipype.rst │ ├── testing_nipype.rst │ └── writing_custom_interfaces.rst ├── developers.rst ├── examples.rst ├── images │ ├── nipype_architecture_overview2.png │ └── nipype_architecture_overview2.svg ├── index.rst ├── interfaces.rst ├── links_names.txt ├── quickstart.rst ├── requirements.txt ├── searchresults.rst ├── users │ └── install.rst └── version.rst ├── docker ├── files │ ├── neurodebian.gpg │ ├── run_builddocs.sh │ ├── run_examples.sh │ └── run_pytests.sh ├── generate_dockerfiles.sh └── prune_dockerfile.sh ├── examples └── README.md ├── nipype ├── COMMIT_INFO.txt ├── __init__.py ├── algorithms │ ├── __init__.py │ ├── confounds.py │ ├── icc.py │ ├── mesh.py │ ├── metrics.py │ ├── misc.py │ ├── modelgen.py │ ├── rapidart.py │ ├── stats.py │ └── tests │ │ ├── __init__.py │ │ ├── test_CompCor.py │ │ ├── test_ErrorMap.py │ │ ├── test_Overlap.py │ │ ├── test_TSNR.py │ │ ├── test_auto_ACompCor.py │ │ ├── test_auto_ActivationCount.py │ │ ├── test_auto_AddCSVColumn.py │ │ ├── test_auto_AddCSVRow.py │ │ ├── test_auto_AddNoise.py │ │ ├── test_auto_ArtifactDetect.py │ │ ├── test_auto_CalculateMedian.py │ │ ├── test_auto_CalculateNormalizedMoments.py │ │ ├── test_auto_ComputeDVARS.py │ │ ├── test_auto_ComputeMeshWarp.py │ │ ├── test_auto_CreateNifti.py │ │ ├── test_auto_Distance.py │ │ ├── test_auto_FramewiseDisplacement.py │ │ ├── test_auto_FuzzyOverlap.py │ │ ├── test_auto_Gunzip.py │ │ ├── test_auto_Gzip.py │ │ ├── test_auto_ICC.py │ │ ├── test_auto_Matlab2CSV.py │ │ ├── test_auto_MergeCSVFiles.py │ │ ├── test_auto_MergeROIs.py │ │ ├── test_auto_MeshWarpMaths.py │ │ ├── test_auto_ModifyAffine.py │ │ ├── test_auto_NonSteadyStateDetector.py │ │ ├── test_auto_NormalizeProbabilityMapSet.py │ │ ├── test_auto_P2PDistance.py │ │ ├── test_auto_PickAtlas.py │ │ ├── test_auto_Similarity.py │ │ ├── test_auto_SimpleThreshold.py │ │ ├── test_auto_SpecifyModel.py │ │ ├── test_auto_SpecifySPMModel.py │ │ ├── test_auto_SpecifySparseModel.py │ │ ├── test_auto_SplitROIs.py │ │ ├── test_auto_StimulusCorrelation.py │ │ ├── test_auto_TCompCor.py │ │ ├── test_auto_TVTKBaseInterface.py │ │ ├── test_auto_WarpPoints.py │ │ ├── test_confounds.py │ │ ├── test_icc_anova.py │ │ ├── test_mesh_ops.py │ │ ├── test_metrics.py │ │ ├── test_misc.py │ │ ├── test_modelgen.py │ │ ├── test_moments.py │ │ ├── test_normalize_tpms.py │ │ ├── test_rapidart.py │ │ ├── test_splitmerge.py │ │ └── test_stats.py ├── caching │ ├── __init__.py │ ├── memory.py │ └── tests │ │ ├── __init__.py │ │ └── test_memory.py ├── conftest.py ├── external │ ├── __init__.py │ ├── cloghandler.py │ ├── d3.js │ ├── due.py │ └── fsl_imglob.py ├── info.py ├── interfaces │ ├── __init__.py │ ├── afni │ │ ├── __init__.py │ │ ├── base.py │ │ ├── model.py │ │ ├── preprocess.py │ │ ├── svm.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_ABoverlap.py │ │ │ ├── test_auto_AFNICommand.py │ │ │ ├── test_auto_AFNICommandBase.py │ │ │ ├── test_auto_AFNIPythonCommand.py │ │ │ ├── test_auto_AFNItoNIFTI.py │ │ │ ├── test_auto_AlignEpiAnatPy.py │ │ │ ├── test_auto_Allineate.py │ │ │ ├── test_auto_AutoTLRC.py │ │ │ ├── test_auto_AutoTcorrelate.py │ │ │ ├── test_auto_Autobox.py │ │ │ ├── test_auto_Automask.py │ │ │ ├── test_auto_Axialize.py │ │ │ ├── test_auto_Bandpass.py │ │ │ ├── test_auto_BlurInMask.py │ │ │ ├── test_auto_BlurToFWHM.py │ │ │ ├── test_auto_BrickStat.py │ │ │ ├── test_auto_Bucket.py │ │ │ ├── test_auto_Calc.py │ │ │ ├── test_auto_Cat.py │ │ │ ├── test_auto_CatMatvec.py │ │ │ ├── test_auto_CenterMass.py │ │ │ ├── test_auto_ClipLevel.py │ │ │ ├── test_auto_ConvertDset.py │ │ │ ├── test_auto_Copy.py │ │ │ ├── test_auto_Deconvolve.py │ │ │ ├── test_auto_DegreeCentrality.py │ │ │ ├── test_auto_Despike.py │ │ │ ├── test_auto_Detrend.py │ │ │ ├── test_auto_Dot.py │ │ │ ├── test_auto_ECM.py │ │ │ ├── test_auto_Edge3.py │ │ │ ├── test_auto_Eval.py │ │ │ ├── test_auto_FWHMx.py │ │ │ ├── test_auto_Fim.py │ │ │ ├── test_auto_Fourier.py │ │ │ ├── test_auto_GCOR.py │ │ │ ├── test_auto_Hist.py │ │ │ ├── test_auto_LFCD.py │ │ │ ├── test_auto_LocalBistat.py │ │ │ ├── test_auto_Localstat.py │ │ │ ├── test_auto_MaskTool.py │ │ │ ├── test_auto_Maskave.py │ │ │ ├── test_auto_Means.py │ │ │ ├── test_auto_Merge.py │ │ │ ├── test_auto_NetCorr.py │ │ │ ├── test_auto_Notes.py │ │ │ ├── test_auto_NwarpAdjust.py │ │ │ ├── test_auto_NwarpApply.py │ │ │ ├── test_auto_NwarpCat.py │ │ │ ├── test_auto_OneDToolPy.py │ │ │ ├── test_auto_OutlierCount.py │ │ │ ├── test_auto_QualityIndex.py │ │ │ ├── test_auto_Qwarp.py │ │ │ ├── test_auto_QwarpPlusMinus.py │ │ │ ├── test_auto_ROIStats.py │ │ │ ├── test_auto_ReHo.py │ │ │ ├── test_auto_Refit.py │ │ │ ├── test_auto_Remlfit.py │ │ │ ├── test_auto_Resample.py │ │ │ ├── test_auto_Retroicor.py │ │ │ ├── test_auto_SVMTest.py │ │ │ ├── test_auto_SVMTrain.py │ │ │ ├── test_auto_Seg.py │ │ │ ├── test_auto_SkullStrip.py │ │ │ ├── test_auto_Synthesize.py │ │ │ ├── test_auto_TCat.py │ │ │ ├── test_auto_TCatSubBrick.py │ │ │ ├── test_auto_TCorr1D.py │ │ │ ├── test_auto_TCorrMap.py │ │ │ ├── test_auto_TCorrelate.py │ │ │ ├── test_auto_TNorm.py │ │ │ ├── test_auto_TProject.py │ │ │ ├── test_auto_TShift.py │ │ │ ├── test_auto_TSmooth.py │ │ │ ├── test_auto_TStat.py │ │ │ ├── test_auto_To3D.py │ │ │ ├── test_auto_Undump.py │ │ │ ├── test_auto_Unifize.py │ │ │ ├── test_auto_Volreg.py │ │ │ ├── test_auto_Warp.py │ │ │ ├── test_auto_ZCutUp.py │ │ │ ├── test_auto_Zcat.py │ │ │ ├── test_auto_Zeropad.py │ │ │ └── test_extra_Deconvolve.py │ │ └── utils.py │ ├── ants │ │ ├── __init__.py │ │ ├── base.py │ │ ├── legacy.py │ │ ├── registration.py │ │ ├── resampling.py │ │ ├── segmentation.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_AI.py │ │ │ ├── test_auto_ANTS.py │ │ │ ├── test_auto_ANTSCommand.py │ │ │ ├── test_auto_AffineInitializer.py │ │ │ ├── test_auto_ApplyTransforms.py │ │ │ ├── test_auto_ApplyTransformsToPoints.py │ │ │ ├── test_auto_Atropos.py │ │ │ ├── test_auto_AverageAffineTransform.py │ │ │ ├── test_auto_AverageImages.py │ │ │ ├── test_auto_BrainExtraction.py │ │ │ ├── test_auto_ComposeMultiTransform.py │ │ │ ├── test_auto_CompositeTransformUtil.py │ │ │ ├── test_auto_ConvertScalarImageToRGB.py │ │ │ ├── test_auto_CorticalThickness.py │ │ │ ├── test_auto_CreateJacobianDeterminantImage.py │ │ │ ├── test_auto_CreateTiledMosaic.py │ │ │ ├── test_auto_DenoiseImage.py │ │ │ ├── test_auto_GenWarpFields.py │ │ │ ├── test_auto_ImageMath.py │ │ │ ├── test_auto_JointFusion.py │ │ │ ├── test_auto_KellyKapowski.py │ │ │ ├── test_auto_LabelGeometry.py │ │ │ ├── test_auto_LaplacianThickness.py │ │ │ ├── test_auto_MeasureImageSimilarity.py │ │ │ ├── test_auto_MultiplyImages.py │ │ │ ├── test_auto_N4BiasFieldCorrection.py │ │ │ ├── test_auto_Registration.py │ │ │ ├── test_auto_RegistrationSynQuick.py │ │ │ ├── test_auto_ResampleImageBySpacing.py │ │ │ ├── test_auto_ThresholdImage.py │ │ │ ├── test_auto_WarpImageMultiTransform.py │ │ │ ├── test_auto_WarpTimeSeriesImageMultiTransform.py │ │ │ ├── test_auto_antsIntroduction.py │ │ │ ├── test_auto_buildtemplateparallel.py │ │ │ ├── test_base.py │ │ │ ├── test_extra_Registration.py │ │ │ ├── test_resampling.py │ │ │ └── test_segmentation.py │ │ ├── utils.py │ │ └── visualization.py │ ├── base │ │ ├── __init__.py │ │ ├── core.py │ │ ├── specs.py │ │ ├── support.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_BaseInterface.py │ │ │ ├── test_auto_CommandLine.py │ │ │ ├── test_auto_LibraryBaseInterface.py │ │ │ ├── test_auto_MpiCommandLine.py │ │ │ ├── test_auto_SEMLikeCommandLine.py │ │ │ ├── test_auto_SimpleInterface.py │ │ │ ├── test_auto_StdOutCommandLine.py │ │ │ ├── test_core.py │ │ │ ├── test_resource_monitor.py │ │ │ ├── test_specs.py │ │ │ ├── test_support.py │ │ │ └── test_traits_extension.py │ │ └── traits_extension.py │ ├── brainsuite │ │ ├── __init__.py │ │ ├── brainsuite.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_BDP.py │ │ │ ├── test_auto_Bfc.py │ │ │ ├── test_auto_Bse.py │ │ │ ├── test_auto_Cerebro.py │ │ │ ├── test_auto_Cortex.py │ │ │ ├── test_auto_Dewisp.py │ │ │ ├── test_auto_Dfs.py │ │ │ ├── test_auto_Hemisplit.py │ │ │ ├── test_auto_Pialmesh.py │ │ │ ├── test_auto_Pvc.py │ │ │ ├── test_auto_SVReg.py │ │ │ ├── test_auto_Scrubmask.py │ │ │ ├── test_auto_Skullfinder.py │ │ │ ├── test_auto_Tca.py │ │ │ └── test_auto_ThicknessPVC.py │ ├── bru2nii.py │ ├── c3.py │ ├── camino │ │ ├── __init__.py │ │ ├── calib.py │ │ ├── connectivity.py │ │ ├── convert.py │ │ ├── dti.py │ │ ├── odf.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_AnalyzeHeader.py │ │ │ ├── test_auto_ComputeEigensystem.py │ │ │ ├── test_auto_ComputeFractionalAnisotropy.py │ │ │ ├── test_auto_ComputeMeanDiffusivity.py │ │ │ ├── test_auto_ComputeTensorTrace.py │ │ │ ├── test_auto_Conmat.py │ │ │ ├── test_auto_DT2NIfTI.py │ │ │ ├── test_auto_DTIFit.py │ │ │ ├── test_auto_DTLUTGen.py │ │ │ ├── test_auto_DTMetric.py │ │ │ ├── test_auto_FSL2Scheme.py │ │ │ ├── test_auto_Image2Voxel.py │ │ │ ├── test_auto_ImageStats.py │ │ │ ├── test_auto_LinRecon.py │ │ │ ├── test_auto_MESD.py │ │ │ ├── test_auto_ModelFit.py │ │ │ ├── test_auto_NIfTIDT2Camino.py │ │ │ ├── test_auto_PicoPDFs.py │ │ │ ├── test_auto_ProcStreamlines.py │ │ │ ├── test_auto_QBallMX.py │ │ │ ├── test_auto_SFLUTGen.py │ │ │ ├── test_auto_SFPICOCalibData.py │ │ │ ├── test_auto_SFPeaks.py │ │ │ ├── test_auto_Shredder.py │ │ │ ├── test_auto_Track.py │ │ │ ├── test_auto_TrackBallStick.py │ │ │ ├── test_auto_TrackBayesDirac.py │ │ │ ├── test_auto_TrackBedpostxDeter.py │ │ │ ├── test_auto_TrackBedpostxProba.py │ │ │ ├── test_auto_TrackBootstrap.py │ │ │ ├── test_auto_TrackDT.py │ │ │ ├── test_auto_TrackPICo.py │ │ │ ├── test_auto_TractShredder.py │ │ │ └── test_auto_VtkStreamlines.py │ │ └── utils.py │ ├── camino2trackvis │ │ ├── __init__.py │ │ ├── convert.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_Camino2Trackvis.py │ │ │ └── test_auto_Trackvis2Camino.py │ ├── cat12 │ │ ├── __init__.py │ │ ├── base.py │ │ ├── preprocess.py │ │ ├── surface.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_CAT12SANLMDenoising.py │ │ │ ├── test_auto_CAT12Segment.py │ │ │ ├── test_auto_ExtractAdditionalSurfaceParameters.py │ │ │ └── test_auto_ExtractROIBasedSurfaceMeasures.py │ ├── cmtk │ │ ├── __init__.py │ │ ├── base.py │ │ ├── cmtk.py │ │ ├── convert.py │ │ ├── nbs.py │ │ ├── nx.py │ │ ├── parcellation.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_AverageNetworks.py │ │ │ ├── test_auto_CFFBaseInterface.py │ │ │ ├── test_auto_CFFConverter.py │ │ │ ├── test_auto_CreateMatrix.py │ │ │ ├── test_auto_CreateNodes.py │ │ │ ├── test_auto_MergeCNetworks.py │ │ │ ├── test_auto_NetworkBasedStatistic.py │ │ │ ├── test_auto_NetworkXMetrics.py │ │ │ ├── test_auto_Parcellate.py │ │ │ ├── test_auto_ROIGen.py │ │ │ └── test_nbs.py │ ├── dcm2nii.py │ ├── dcmstack.py │ ├── diffusion_toolkit │ │ ├── __init__.py │ │ ├── base.py │ │ ├── dti.py │ │ ├── odf.py │ │ ├── postproc.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_DTIRecon.py │ │ │ ├── test_auto_DTITracker.py │ │ │ ├── test_auto_HARDIMat.py │ │ │ ├── test_auto_ODFRecon.py │ │ │ ├── test_auto_ODFTracker.py │ │ │ ├── test_auto_SplineFilter.py │ │ │ └── test_auto_TrackMerge.py │ ├── dipy │ │ ├── __init__.py │ │ ├── anisotropic_power.py │ │ ├── base.py │ │ ├── preprocess.py │ │ ├── reconstruction.py │ │ ├── registration.py │ │ ├── setup.py │ │ ├── simulate.py │ │ ├── stats.py │ │ ├── tensors.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_APMQball.py │ │ │ ├── test_auto_CSD.py │ │ │ ├── test_auto_DTI.py │ │ │ ├── test_auto_Denoise.py │ │ │ ├── test_auto_DipyBaseInterface.py │ │ │ ├── test_auto_DipyDiffusionInterface.py │ │ │ ├── test_auto_EstimateResponseSH.py │ │ │ ├── test_auto_RESTORE.py │ │ │ ├── test_auto_Resample.py │ │ │ ├── test_auto_SimulateMultiTensor.py │ │ │ ├── test_auto_StreamlineTractography.py │ │ │ ├── test_auto_TensorMode.py │ │ │ ├── test_auto_TrackDensityMap.py │ │ │ └── test_base.py │ │ └── tracks.py │ ├── dtitk │ │ ├── __init__.py │ │ ├── base.py │ │ ├── registration.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_AffScalarVol.py │ │ │ ├── test_auto_AffSymTensor3DVol.py │ │ │ ├── test_auto_Affine.py │ │ │ ├── test_auto_AffineTask.py │ │ │ ├── test_auto_BinThresh.py │ │ │ ├── test_auto_BinThreshTask.py │ │ │ ├── test_auto_CommandLineDtitk.py │ │ │ ├── test_auto_ComposeXfm.py │ │ │ ├── test_auto_ComposeXfmTask.py │ │ │ ├── test_auto_Diffeo.py │ │ │ ├── test_auto_DiffeoScalarVol.py │ │ │ ├── test_auto_DiffeoSymTensor3DVol.py │ │ │ ├── test_auto_DiffeoTask.py │ │ │ ├── test_auto_Rigid.py │ │ │ ├── test_auto_RigidTask.py │ │ │ ├── test_auto_SVAdjustVoxSp.py │ │ │ ├── test_auto_SVAdjustVoxSpTask.py │ │ │ ├── test_auto_SVResample.py │ │ │ ├── test_auto_SVResampleTask.py │ │ │ ├── test_auto_TVAdjustOriginTask.py │ │ │ ├── test_auto_TVAdjustVoxSp.py │ │ │ ├── test_auto_TVAdjustVoxSpTask.py │ │ │ ├── test_auto_TVResample.py │ │ │ ├── test_auto_TVResampleTask.py │ │ │ ├── test_auto_TVtool.py │ │ │ ├── test_auto_TVtoolTask.py │ │ │ ├── test_auto_affScalarVolTask.py │ │ │ ├── test_auto_affSymTensor3DVolTask.py │ │ │ ├── test_auto_diffeoScalarVolTask.py │ │ │ └── test_auto_diffeoSymTensor3DVolTask.py │ │ └── utils.py │ ├── dynamic_slicer.py │ ├── elastix │ │ ├── __init__.py │ │ ├── base.py │ │ ├── registration.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_AnalyzeWarp.py │ │ │ ├── test_auto_ApplyWarp.py │ │ │ ├── test_auto_EditTransform.py │ │ │ ├── test_auto_PointsWarp.py │ │ │ └── test_auto_Registration.py │ │ └── utils.py │ ├── freesurfer │ │ ├── __init__.py │ │ ├── base.py │ │ ├── longitudinal.py │ │ ├── model.py │ │ ├── petsurfer.py │ │ ├── preprocess.py │ │ ├── registration.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_BBRegister.py │ │ │ ├── test_FSSurfaceCommand.py │ │ │ ├── test_auto_AddXFormToHeader.py │ │ │ ├── test_auto_Aparc2Aseg.py │ │ │ ├── test_auto_Apas2Aseg.py │ │ │ ├── test_auto_ApplyMask.py │ │ │ ├── test_auto_ApplyVolTransform.py │ │ │ ├── test_auto_Binarize.py │ │ │ ├── test_auto_CALabel.py │ │ │ ├── test_auto_CANormalize.py │ │ │ ├── test_auto_CARegister.py │ │ │ ├── test_auto_CheckTalairachAlignment.py │ │ │ ├── test_auto_Concatenate.py │ │ │ ├── test_auto_ConcatenateLTA.py │ │ │ ├── test_auto_Contrast.py │ │ │ ├── test_auto_Curvature.py │ │ │ ├── test_auto_CurvatureStats.py │ │ │ ├── test_auto_DICOMConvert.py │ │ │ ├── test_auto_EMRegister.py │ │ │ ├── test_auto_EditWMwithAseg.py │ │ │ ├── test_auto_EulerNumber.py │ │ │ ├── test_auto_ExtractMainComponent.py │ │ │ ├── test_auto_FSCommand.py │ │ │ ├── test_auto_FSCommandOpenMP.py │ │ │ ├── test_auto_FSScriptCommand.py │ │ │ ├── test_auto_FitMSParams.py │ │ │ ├── test_auto_FixTopology.py │ │ │ ├── test_auto_FuseSegmentations.py │ │ │ ├── test_auto_GLMFit.py │ │ │ ├── test_auto_GTMPVC.py │ │ │ ├── test_auto_GTMSeg.py │ │ │ ├── test_auto_ImageInfo.py │ │ │ ├── test_auto_Jacobian.py │ │ │ ├── test_auto_LTAConvert.py │ │ │ ├── test_auto_Label2Annot.py │ │ │ ├── test_auto_Label2Label.py │ │ │ ├── test_auto_Label2Vol.py │ │ │ ├── test_auto_Logan.py │ │ │ ├── test_auto_MNIBiasCorrection.py │ │ │ ├── test_auto_MPRtoMNI305.py │ │ │ ├── test_auto_MRIConvert.py │ │ │ ├── test_auto_MRICoreg.py │ │ │ ├── test_auto_MRIFill.py │ │ │ ├── test_auto_MRIMarchingCubes.py │ │ │ ├── test_auto_MRIPretess.py │ │ │ ├── test_auto_MRISPreproc.py │ │ │ ├── test_auto_MRISPreprocReconAll.py │ │ │ ├── test_auto_MRITessellate.py │ │ │ ├── test_auto_MRIsCALabel.py │ │ │ ├── test_auto_MRIsCalc.py │ │ │ ├── test_auto_MRIsCombine.py │ │ │ ├── test_auto_MRIsConvert.py │ │ │ ├── test_auto_MRIsExpand.py │ │ │ ├── test_auto_MRIsInflate.py │ │ │ ├── test_auto_MRTM1.py │ │ │ ├── test_auto_MRTM2.py │ │ │ ├── test_auto_MS_LDA.py │ │ │ ├── test_auto_MakeAverageSubject.py │ │ │ ├── test_auto_MakeSurfaces.py │ │ │ ├── test_auto_Normalize.py │ │ │ ├── test_auto_OneSampleTTest.py │ │ │ ├── test_auto_Paint.py │ │ │ ├── test_auto_ParcellationStats.py │ │ │ ├── test_auto_ParseDICOMDir.py │ │ │ ├── test_auto_ReconAll.py │ │ │ ├── test_auto_Register.py │ │ │ ├── test_auto_RegisterAVItoTalairach.py │ │ │ ├── test_auto_RelabelHypointensities.py │ │ │ ├── test_auto_RemoveIntersection.py │ │ │ ├── test_auto_RemoveNeck.py │ │ │ ├── test_auto_Resample.py │ │ │ ├── test_auto_RobustRegister.py │ │ │ ├── test_auto_RobustTemplate.py │ │ │ ├── test_auto_SampleToSurface.py │ │ │ ├── test_auto_SegStats.py │ │ │ ├── test_auto_SegStatsReconAll.py │ │ │ ├── test_auto_SegmentCC.py │ │ │ ├── test_auto_SegmentWM.py │ │ │ ├── test_auto_Smooth.py │ │ │ ├── test_auto_SmoothTessellation.py │ │ │ ├── test_auto_Sphere.py │ │ │ ├── test_auto_SphericalAverage.py │ │ │ ├── test_auto_Surface2VolTransform.py │ │ │ ├── test_auto_SurfaceSmooth.py │ │ │ ├── test_auto_SurfaceSnapshots.py │ │ │ ├── test_auto_SurfaceTransform.py │ │ │ ├── test_auto_SynthesizeFLASH.py │ │ │ ├── test_auto_TalairachAVI.py │ │ │ ├── test_auto_TalairachQC.py │ │ │ ├── test_auto_Tkregister2.py │ │ │ ├── test_auto_UnpackSDICOMDir.py │ │ │ ├── test_auto_VolumeMask.py │ │ │ ├── test_auto_WatershedSkullStrip.py │ │ │ ├── test_model.py │ │ │ ├── test_preprocess.py │ │ │ └── test_utils.py │ │ └── utils.py │ ├── fsl │ │ ├── __init__.py │ │ ├── aroma.py │ │ ├── base.py │ │ ├── dti.py │ │ ├── epi.py │ │ ├── fix.py │ │ ├── maths.py │ │ ├── model.py │ │ ├── model_templates │ │ │ ├── feat_contrast_element.tcl │ │ │ ├── feat_contrast_ftest_element.tcl │ │ │ ├── feat_contrast_header.tcl │ │ │ ├── feat_contrast_prolog.tcl │ │ │ ├── feat_contrastmask_element.tcl │ │ │ ├── feat_contrastmask_footer.tcl │ │ │ ├── feat_contrastmask_header.tcl │ │ │ ├── feat_contrasts.tcl │ │ │ ├── feat_ev_custom.tcl │ │ │ ├── feat_ev_gamma.tcl │ │ │ ├── feat_ev_hrf.tcl │ │ │ ├── feat_ev_none.tcl │ │ │ ├── feat_ev_ortho.tcl │ │ │ ├── feat_fe_copes.tcl │ │ │ ├── feat_fe_ev_element.tcl │ │ │ ├── feat_fe_ev_header.tcl │ │ │ ├── feat_fe_featdirs.tcl │ │ │ ├── feat_fe_footer.tcl │ │ │ ├── feat_fe_header.tcl │ │ │ ├── feat_header.tcl │ │ │ ├── feat_header_l1.tcl │ │ │ ├── feat_nongui.tcl │ │ │ └── featreg_header.tcl │ │ ├── possum.py │ │ ├── preprocess.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_FILMGLS.py │ │ │ ├── test_Level1Design_functions.py │ │ │ ├── test_auto_AR1Image.py │ │ │ ├── test_auto_AccuracyTester.py │ │ │ ├── test_auto_ApplyMask.py │ │ │ ├── test_auto_ApplyTOPUP.py │ │ │ ├── test_auto_ApplyWarp.py │ │ │ ├── test_auto_ApplyXFM.py │ │ │ ├── test_auto_AvScale.py │ │ │ ├── test_auto_B0Calc.py │ │ │ ├── test_auto_BEDPOSTX5.py │ │ │ ├── test_auto_BET.py │ │ │ ├── test_auto_BinaryMaths.py │ │ │ ├── test_auto_ChangeDataType.py │ │ │ ├── test_auto_Classifier.py │ │ │ ├── test_auto_Cleaner.py │ │ │ ├── test_auto_Cluster.py │ │ │ ├── test_auto_Complex.py │ │ │ ├── test_auto_ContrastMgr.py │ │ │ ├── test_auto_ConvertWarp.py │ │ │ ├── test_auto_ConvertXFM.py │ │ │ ├── test_auto_CopyGeom.py │ │ │ ├── test_auto_DTIFit.py │ │ │ ├── test_auto_DilateImage.py │ │ │ ├── test_auto_DistanceMap.py │ │ │ ├── test_auto_DualRegression.py │ │ │ ├── test_auto_EPIDeWarp.py │ │ │ ├── test_auto_Eddy.py │ │ │ ├── test_auto_EddyCorrect.py │ │ │ ├── test_auto_EddyQuad.py │ │ │ ├── test_auto_EpiReg.py │ │ │ ├── test_auto_ErodeImage.py │ │ │ ├── test_auto_ExtractROI.py │ │ │ ├── test_auto_FAST.py │ │ │ ├── test_auto_FEAT.py │ │ │ ├── test_auto_FEATModel.py │ │ │ ├── test_auto_FEATRegister.py │ │ │ ├── test_auto_FIRST.py │ │ │ ├── test_auto_FLAMEO.py │ │ │ ├── test_auto_FLIRT.py │ │ │ ├── test_auto_FNIRT.py │ │ │ ├── test_auto_FSLCommand.py │ │ │ ├── test_auto_FSLXCommand.py │ │ │ ├── test_auto_FUGUE.py │ │ │ ├── test_auto_FeatureExtractor.py │ │ │ ├── test_auto_FilterRegressor.py │ │ │ ├── test_auto_FindTheBiggest.py │ │ │ ├── test_auto_GLM.py │ │ │ ├── test_auto_ICA_AROMA.py │ │ │ ├── test_auto_ImageMaths.py │ │ │ ├── test_auto_ImageMeants.py │ │ │ ├── test_auto_ImageStats.py │ │ │ ├── test_auto_InvWarp.py │ │ │ ├── test_auto_IsotropicSmooth.py │ │ │ ├── test_auto_L2Model.py │ │ │ ├── test_auto_Level1Design.py │ │ │ ├── test_auto_MCFLIRT.py │ │ │ ├── test_auto_MELODIC.py │ │ │ ├── test_auto_MakeDyadicVectors.py │ │ │ ├── test_auto_MathsCommand.py │ │ │ ├── test_auto_MaxImage.py │ │ │ ├── test_auto_MaxnImage.py │ │ │ ├── test_auto_MeanImage.py │ │ │ ├── test_auto_MedianImage.py │ │ │ ├── test_auto_Merge.py │ │ │ ├── test_auto_MinImage.py │ │ │ ├── test_auto_MotionOutliers.py │ │ │ ├── test_auto_MultiImageMaths.py │ │ │ ├── test_auto_MultipleRegressDesign.py │ │ │ ├── test_auto_Overlay.py │ │ │ ├── test_auto_PRELUDE.py │ │ │ ├── test_auto_PercentileImage.py │ │ │ ├── test_auto_PlotMotionParams.py │ │ │ ├── test_auto_PlotTimeSeries.py │ │ │ ├── test_auto_PowerSpectrum.py │ │ │ ├── test_auto_PrepareFieldmap.py │ │ │ ├── test_auto_ProbTrackX.py │ │ │ ├── test_auto_ProbTrackX2.py │ │ │ ├── test_auto_ProjThresh.py │ │ │ ├── test_auto_Randomise.py │ │ │ ├── test_auto_Reorient2Std.py │ │ │ ├── test_auto_RobustFOV.py │ │ │ ├── test_auto_SMM.py │ │ │ ├── test_auto_SUSAN.py │ │ │ ├── test_auto_SigLoss.py │ │ │ ├── test_auto_Slice.py │ │ │ ├── test_auto_SliceTimer.py │ │ │ ├── test_auto_Slicer.py │ │ │ ├── test_auto_Smooth.py │ │ │ ├── test_auto_SmoothEstimate.py │ │ │ ├── test_auto_SpatialFilter.py │ │ │ ├── test_auto_Split.py │ │ │ ├── test_auto_StdImage.py │ │ │ ├── test_auto_SwapDimensions.py │ │ │ ├── test_auto_TOPUP.py │ │ │ ├── test_auto_TemporalFilter.py │ │ │ ├── test_auto_Text2Vest.py │ │ │ ├── test_auto_Threshold.py │ │ │ ├── test_auto_TractSkeleton.py │ │ │ ├── test_auto_Training.py │ │ │ ├── test_auto_TrainingSetCreator.py │ │ │ ├── test_auto_UnaryMaths.py │ │ │ ├── test_auto_VecReg.py │ │ │ ├── test_auto_Vest2Text.py │ │ │ ├── test_auto_WarpPoints.py │ │ │ ├── test_auto_WarpPointsFromStd.py │ │ │ ├── test_auto_WarpPointsToStd.py │ │ │ ├── test_auto_WarpUtils.py │ │ │ ├── test_auto_XFibres5.py │ │ │ ├── test_base.py │ │ │ ├── test_dti.py │ │ │ ├── test_epi.py │ │ │ ├── test_maths.py │ │ │ ├── test_model.py │ │ │ ├── test_preprocess.py │ │ │ └── test_utils.py │ │ └── utils.py │ ├── image.py │ ├── io.py │ ├── matlab.py │ ├── meshfix.py │ ├── minc │ │ ├── __init__.py │ │ ├── base.py │ │ ├── minc.py │ │ ├── testdata.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_Average.py │ │ │ ├── test_auto_BBox.py │ │ │ ├── test_auto_Beast.py │ │ │ ├── test_auto_BestLinReg.py │ │ │ ├── test_auto_BigAverage.py │ │ │ ├── test_auto_Blob.py │ │ │ ├── test_auto_Blur.py │ │ │ ├── test_auto_Calc.py │ │ │ ├── test_auto_Convert.py │ │ │ ├── test_auto_Copy.py │ │ │ ├── test_auto_Dump.py │ │ │ ├── test_auto_Extract.py │ │ │ ├── test_auto_Gennlxfm.py │ │ │ ├── test_auto_Math.py │ │ │ ├── test_auto_NlpFit.py │ │ │ ├── test_auto_Norm.py │ │ │ ├── test_auto_Pik.py │ │ │ ├── test_auto_Resample.py │ │ │ ├── test_auto_Reshape.py │ │ │ ├── test_auto_ToEcat.py │ │ │ ├── test_auto_ToRaw.py │ │ │ ├── test_auto_VolSymm.py │ │ │ ├── test_auto_Volcentre.py │ │ │ ├── test_auto_Voliso.py │ │ │ ├── test_auto_Volpad.py │ │ │ ├── test_auto_XfmAvg.py │ │ │ ├── test_auto_XfmConcat.py │ │ │ └── test_auto_XfmInvert.py │ ├── mipav │ │ ├── __init__.py │ │ ├── developer.py │ │ ├── generate_classes.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_JistBrainMgdmSegmentation.py │ │ │ ├── test_auto_JistBrainMp2rageDuraEstimation.py │ │ │ ├── test_auto_JistBrainMp2rageSkullStripping.py │ │ │ ├── test_auto_JistBrainPartialVolumeFilter.py │ │ │ ├── test_auto_JistCortexSurfaceMeshInflation.py │ │ │ ├── test_auto_JistIntensityMp2rageMasking.py │ │ │ ├── test_auto_JistLaminarProfileCalculator.py │ │ │ ├── test_auto_JistLaminarProfileGeometry.py │ │ │ ├── test_auto_JistLaminarProfileSampling.py │ │ │ ├── test_auto_JistLaminarROIAveraging.py │ │ │ ├── test_auto_JistLaminarVolumetricLayering.py │ │ │ ├── test_auto_MedicAlgorithmImageCalculator.py │ │ │ ├── test_auto_MedicAlgorithmLesionToads.py │ │ │ ├── test_auto_MedicAlgorithmMipavReorient.py │ │ │ ├── test_auto_MedicAlgorithmN3.py │ │ │ ├── test_auto_MedicAlgorithmSPECTRE2010.py │ │ │ ├── test_auto_MedicAlgorithmThresholdToBinaryMask.py │ │ │ └── test_auto_RandomVol.py │ ├── mixins │ │ ├── __init__.py │ │ ├── fixheader.py │ │ ├── reporting.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_CopyHeaderInterface.py │ │ │ └── test_auto_ReportCapableInterface.py │ ├── mne │ │ ├── __init__.py │ │ ├── base.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ └── test_auto_WatershedBEM.py │ ├── mrtrix │ │ ├── __init__.py │ │ ├── convert.py │ │ ├── defhdr.mat │ │ ├── preprocess.py │ │ ├── tensors.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_ConstrainedSphericalDeconvolution.py │ │ │ ├── test_auto_DWI2SphericalHarmonicsImage.py │ │ │ ├── test_auto_DWI2Tensor.py │ │ │ ├── test_auto_DiffusionTensorStreamlineTrack.py │ │ │ ├── test_auto_Directions2Amplitude.py │ │ │ ├── test_auto_Erode.py │ │ │ ├── test_auto_EstimateResponseForSH.py │ │ │ ├── test_auto_FSL2MRTrix.py │ │ │ ├── test_auto_FilterTracks.py │ │ │ ├── test_auto_FindShPeaks.py │ │ │ ├── test_auto_GenerateDirections.py │ │ │ ├── test_auto_GenerateWhiteMatterMask.py │ │ │ ├── test_auto_MRConvert.py │ │ │ ├── test_auto_MRMultiply.py │ │ │ ├── test_auto_MRTransform.py │ │ │ ├── test_auto_MRTrix2TrackVis.py │ │ │ ├── test_auto_MRTrixInfo.py │ │ │ ├── test_auto_MRTrixViewer.py │ │ │ ├── test_auto_MedianFilter3D.py │ │ │ ├── test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py │ │ │ ├── test_auto_SphericallyDeconvolutedStreamlineTrack.py │ │ │ ├── test_auto_StreamlineTrack.py │ │ │ ├── test_auto_Tensor2ApparentDiffusion.py │ │ │ ├── test_auto_Tensor2FractionalAnisotropy.py │ │ │ ├── test_auto_Tensor2Vector.py │ │ │ ├── test_auto_Threshold.py │ │ │ └── test_auto_Tracks2Prob.py │ │ └── tracking.py │ ├── mrtrix3 │ │ ├── __init__.py │ │ ├── base.py │ │ ├── connectivity.py │ │ ├── preprocess.py │ │ ├── reconst.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_ACTPrepareFSL.py │ │ │ ├── test_auto_BrainMask.py │ │ │ ├── test_auto_BuildConnectome.py │ │ │ ├── test_auto_ComputeTDI.py │ │ │ ├── test_auto_ConstrainedSphericalDeconvolution.py │ │ │ ├── test_auto_DWIBiasCorrect.py │ │ │ ├── test_auto_DWIDenoise.py │ │ │ ├── test_auto_DWIExtract.py │ │ │ ├── test_auto_DWIPreproc.py │ │ │ ├── test_auto_EstimateFOD.py │ │ │ ├── test_auto_FitTensor.py │ │ │ ├── test_auto_Generate5tt.py │ │ │ ├── test_auto_Generate5tt2gmwmi.py │ │ │ ├── test_auto_LabelConfig.py │ │ │ ├── test_auto_LabelConvert.py │ │ │ ├── test_auto_MRCat.py │ │ │ ├── test_auto_MRConvert.py │ │ │ ├── test_auto_MRDeGibbs.py │ │ │ ├── test_auto_MRMath.py │ │ │ ├── test_auto_MRResize.py │ │ │ ├── test_auto_MRTransform.py │ │ │ ├── test_auto_MRTrix3Base.py │ │ │ ├── test_auto_MTNormalise.py │ │ │ ├── test_auto_MaskFilter.py │ │ │ ├── test_auto_Mesh2PVE.py │ │ │ ├── test_auto_ReplaceFSwithFIRST.py │ │ │ ├── test_auto_ResponseSD.py │ │ │ ├── test_auto_SH2Amp.py │ │ │ ├── test_auto_SHConv.py │ │ │ ├── test_auto_TCK2VTK.py │ │ │ ├── test_auto_TensorMetrics.py │ │ │ ├── test_auto_Tractography.py │ │ │ └── test_auto_TransformFSLConvert.py │ │ ├── tracking.py │ │ └── utils.py │ ├── niftyfit │ │ ├── __init__.py │ │ ├── asl.py │ │ ├── base.py │ │ ├── dwi.py │ │ ├── qt1.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_asl.py │ │ │ ├── test_auto_DwiTool.py │ │ │ ├── test_auto_FitAsl.py │ │ │ ├── test_auto_FitDwi.py │ │ │ ├── test_auto_FitQt1.py │ │ │ ├── test_auto_NiftyFitCommand.py │ │ │ ├── test_dwi.py │ │ │ └── test_qt1.py │ ├── niftyreg │ │ ├── __init__.py │ │ ├── base.py │ │ ├── reg.py │ │ ├── regutils.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_NiftyRegCommand.py │ │ │ ├── test_auto_RegAladin.py │ │ │ ├── test_auto_RegAverage.py │ │ │ ├── test_auto_RegF3D.py │ │ │ ├── test_auto_RegJacobian.py │ │ │ ├── test_auto_RegMeasure.py │ │ │ ├── test_auto_RegResample.py │ │ │ ├── test_auto_RegTools.py │ │ │ ├── test_auto_RegTransform.py │ │ │ ├── test_reg.py │ │ │ └── test_regutils.py │ ├── niftyseg │ │ ├── __init__.py │ │ ├── base.py │ │ ├── em.py │ │ ├── label_fusion.py │ │ ├── lesions.py │ │ ├── maths.py │ │ ├── patchmatch.py │ │ ├── stats.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_BinaryMaths.py │ │ │ ├── test_auto_BinaryMathsInteger.py │ │ │ ├── test_auto_BinaryStats.py │ │ │ ├── test_auto_CalcTopNCC.py │ │ │ ├── test_auto_EM.py │ │ │ ├── test_auto_FillLesions.py │ │ │ ├── test_auto_LabelFusion.py │ │ │ ├── test_auto_MathsCommand.py │ │ │ ├── test_auto_Merge.py │ │ │ ├── test_auto_NiftySegCommand.py │ │ │ ├── test_auto_PatchMatch.py │ │ │ ├── test_auto_StatsCommand.py │ │ │ ├── test_auto_TupleMaths.py │ │ │ ├── test_auto_UnaryMaths.py │ │ │ ├── test_auto_UnaryStats.py │ │ │ ├── test_em_interfaces.py │ │ │ ├── test_extra_PatchMatch.py │ │ │ ├── test_label_fusion.py │ │ │ ├── test_lesions.py │ │ │ ├── test_maths.py │ │ │ └── test_stats.py │ ├── nilearn.py │ ├── nipy │ │ ├── __init__.py │ │ ├── base.py │ │ ├── model.py │ │ ├── preprocess.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_ComputeMask.py │ │ │ ├── test_auto_EstimateContrast.py │ │ │ ├── test_auto_FitGLM.py │ │ │ ├── test_auto_NipyBaseInterface.py │ │ │ ├── test_auto_Similarity.py │ │ │ ├── test_auto_SpaceTimeRealigner.py │ │ │ └── test_auto_Trim.py │ │ └── utils.py │ ├── nitime │ │ ├── __init__.py │ │ ├── analysis.py │ │ ├── base.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_CoherenceAnalyzer.py │ │ │ ├── test_auto_NitimeBaseInterface.py │ │ │ └── test_nitime.py │ ├── petpvc.py │ ├── quickshear.py │ ├── r.py │ ├── robex │ │ ├── __init__.py │ │ ├── preprocess.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ └── test_auto_RobexSegment.py │ ├── semtools │ │ ├── __init__.py │ │ ├── brains │ │ │ ├── __init__.py │ │ │ ├── classify.py │ │ │ ├── segmentation.py │ │ │ ├── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_auto_BRAINSPosteriorToContinuousClass.py │ │ │ │ ├── test_auto_BRAINSTalairach.py │ │ │ │ ├── test_auto_BRAINSTalairachMask.py │ │ │ │ ├── test_auto_GenerateEdgeMapImage.py │ │ │ │ ├── test_auto_GeneratePurePlugMask.py │ │ │ │ ├── test_auto_HistogramMatchingFilter.py │ │ │ │ └── test_auto_SimilarityIndex.py │ │ │ └── utilities.py │ │ ├── converters.py │ │ ├── diffusion │ │ │ ├── __init__.py │ │ │ ├── diffusion.py │ │ │ ├── gtract.py │ │ │ ├── maxcurvature.py │ │ │ ├── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_auto_DWIConvert.py │ │ │ │ ├── test_auto_compareTractInclusion.py │ │ │ │ ├── test_auto_dtiaverage.py │ │ │ │ ├── test_auto_dtiestim.py │ │ │ │ ├── test_auto_dtiprocess.py │ │ │ │ ├── test_auto_extractNrrdVectorIndex.py │ │ │ │ ├── test_auto_gtractAnisotropyMap.py │ │ │ │ ├── test_auto_gtractAverageBvalues.py │ │ │ │ ├── test_auto_gtractClipAnisotropy.py │ │ │ │ ├── test_auto_gtractCoRegAnatomy.py │ │ │ │ ├── test_auto_gtractConcatDwi.py │ │ │ │ ├── test_auto_gtractCopyImageOrientation.py │ │ │ │ ├── test_auto_gtractCoregBvalues.py │ │ │ │ ├── test_auto_gtractCostFastMarching.py │ │ │ │ ├── test_auto_gtractCreateGuideFiber.py │ │ │ │ ├── test_auto_gtractFastMarchingTracking.py │ │ │ │ ├── test_auto_gtractFiberTracking.py │ │ │ │ ├── test_auto_gtractImageConformity.py │ │ │ │ ├── test_auto_gtractInvertBSplineTransform.py │ │ │ │ ├── test_auto_gtractInvertDisplacementField.py │ │ │ │ ├── test_auto_gtractInvertRigidTransform.py │ │ │ │ ├── test_auto_gtractResampleAnisotropy.py │ │ │ │ ├── test_auto_gtractResampleB0.py │ │ │ │ ├── test_auto_gtractResampleCodeImage.py │ │ │ │ ├── test_auto_gtractResampleDWIInPlace.py │ │ │ │ ├── test_auto_gtractResampleFibers.py │ │ │ │ ├── test_auto_gtractTensor.py │ │ │ │ ├── test_auto_gtractTransformToDisplacementField.py │ │ │ │ └── test_auto_maxcurvature.py │ │ │ └── tractography │ │ │ │ ├── __init__.py │ │ │ │ ├── commandlineonly.py │ │ │ │ ├── fiberprocess.py │ │ │ │ ├── fibertrack.py │ │ │ │ ├── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_auto_UKFTractography.py │ │ │ │ ├── test_auto_fiberprocess.py │ │ │ │ ├── test_auto_fiberstats.py │ │ │ │ └── test_auto_fibertrack.py │ │ │ │ └── ukftractography.py │ │ ├── featurecreator.py │ │ ├── filtering │ │ │ ├── __init__.py │ │ │ ├── denoising.py │ │ │ ├── featuredetection.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_auto_CannyEdge.py │ │ │ │ ├── test_auto_CannySegmentationLevelSetImageFilter.py │ │ │ │ ├── test_auto_DilateImage.py │ │ │ │ ├── test_auto_DilateMask.py │ │ │ │ ├── test_auto_DistanceMaps.py │ │ │ │ ├── test_auto_DumpBinaryTrainingVectors.py │ │ │ │ ├── test_auto_ErodeImage.py │ │ │ │ ├── test_auto_FlippedDifference.py │ │ │ │ ├── test_auto_GenerateBrainClippedImage.py │ │ │ │ ├── test_auto_GenerateSummedGradientImage.py │ │ │ │ ├── test_auto_GenerateTestImage.py │ │ │ │ ├── test_auto_GradientAnisotropicDiffusionImageFilter.py │ │ │ │ ├── test_auto_HammerAttributeCreator.py │ │ │ │ ├── test_auto_NeighborhoodMean.py │ │ │ │ ├── test_auto_NeighborhoodMedian.py │ │ │ │ ├── test_auto_STAPLEAnalysis.py │ │ │ │ ├── test_auto_TextureFromNoiseImageFilter.py │ │ │ │ ├── test_auto_TextureMeasureFilter.py │ │ │ │ └── test_auto_UnbiasedNonLocalMeans.py │ │ ├── generated.sh │ │ ├── legacy │ │ │ ├── __init__.py │ │ │ ├── registration.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ └── test_auto_scalartransform.py │ │ ├── registration │ │ │ ├── __init__.py │ │ │ ├── brainsfit.py │ │ │ ├── brainsresample.py │ │ │ ├── brainsresize.py │ │ │ ├── specialized.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_auto_BRAINSDemonWarp.py │ │ │ │ ├── test_auto_BRAINSFit.py │ │ │ │ ├── test_auto_BRAINSResample.py │ │ │ │ ├── test_auto_BRAINSResize.py │ │ │ │ ├── test_auto_BRAINSTransformFromFiducials.py │ │ │ │ └── test_auto_VBRAINSDemonWarp.py │ │ ├── segmentation │ │ │ ├── __init__.py │ │ │ ├── specialized.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_auto_BRAINSABC.py │ │ │ │ ├── test_auto_BRAINSConstellationDetector.py │ │ │ │ ├── test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py │ │ │ │ ├── test_auto_BRAINSCut.py │ │ │ │ ├── test_auto_BRAINSMultiSTAPLE.py │ │ │ │ ├── test_auto_BRAINSROIAuto.py │ │ │ │ ├── test_auto_BinaryMaskEditorBasedOnLandmarks.py │ │ │ │ └── test_auto_ESLR.py │ │ ├── testing │ │ │ ├── __init__.py │ │ │ ├── featuredetection.py │ │ │ ├── generateaveragelmkfile.py │ │ │ └── landmarkscompare.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_DWICompare.py │ │ │ ├── test_auto_DWISimpleCompare.py │ │ │ └── test_auto_GenerateCsfClippedFromClassifiedImage.py │ │ └── utilities │ │ │ ├── __init__.py │ │ │ ├── brains.py │ │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_BRAINSAlignMSP.py │ │ │ ├── test_auto_BRAINSClipInferior.py │ │ │ ├── test_auto_BRAINSConstellationModeler.py │ │ │ ├── test_auto_BRAINSEyeDetector.py │ │ │ ├── test_auto_BRAINSInitializedControlPoints.py │ │ │ ├── test_auto_BRAINSLandmarkInitializer.py │ │ │ ├── test_auto_BRAINSLinearModelerEPCA.py │ │ │ ├── test_auto_BRAINSLmkTransform.py │ │ │ ├── test_auto_BRAINSMush.py │ │ │ ├── test_auto_BRAINSSnapShotWriter.py │ │ │ ├── test_auto_BRAINSTransformConvert.py │ │ │ ├── test_auto_BRAINSTrimForegroundInDirection.py │ │ │ ├── test_auto_CleanUpOverlapLabels.py │ │ │ ├── test_auto_FindCenterOfBrain.py │ │ │ ├── test_auto_GenerateLabelMapFromProbabilityMap.py │ │ │ ├── test_auto_ImageRegionPlotter.py │ │ │ ├── test_auto_JointHistogram.py │ │ │ ├── test_auto_ShuffleVectorsModule.py │ │ │ ├── test_auto_fcsv_to_hdf5.py │ │ │ ├── test_auto_insertMidACPCpoint.py │ │ │ ├── test_auto_landmarksConstellationAligner.py │ │ │ └── test_auto_landmarksConstellationWeights.py │ ├── slicer │ │ ├── __init__.py │ │ ├── base.py │ │ ├── converters.py │ │ ├── diffusion │ │ │ ├── __init__.py │ │ │ ├── diffusion.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_auto_DTIexport.py │ │ │ │ ├── test_auto_DTIimport.py │ │ │ │ ├── test_auto_DWIJointRicianLMMSEFilter.py │ │ │ │ ├── test_auto_DWIRicianLMMSEFilter.py │ │ │ │ ├── test_auto_DWIToDTIEstimation.py │ │ │ │ ├── test_auto_DiffusionTensorScalarMeasurements.py │ │ │ │ ├── test_auto_DiffusionWeightedVolumeMasking.py │ │ │ │ ├── test_auto_ResampleDTIVolume.py │ │ │ │ └── test_auto_TractographyLabelMapSeeding.py │ │ ├── filtering │ │ │ ├── __init__.py │ │ │ ├── arithmetic.py │ │ │ ├── checkerboardfilter.py │ │ │ ├── denoising.py │ │ │ ├── extractskeleton.py │ │ │ ├── histogrammatching.py │ │ │ ├── imagelabelcombine.py │ │ │ ├── morphology.py │ │ │ ├── n4itkbiasfieldcorrection.py │ │ │ ├── resamplescalarvectordwivolume.py │ │ │ ├── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_auto_AddScalarVolumes.py │ │ │ │ ├── test_auto_CastScalarVolume.py │ │ │ │ ├── test_auto_CheckerBoardFilter.py │ │ │ │ ├── test_auto_CurvatureAnisotropicDiffusion.py │ │ │ │ ├── test_auto_ExtractSkeleton.py │ │ │ │ ├── test_auto_GaussianBlurImageFilter.py │ │ │ │ ├── test_auto_GradientAnisotropicDiffusion.py │ │ │ │ ├── test_auto_GrayscaleFillHoleImageFilter.py │ │ │ │ ├── test_auto_GrayscaleGrindPeakImageFilter.py │ │ │ │ ├── test_auto_HistogramMatching.py │ │ │ │ ├── test_auto_ImageLabelCombine.py │ │ │ │ ├── test_auto_MaskScalarVolume.py │ │ │ │ ├── test_auto_MedianImageFilter.py │ │ │ │ ├── test_auto_MultiplyScalarVolumes.py │ │ │ │ ├── test_auto_N4ITKBiasFieldCorrection.py │ │ │ │ ├── test_auto_ResampleScalarVectorDWIVolume.py │ │ │ │ ├── test_auto_SubtractScalarVolumes.py │ │ │ │ ├── test_auto_ThresholdScalarVolume.py │ │ │ │ └── test_auto_VotingBinaryHoleFillingImageFilter.py │ │ │ ├── thresholdscalarvolume.py │ │ │ └── votingbinaryholefillingimagefilter.py │ │ ├── generate_classes.py │ │ ├── legacy │ │ │ ├── __init__.py │ │ │ ├── converters.py │ │ │ ├── diffusion │ │ │ │ ├── __init__.py │ │ │ │ ├── denoising.py │ │ │ │ └── tests │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── test_auto_DWIUnbiasedNonLocalMeansFilter.py │ │ │ ├── filtering.py │ │ │ ├── registration.py │ │ │ ├── segmentation.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_auto_AffineRegistration.py │ │ │ │ ├── test_auto_BSplineDeformableRegistration.py │ │ │ │ ├── test_auto_BSplineToDeformationField.py │ │ │ │ ├── test_auto_ExpertAutomatedRegistration.py │ │ │ │ ├── test_auto_LinearRegistration.py │ │ │ │ ├── test_auto_MultiResolutionAffineRegistration.py │ │ │ │ ├── test_auto_OtsuThresholdImageFilter.py │ │ │ │ ├── test_auto_OtsuThresholdSegmentation.py │ │ │ │ ├── test_auto_ResampleScalarVolume.py │ │ │ │ └── test_auto_RigidRegistration.py │ │ ├── quantification │ │ │ ├── __init__.py │ │ │ ├── changequantification.py │ │ │ ├── petstandarduptakevaluecomputation.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_auto_IntensityDifferenceMetric.py │ │ │ │ └── test_auto_PETStandardUptakeValueComputation.py │ │ ├── registration │ │ │ ├── __init__.py │ │ │ ├── brainsfit.py │ │ │ ├── brainsresample.py │ │ │ ├── specialized.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_auto_ACPCTransform.py │ │ │ │ ├── test_auto_BRAINSDemonWarp.py │ │ │ │ ├── test_auto_BRAINSFit.py │ │ │ │ ├── test_auto_BRAINSResample.py │ │ │ │ ├── test_auto_FiducialRegistration.py │ │ │ │ └── test_auto_VBRAINSDemonWarp.py │ │ ├── segmentation │ │ │ ├── __init__.py │ │ │ ├── simpleregiongrowingsegmentation.py │ │ │ ├── specialized.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── test_auto_BRAINSROIAuto.py │ │ │ │ ├── test_auto_EMSegmentCommandLine.py │ │ │ │ ├── test_auto_RobustStatisticsSegmenter.py │ │ │ │ └── test_auto_SimpleRegionGrowingSegmentation.py │ │ ├── surface.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_DicomToNrrdConverter.py │ │ │ ├── test_auto_EMSegmentTransformToNewFormat.py │ │ │ ├── test_auto_GrayscaleModelMaker.py │ │ │ ├── test_auto_LabelMapSmoothing.py │ │ │ ├── test_auto_MergeModels.py │ │ │ ├── test_auto_ModelMaker.py │ │ │ ├── test_auto_ModelToLabelMap.py │ │ │ ├── test_auto_OrientScalarVolume.py │ │ │ ├── test_auto_ProbeVolumeWithModel.py │ │ │ └── test_auto_SlicerCommandLine.py │ │ └── utilities.py │ ├── spm │ │ ├── __init__.py │ │ ├── base.py │ │ ├── model.py │ │ ├── preprocess.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_Analyze2nii.py │ │ │ ├── test_auto_ApplyDeformations.py │ │ │ ├── test_auto_ApplyInverseDeformation.py │ │ │ ├── test_auto_ApplyTransform.py │ │ │ ├── test_auto_ApplyVDM.py │ │ │ ├── test_auto_CalcCoregAffine.py │ │ │ ├── test_auto_Coregister.py │ │ │ ├── test_auto_CreateWarped.py │ │ │ ├── test_auto_DARTEL.py │ │ │ ├── test_auto_DARTELNorm2MNI.py │ │ │ ├── test_auto_DicomImport.py │ │ │ ├── test_auto_EstimateContrast.py │ │ │ ├── test_auto_EstimateModel.py │ │ │ ├── test_auto_FactorialDesign.py │ │ │ ├── test_auto_FieldMap.py │ │ │ ├── test_auto_Level1Design.py │ │ │ ├── test_auto_MultiChannelNewSegment.py │ │ │ ├── test_auto_MultipleRegressionDesign.py │ │ │ ├── test_auto_NewSegment.py │ │ │ ├── test_auto_Normalize.py │ │ │ ├── test_auto_Normalize12.py │ │ │ ├── test_auto_OneSampleTTestDesign.py │ │ │ ├── test_auto_PairedTTestDesign.py │ │ │ ├── test_auto_Realign.py │ │ │ ├── test_auto_RealignUnwarp.py │ │ │ ├── test_auto_Reslice.py │ │ │ ├── test_auto_ResliceToReference.py │ │ │ ├── test_auto_SPMCommand.py │ │ │ ├── test_auto_Segment.py │ │ │ ├── test_auto_SliceTiming.py │ │ │ ├── test_auto_Smooth.py │ │ │ ├── test_auto_Threshold.py │ │ │ ├── test_auto_ThresholdStatistics.py │ │ │ ├── test_auto_TwoSampleTTestDesign.py │ │ │ ├── test_auto_VBMSegment.py │ │ │ ├── test_base.py │ │ │ ├── test_model.py │ │ │ ├── test_preprocess.py │ │ │ └── test_utils.py │ │ └── utils.py │ ├── tests │ │ ├── __init__.py │ │ ├── test_auto_BIDSDataGrabber.py │ │ ├── test_auto_Bru2.py │ │ ├── test_auto_C3d.py │ │ ├── test_auto_C3dAffineTool.py │ │ ├── test_auto_CopyMeta.py │ │ ├── test_auto_DataFinder.py │ │ ├── test_auto_DataGrabber.py │ │ ├── test_auto_DataSink.py │ │ ├── test_auto_Dcm2nii.py │ │ ├── test_auto_Dcm2niix.py │ │ ├── test_auto_DcmStack.py │ │ ├── test_auto_ExportFile.py │ │ ├── test_auto_FreeSurferSource.py │ │ ├── test_auto_GroupAndStack.py │ │ ├── test_auto_IOBase.py │ │ ├── test_auto_JSONFileGrabber.py │ │ ├── test_auto_JSONFileSink.py │ │ ├── test_auto_LookupMeta.py │ │ ├── test_auto_MatlabCommand.py │ │ ├── test_auto_MergeNifti.py │ │ ├── test_auto_MeshFix.py │ │ ├── test_auto_MySQLSink.py │ │ ├── test_auto_NiftiGeneratorBase.py │ │ ├── test_auto_NilearnBaseInterface.py │ │ ├── test_auto_PETPVC.py │ │ ├── test_auto_Quickshear.py │ │ ├── test_auto_RCommand.py │ │ ├── test_auto_Reorient.py │ │ ├── test_auto_Rescale.py │ │ ├── test_auto_S3DataGrabber.py │ │ ├── test_auto_SQLiteSink.py │ │ ├── test_auto_SSHDataGrabber.py │ │ ├── test_auto_SelectFiles.py │ │ ├── test_auto_SignalExtraction.py │ │ ├── test_auto_SlicerCommandLine.py │ │ ├── test_auto_SplitNifti.py │ │ ├── test_auto_XNATSink.py │ │ ├── test_auto_XNATSource.py │ │ ├── test_dcm2nii.py │ │ ├── test_extra_dcm2nii.py │ │ ├── test_image.py │ │ ├── test_io.py │ │ ├── test_matlab.py │ │ ├── test_nilearn.py │ │ └── test_r.py │ ├── utility │ │ ├── __init__.py │ │ ├── base.py │ │ ├── csv.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_AssertEqual.py │ │ │ ├── test_auto_CSVReader.py │ │ │ ├── test_auto_Function.py │ │ │ ├── test_auto_IdentityInterface.py │ │ │ ├── test_auto_Merge.py │ │ │ ├── test_auto_Rename.py │ │ │ ├── test_auto_Select.py │ │ │ ├── test_auto_Split.py │ │ │ ├── test_base.py │ │ │ ├── test_csv.py │ │ │ └── test_wrappers.py │ │ └── wrappers.py │ ├── vista │ │ ├── __init__.py │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_auto_Vnifti2Image.py │ │ │ └── test_auto_VtoMat.py │ │ └── vista.py │ ├── vtkbase.py │ └── workbench │ │ ├── __init__.py │ │ ├── base.py │ │ ├── cifti.py │ │ ├── metric.py │ │ └── tests │ │ ├── __init__.py │ │ ├── test_auto_CiftiSmooth.py │ │ ├── test_auto_MetricResample.py │ │ └── test_auto_WBCommand.py ├── pipeline │ ├── __init__.py │ ├── engine │ │ ├── __init__.py │ │ ├── base.py │ │ ├── nodes.py │ │ ├── report_template.html │ │ ├── report_template2.html │ │ ├── tests │ │ │ ├── __init__.py │ │ │ ├── test_base.py │ │ │ ├── test_engine.py │ │ │ ├── test_join.py │ │ │ ├── test_nodes.py │ │ │ ├── test_utils.py │ │ │ └── test_workflows.py │ │ ├── utils.py │ │ └── workflows.py │ └── plugins │ │ ├── __init__.py │ │ ├── base.py │ │ ├── condor.py │ │ ├── dagman.py │ │ ├── debug.py │ │ ├── ipython.py │ │ ├── legacymultiproc.py │ │ ├── linear.py │ │ ├── lsf.py │ │ ├── multiproc.py │ │ ├── oar.py │ │ ├── pbs.py │ │ ├── pbsgraph.py │ │ ├── semaphore_singleton.py │ │ ├── sge.py │ │ ├── sgegraph.py │ │ ├── slurm.py │ │ ├── slurmgraph.py │ │ ├── somaflow.py │ │ ├── tests │ │ ├── __init__.py │ │ ├── test_base.py │ │ ├── test_callback.py │ │ ├── test_debug.py │ │ ├── test_legacymultiproc_nondaemon.py │ │ ├── test_linear.py │ │ ├── test_multiproc.py │ │ ├── test_oar.py │ │ ├── test_pbs.py │ │ ├── test_sgelike.py │ │ ├── test_somaflow.py │ │ └── test_tools.py │ │ └── tools.py ├── pkg_info.py ├── pytest.ini ├── refs.py ├── scripts │ ├── __init__.py │ ├── cli.py │ ├── crash_files.py │ ├── instance.py │ └── utils.py ├── sphinxext │ ├── __init__.py │ ├── apidoc │ │ ├── __init__.py │ │ └── docstring.py │ ├── documenter.py │ ├── gh.py │ └── plot_workflow.py ├── testing │ ├── __init__.py │ ├── data │ │ ├── 4d_dwi.nii │ │ ├── 5tt_in.mif │ │ ├── A.scheme │ │ ├── A_qmat.Bdouble │ │ ├── A_recon_params.Bdouble │ │ ├── AffineTransform.mat │ │ ├── BrainSegmentationPrior01.nii.gz │ │ ├── BrainSegmentationPrior02.nii.gz │ │ ├── BrainSegmentationPrior03.nii.gz │ │ ├── BrainSegmentationPrior04.nii.gz │ │ ├── DisplacementFieldTransform.nii.gz │ │ ├── FLASH1.mgz │ │ ├── FLASH2.mgz │ │ ├── FLASH3.mgz │ │ ├── Fred+orig │ │ ├── FreeSurferColorLUT.txt │ │ ├── FreeSurferColorLUT_adapted_aparc+aseg_out.pck │ │ ├── MASK_average_thal_right.nii │ │ ├── NWARP │ │ ├── PD.mgz │ │ ├── ProbabilityMaskOfStudyTemplate.nii.gz │ │ ├── Q25_warp+tlrc.HEAD │ │ ├── QSH_peaks.Bdouble │ │ ├── README │ │ ├── ROI_scale500.nii.gz │ │ ├── SPM.mat │ │ ├── SubjectA.Bfloat │ │ ├── T1.mgz │ │ ├── T1.nii │ │ ├── T1.nii.gz │ │ ├── T1_brain.nii │ │ ├── T1map.nii.gz │ │ ├── T2.nii │ │ ├── TI4D.nii.gz │ │ ├── TPM.nii │ │ ├── Template_1_IXI550_MNI152.nii │ │ ├── Template_6.nii │ │ ├── TransformParameters.0.txt │ │ ├── afni_output.3D │ │ ├── allFA.nii │ │ ├── all_FA.nii.gz │ │ ├── anat_coreg.mif │ │ ├── anatomical.nii │ │ ├── ants_Affine.txt │ │ ├── ants_Warp.nii.gz │ │ ├── ants_deformed.nii.gz │ │ ├── aparc+aseg.nii │ │ ├── aseg.mgz │ │ ├── asl.nii.gz │ │ ├── atlas.nii.gz │ │ ├── b0.nii │ │ ├── b0.nii.gz │ │ ├── b0_b0rev.nii │ │ ├── ballstickfit_data.Bfloat │ │ ├── bedpostxout │ │ │ └── do_not_delete.txt │ │ ├── brain_mask.nii │ │ ├── brain_study_template.nii.gz │ │ ├── brain_track.Bdouble │ │ ├── brukerdir │ │ │ ├── fid │ │ │ └── pdata │ │ │ │ └── 1 │ │ │ │ └── 2dseq │ │ ├── bvals │ │ ├── bvals.scheme │ │ ├── bvecs │ │ ├── bvecs.scheme │ │ ├── c1s1.nii │ │ ├── c1s3.nii │ │ ├── clustering.mat │ │ ├── cmatrix.mat │ │ ├── complex.nii │ │ ├── config.ini │ │ ├── cont1.nii │ │ ├── cont1a.nii │ │ ├── cont2.nii │ │ ├── cont2a.nii │ │ ├── converted.trk │ │ ├── cope.nii.gz │ │ ├── cope1.nii.gz │ │ ├── cope1run1.nii.gz │ │ ├── cope1run2.nii.gz │ │ ├── cope2run1.nii.gz │ │ ├── cope2run2.nii.gz │ │ ├── cortex.label │ │ ├── cov_split.mat │ │ ├── csd.mif │ │ ├── csffod.mif │ │ ├── data.Bfloat │ │ ├── db.xml │ │ ├── degree.csv │ │ ├── degree.mat │ │ ├── design.con │ │ ├── design.mat │ │ ├── design.txt │ │ ├── dicomdir │ │ │ └── 123456-1-1.dcm │ │ ├── diffusion.nii │ │ ├── diffusion_weighted.nii │ │ ├── dilated_wm_mask.nii │ │ ├── dirs.txt │ │ ├── dofrun1 │ │ ├── dofrun2 │ │ ├── ds003_sub-01_mc.DVARS │ │ ├── ds003_sub-01_mc.nii.gz │ │ ├── ds003_sub-01_mc_brainmask.nii.gz │ │ ├── ds005 │ │ │ └── filler.txt │ │ ├── dteig.Bdouble │ │ ├── dti.mif │ │ ├── dwi.mif │ │ ├── dwi.nii.gz │ │ ├── dwi2anat_InverseWarp.nii.gz │ │ ├── dwi2anat_Warp.nii.gz │ │ ├── dwi2anat_coreg_Affine.txt │ │ ├── dwi_CSD_tracked.tck │ │ ├── dwi_FA.mif │ │ ├── dwi_WMProb.mif │ │ ├── dwi_evals.nii │ │ ├── dwi_tensor.mif │ │ ├── elastix.txt │ │ ├── encoding.txt │ │ ├── epi.nii │ │ ├── epi_acqp.txt │ │ ├── epi_index.txt │ │ ├── epi_mask.nii │ │ ├── epi_param.txt │ │ ├── epi_phasediff.nii │ │ ├── epi_rev.nii │ │ ├── epi_slspec.txt │ │ ├── events.tsv │ │ ├── f1.1D │ │ ├── f2.1D │ │ ├── fa.nii.gz │ │ ├── fdir00.nii │ │ ├── fdir01.nii │ │ ├── ffra00.nii │ │ ├── ffra01.nii │ │ ├── fieldmap_mag.nii │ │ ├── fieldmap_mag_brain.nii │ │ ├── fieldmap_phase_fslprepared.nii │ │ ├── first_merged.nii.gz │ │ ├── fitted_data1.Bfloat │ │ ├── fitted_data2.Bfloat │ │ ├── fixed1.nii │ │ ├── fixed2.nii │ │ ├── flash_05.mgz │ │ ├── flash_30.mgz │ │ ├── flirt.mat │ │ ├── fmri_timeseries.csv │ │ ├── fmri_timeseries_nolabels.csv │ │ ├── fods.mif │ │ ├── fsLUT_aparc+aseg.pck │ │ ├── fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii │ │ ├── fs_LR.L.midthickness_va_avg.32k_fs_LR.shape.gii │ │ ├── fsaverage5.L.midthickness_va_avg.10k_fsavg_L.shape.gii │ │ ├── fsaverage5_std_sphere.L.10k_fsavg_L.surf.gii │ │ ├── fsl_mcflirt_movpar.txt │ │ ├── fsl_motion_outliers_fd.txt │ │ ├── func2anat_InverseWarp.nii.gz │ │ ├── func2anat_coreg_Affine.txt │ │ ├── func2anat_coreg_InverseWarp.nii.gz │ │ ├── func_epi_1_1.nii │ │ ├── func_to_struct.mat │ │ ├── functional.HEAD │ │ ├── functional.nii │ │ ├── functional.par │ │ ├── functional.rms │ │ ├── functional2.nii │ │ ├── functional3.nii │ │ ├── functional_1.dcm │ │ ├── functional_2.dcm │ │ ├── gmfod.mif │ │ ├── grad.b │ │ ├── grads.txt │ │ ├── gtmseg.mgz │ │ ├── gtmseg.nii │ │ ├── im1.nii │ │ ├── im2.nii │ │ ├── im3.nii │ │ ├── im_affine.aff │ │ ├── im_warp.df.nii │ │ ├── image.nii │ │ ├── image.v │ │ ├── indices-labels.txt │ │ ├── indices.txt │ │ ├── input1.xfm │ │ ├── jsongrabber.txt │ │ ├── label.mgz │ │ ├── lh-pial.stl │ │ ├── lh.aparc_a2009s.freesurfer.annot │ │ ├── lh.area.structural │ │ ├── lh.central.structural.gii │ │ ├── lh.cope1.mgz │ │ ├── lh.cope1.nii.gz │ │ ├── lh.hippocampus.stl │ │ ├── lh.pbt.structural │ │ ├── lh.pial │ │ ├── lh.pial_converted.gii │ │ ├── lh.sphere.reg.structural.gii │ │ ├── lh.sphere.structural.gii │ │ ├── lh.white │ │ ├── lta1.lta │ │ ├── lta2.lta │ │ ├── lut_file │ │ ├── magnitude.nii │ │ ├── maps.nii │ │ ├── mask.1D │ │ ├── mask.mif │ │ ├── mask.nii │ │ ├── mask.nii.gz │ │ ├── mean_func.nii.gz │ │ ├── merged_f1samples.nii.gz │ │ ├── merged_fsamples.nii │ │ ├── merged_ph1samples.nii.gz │ │ ├── merged_phsamples.nii │ │ ├── merged_th1samples.nii.gz │ │ ├── merged_thsamples.nii │ │ ├── minc_initial.xfm │ │ ├── minc_nlp.conf │ │ ├── minc_test_2D_00.mnc │ │ ├── minc_test_2D_01.mnc │ │ ├── minc_test_2D_02.mnc │ │ ├── minc_test_2D_03.mnc │ │ ├── minc_test_2D_04.mnc │ │ ├── minc_test_2D_05.mnc │ │ ├── minc_test_2D_06.mnc │ │ ├── minc_test_2D_07.mnc │ │ ├── minc_test_2D_08.mnc │ │ ├── minc_test_2D_09.mnc │ │ ├── minc_test_3D_00.mnc │ │ ├── minc_test_3D_01.mnc │ │ ├── minc_test_3D_02.mnc │ │ ├── minc_test_3D_03.mnc │ │ ├── minc_test_3D_04.mnc │ │ ├── minc_test_3D_05.mnc │ │ ├── minc_test_3D_06.mnc │ │ ├── minc_test_3D_07.mnc │ │ ├── minc_test_3D_08.mnc │ │ ├── minc_test_3D_09.mnc │ │ ├── mni.nii │ │ ├── mni2t1.nii │ │ ├── model.pklz │ │ ├── moving.csv │ │ ├── moving1.nii │ │ ├── moving2.nii │ │ ├── mrtrix3_labelconfig.txt │ │ ├── my_database.db │ │ ├── network0.aparc+aseg.nii │ │ ├── network0.gpickle │ │ ├── nipype2boutiques_example.json │ │ ├── nodif_brain_mask.nii.gz │ │ ├── norm.mgz │ │ ├── output.csv │ │ ├── output_Composite.h5 │ │ ├── pdfs.Bfloat │ │ ├── peak_directions.mif │ │ ├── pet.nii.gz │ │ ├── pet_resliced.nii │ │ ├── phase.nii │ │ ├── rc1s1.nii │ │ ├── rc1s2.nii │ │ ├── rc2s1.nii │ │ ├── rc2s2.nii │ │ ├── realign_json.json │ │ ├── ref_class0.nii │ │ ├── ref_class1.nii │ │ ├── ref_tac.dat │ │ ├── register.dat │ │ ├── register.mat │ │ ├── resp.1D │ │ ├── response.txt │ │ ├── resting.nii │ │ ├── resting2anat_Warp.nii.gz │ │ ├── resting2anat_coreg_Affine.txt │ │ ├── rgb.nii.gz │ │ ├── rh-pial.stl │ │ ├── rh.aparc_a2009s.freesurfer.annot │ │ ├── rh.central.structural.gii │ │ ├── rh.pbt.structural │ │ ├── rh.pial │ │ ├── rh.pial_converted.gii │ │ ├── rh.sphere.reg.structural.gii │ │ ├── rh.sphere.structural.gii │ │ ├── roi01.nii │ │ ├── roi01_idx.npz │ │ ├── roi02.nii │ │ ├── roi02_idx.npz │ │ ├── roi03.nii │ │ ├── roi03_idx.npz │ │ ├── roi04.nii │ │ ├── roi04_idx.npz │ │ ├── roi05.nii │ │ ├── roi05_idx.npz │ │ ├── run1+orig │ │ ├── run1+orig_model │ │ ├── run1_categories.1D │ │ ├── run2+orig │ │ ├── run2_categories.1D │ │ ├── seed.1D │ │ ├── seed_mask.nii │ │ ├── seed_source.nii.gz │ │ ├── seeds_to_M1.nii │ │ ├── seeds_to_M2.nii │ │ ├── segmentation0.nii.gz │ │ ├── segmentation1.nii.gz │ │ ├── session_info.npz │ │ ├── sh.mif │ │ ├── skeleton_mask.nii.gz │ │ ├── smri_ants_registration_settings.json │ │ ├── spmT_0001.img │ │ ├── spminfo │ │ ├── streamlines.trk │ │ ├── struct2mni.nii │ │ ├── struct_to_func.mat │ │ ├── struct_to_template.mat │ │ ├── structural.nii │ │ ├── study_template.nii.gz │ │ ├── sub-01.L.midthickness.32k_fs_LR.surf.gii │ │ ├── sub-01.R.midthickness.32k_fs_LR.surf.gii │ │ ├── sub-01_dir-LR_epi.nii.gz │ │ ├── sub-01_dir-RL_epi.nii.gz │ │ ├── sub-01_ses-baseline_pet.nii.gz │ │ ├── sub-01_ses-baseline_pet_mean_reg.lta │ │ ├── sub-01_task-rest.dtseries.nii │ │ ├── sub-01_task-rest_bold_space-fsaverage5.L.func.gii │ │ ├── subj1.cff │ │ ├── subj1.pck │ │ ├── subj2.cff │ │ ├── subj2.pck │ │ ├── subjectDesign.con │ │ ├── subjectDesign.mat │ │ ├── surf.txt │ │ ├── surf01.vtk │ │ ├── surf1.vtk │ │ ├── surf2.vtk │ │ ├── tac.nii │ │ ├── targets_MASK1.nii │ │ ├── targets_MASK2.nii │ │ ├── tbss_dir │ │ │ └── do_not_delete.txt │ │ ├── tdi.mif │ │ ├── tensor_fitted_data.Bdouble │ │ ├── timeDesign.con │ │ ├── timeDesign.mat │ │ ├── timeseries.txt │ │ ├── timing.dat │ │ ├── tissue+air_map.nii │ │ ├── tissues.nii.gz │ │ ├── topup_encoding.txt │ │ ├── topup_fieldcoef.nii.gz │ │ ├── topup_movpar.txt │ │ ├── tpm_00.nii.gz │ │ ├── tpm_01.nii.gz │ │ ├── tpm_02.nii.gz │ │ ├── tpms_msk.nii.gz │ │ ├── track1.trk │ │ ├── track2.trk │ │ ├── tracks.tck │ │ ├── tracks.trk │ │ ├── tract_data.Bfloat │ │ ├── tracts.Bdouble │ │ ├── trans.mat │ │ ├── tst_class0.nii │ │ ├── tst_class1.nii │ │ ├── u_rc1s1_Template.nii │ │ ├── u_rc1s2_Template.nii │ │ ├── u_rc1s3_Template.nii │ │ ├── varcope.nii.gz │ │ ├── varcope1run1.nii.gz │ │ ├── varcope1run2.nii.gz │ │ ├── varcope2run1.nii.gz │ │ ├── varcope2run2.nii.gz │ │ ├── voxel-order_data.Bfloat │ │ ├── voxeldisplacemap.vdm │ │ ├── vsm.nii │ │ ├── warpfield.nii │ │ ├── weights.txt │ │ ├── wm.mgz │ │ ├── wm_mask.mif │ │ ├── wm_undersampled.nii │ │ ├── wmfod.mif │ │ └── zstat1.nii.gz │ ├── fixtures.py │ ├── tests │ │ └── test_utils.py │ └── utils.py ├── tests │ ├── __init__.py │ └── test_nipype.py ├── utils │ ├── README.txt │ ├── __init__.py │ ├── config.py │ ├── datetime.py │ ├── docparse.py │ ├── draw_gantt_chart.py │ ├── filemanip.py │ ├── functions.py │ ├── gpu_count.py │ ├── imagemanip.py │ ├── logger.py │ ├── matlabtools.py │ ├── misc.py │ ├── nipype2boutiques.py │ ├── nipype_cmd.py │ ├── onetime.py │ ├── profiler.py │ ├── provenance.py │ ├── spm_docs.py │ ├── spm_flat_config.m │ ├── spm_get_doc.m │ ├── subprocess.py │ ├── tests │ │ ├── __init__.py │ │ ├── test_cmd.py │ │ ├── test_config.py │ │ ├── test_docparse.py │ │ ├── test_filemanip.py │ │ ├── test_functions.py │ │ ├── test_imagemanip.py │ │ ├── test_misc.py │ │ ├── test_nipype2boutiques.py │ │ ├── test_provenance.py │ │ └── use_resources │ └── tmpdirs.py └── workflows │ └── __init__.py ├── pyproject.toml ├── requirements.txt ├── setup.cfg ├── setup.py ├── tools ├── checkspecs.py ├── ci │ ├── activate.sh │ ├── build_archive.sh │ ├── check.sh │ ├── create_venv.sh │ ├── env.sh │ ├── install.sh │ ├── install_deb_dependencies.sh │ └── install_dependencies.sh ├── ex2rst ├── feedstock.sh ├── gitwash_dumper.py ├── install_spm_mcr.sh ├── retry_cmd.sh ├── run_examples.py ├── update_changes.sh ├── update_mailmap.sh ├── update_requirements.py └── update_zenodo.py └── tox.ini /.circleci/test_pytest.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e CI_SKIP_TEST=1 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py38" /usr/bin/run_pytests.sh 4 | -------------------------------------------------------------------------------- /.codespellrc: -------------------------------------------------------------------------------- 1 | [codespell] 2 | skip = .git,*.pdf,*.svg,external 3 | # nd,nam - import module short 4 | # fith - oddness coming from AFNI 5 | # whos - smth used in matlab things 6 | # SMAL - Stanford CNI MRS Library 7 | # Suh - name 8 | # noo,crasher,afile - field/var name used 9 | # Reson - short journal name 10 | # ALS, FWE - neuroimaging specific abbrevs 11 | # Comision - foreign word used 12 | # expad - AFNI flag 13 | ignore-words-list = te,inport,objekt,jist,nd,hel,inout,fith,whos,fot,ue,shs,smal,nam,filetest,suh,noo,reson,als,fwe,crasher,comision,afile,expad,burnin 14 | -------------------------------------------------------------------------------- /.coveragerc: -------------------------------------------------------------------------------- 1 | [run] 2 | branch = True 3 | -------------------------------------------------------------------------------- /.dockerignore: -------------------------------------------------------------------------------- 1 | # python cache 2 | __pycache__ 3 | **/__pycache__ 4 | **/*.pyc 5 | *.pyc 6 | 7 | # python distribution 8 | build/**/* 9 | build 10 | dist/**/* 11 | dist 12 | nipype.egg-info/**/* 13 | nipype.egg-info 14 | .eggs/**/* 15 | .eggs 16 | src/**/* 17 | src/ 18 | 19 | # git 20 | .gitignore 21 | .git/**/* 22 | .git 23 | 24 | # other 25 | doc/**/* 26 | doc/ 27 | .cache/ 28 | .circle/**/* 29 | .circle/ 30 | circle.yml 31 | Vagrantfile 32 | .travis.yml 33 | .mailmap 34 | 35 | # Previous coverage results 36 | .coverage 37 | -------------------------------------------------------------------------------- /.et: -------------------------------------------------------------------------------- 1 | { "bad_versions" : [ "1.2.1", 2 | "1.2.3", 3 | "1.3.0"] 4 | } 5 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | nipype/COMMIT_INFO.txt export-subst 2 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE.md: -------------------------------------------------------------------------------- 1 | ### Summary 2 | 3 | ### Actual behavior 4 | 5 | ### Expected behavior 6 | 7 | ### How to replicate the behavior 8 | 9 | ### Script/Workflow details 10 | 11 | Please put URL to code or code here (if not too long). 12 | 13 | ### Platform details: 14 | 15 | 18 | 19 | ``` 20 | 21 | ``` 22 | 23 | ### Execution environment 24 | 25 | Choose one 26 | - Container [Tag: ???] 27 | - My python environment inside container [Base Tag: ???] 28 | - My python environment outside container 29 | -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE.md: -------------------------------------------------------------------------------- 1 | 12 | ## Summary 13 | 15 | 16 | Fixes # . 17 | 18 | ## List of changes proposed in this PR (pull-request) 19 | 20 | -------------------------------------------------------------------------------- /.github/dependabot.yml: -------------------------------------------------------------------------------- 1 | # Dependabot configuration file 2 | version: 2 3 | updates: 4 | - package-ecosystem: "github-actions" 5 | directory: "/" 6 | schedule: 7 | interval: "weekly" 8 | groups: 9 | actions-infrastructure: 10 | patterns: 11 | - "actions/*" 12 | -------------------------------------------------------------------------------- /.github/release-drafter.yml: -------------------------------------------------------------------------------- 1 | template: | 2 | ## What's Changed 3 | 4 | $CHANGES 5 | -------------------------------------------------------------------------------- /.github/workflows/codespell.yml: -------------------------------------------------------------------------------- 1 | --- 2 | name: Codespell 3 | 4 | on: 5 | push: 6 | branches: [master] 7 | pull_request: 8 | branches: [master] 9 | 10 | jobs: 11 | codespell: 12 | name: Check for spelling errors 13 | runs-on: ubuntu-latest 14 | 15 | steps: 16 | - name: Checkout 17 | uses: actions/checkout@v4 18 | - name: Codespell 19 | uses: codespell-project/actions-codespell@v2 20 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | /build 2 | /dist 3 | /nipype.egg-info 4 | /MANIFEST 5 | /nipype/build 6 | /nipype/nipype.egg-info 7 | /doc/_build 8 | /doc/preproc 9 | /doc/users/examples 10 | /doc/api/generated 11 | *.pyc 12 | *.so 13 | .project 14 | .settings 15 | .pydevproject 16 | .eggs 17 | .idea/ 18 | /documentation.zip 19 | .DS_Store 20 | nipype/testing/data/von-ray_errmap.nii.gz 21 | nipype/testing/data/von_errmap.nii.gz 22 | nipype/testing/data/.proc* 23 | crash*.pklz 24 | .coverage 25 | htmlcov/ 26 | __pycache__/ 27 | *~ 28 | .*.swp 29 | .ipynb_checkpoints/ 30 | .ruby-version 31 | .pytest_cache 32 | .vscode/ 33 | venv/ 34 | -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- 1 | # See https://pre-commit.com for more information 2 | # See https://pre-commit.com/hooks.html for more hooks 3 | repos: 4 | - repo: https://github.com/pre-commit/pre-commit-hooks 5 | rev: v4.5.0 6 | hooks: 7 | - id: trailing-whitespace 8 | - id: end-of-file-fixer 9 | - id: check-yaml 10 | - id: check-added-large-files 11 | - repo: https://github.com/psf/black 12 | rev: 24.2.0 13 | hooks: 14 | - id: black 15 | - repo: https://github.com/codespell-project/codespell 16 | rev: v2.2.6 17 | hooks: 18 | - id: codespell 19 | -------------------------------------------------------------------------------- /INSTALL: -------------------------------------------------------------------------------- 1 | .. -*- rst -*- rest mode for emacs 2 | .. _development-quickstart: 3 | 4 | For installation instructions see documentation: 5 | 6 | http://nipy.org/nipype/ 7 | 8 | or doc/users/install.rst 9 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Copyright (c) 2009-2016, Nipype developers 2 | 3 | Licensed under the Apache License, Version 2.0 (the "License"); 4 | you may not use this file except in compliance with the License. 5 | You may obtain a copy of the License at 6 | 7 | http://www.apache.org/licenses/LICENSE-2.0 8 | 9 | Unless required by applicable law or agreed to in writing, software 10 | distributed under the License is distributed on an "AS IS" BASIS, 11 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | See the License for the specific language governing permissions and 13 | limitations under the License. 14 | 15 | Prior to release 0.12, Nipype was licensed under a BSD license. 16 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include INSTALL 2 | include LICENSE 3 | include MANIFEST.in 4 | include README 5 | include THANKS 6 | include Makefile 7 | include setup_egg.py 8 | include doc/documentation.zip 9 | include nipype/COMMIT_INFO.txt 10 | 11 | recursive-include doc * 12 | recursive-include tools * 13 | -------------------------------------------------------------------------------- /codecov.yml: -------------------------------------------------------------------------------- 1 | coverage: 2 | range: "0...100" 3 | status: 4 | patch: 5 | default: 6 | target: 0 7 | threshold: 100 8 | project: 9 | default: 10 | target: 0 11 | threshold: 100 12 | patch: 13 | target: 0 14 | threshold: 100 15 | unittests: 16 | target: 0 17 | threshold: 100 18 | flags: 19 | - "unittests" 20 | smoketests: 21 | target: 0 22 | threshold: 100 23 | flags: 24 | - "smoketests" 25 | ignore: # files and folders that will be removed during processing 26 | - "nipype/external" 27 | - "tools" 28 | - "doc" 29 | - "**/tests" 30 | - "examples" 31 | -------------------------------------------------------------------------------- /doc/.gitignore: -------------------------------------------------------------------------------- 1 | /documentation.zip 2 | _static/python 3 | -------------------------------------------------------------------------------- /doc/_static/nipype-banner-bg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/doc/_static/nipype-banner-bg.png -------------------------------------------------------------------------------- /doc/_templates/navbar.html: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | Home · 10 | Quickstart · 11 | User Guide and Examples · 12 | Interfaces Index · 13 | Developers · 14 | About · 15 | Nipy 16 | -------------------------------------------------------------------------------- /doc/changes.rst: -------------------------------------------------------------------------------- 1 | :orphan: 2 | :tocdepth: 2 3 | 4 | .. _changes: 5 | 6 | ================= 7 | Changes in Nipype 8 | ================= 9 | 10 | .. include:: changelog/1.X.X-changelog.rst 11 | 12 | .. include:: changelog/0.X.X-changelog.rst 13 | 14 | .. include:: links_names.txt 15 | -------------------------------------------------------------------------------- /doc/devel/gitwash/branch_list.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/doc/devel/gitwash/branch_list.png -------------------------------------------------------------------------------- /doc/devel/gitwash/branch_list_compare.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/doc/devel/gitwash/branch_list_compare.png -------------------------------------------------------------------------------- /doc/devel/gitwash/forking_button.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/doc/devel/gitwash/forking_button.png -------------------------------------------------------------------------------- /doc/devel/gitwash/git_development.rst: -------------------------------------------------------------------------------- 1 | .. _git-development: 2 | 3 | ===================== 4 | Git for development 5 | ===================== 6 | 7 | Contents: 8 | 9 | .. toctree:: 10 | :maxdepth: 2 11 | 12 | forking_hell 13 | set_up_fork 14 | configure_git 15 | development_workflow 16 | -------------------------------------------------------------------------------- /doc/devel/gitwash/git_install.rst: -------------------------------------------------------------------------------- 1 | .. _install-git: 2 | 3 | ============= 4 | Install git 5 | ============= 6 | 7 | Overview 8 | ======== 9 | 10 | ================ ============= 11 | Debian / Ubuntu ``sudo apt-get install git-core`` 12 | Fedora ``sudo yum install git-core`` 13 | Windows Download and install msysGit_ 14 | OS X Use the git-osx-installer_ 15 | ================ ============= 16 | 17 | In detail 18 | ========= 19 | 20 | See the git_ page for the most recent information. 21 | 22 | Have a look at the github_ install help pages available from `github help`_ 23 | 24 | There are good instructions here: http://book.git-scm.com/2_installing_git.html 25 | 26 | .. include:: links.inc 27 | -------------------------------------------------------------------------------- /doc/devel/gitwash/git_intro.rst: -------------------------------------------------------------------------------- 1 | ============== 2 | Introduction 3 | ============== 4 | 5 | These pages describe a git_ and github_ workflow for the nipype_ 6 | project. 7 | 8 | There are several different workflows here, for different ways of 9 | working with *nipype*. 10 | 11 | This is not a comprehensive git_ reference, it's just a workflow for our 12 | own project. It's tailored to the github_ hosting service. You may well 13 | find better or quicker ways of getting stuff done with git_, but these 14 | should get you started. 15 | 16 | For general resources for learning git_ see :ref:`git-resources`. 17 | 18 | .. include:: links.inc 19 | -------------------------------------------------------------------------------- /doc/devel/gitwash/index.rst: -------------------------------------------------------------------------------- 1 | .. _using-git: 2 | 3 | Working with *nipype* source code 4 | ====================================== 5 | 6 | Contents: 7 | 8 | .. toctree:: 9 | :maxdepth: 2 10 | 11 | git_intro 12 | git_install 13 | following_latest 14 | patching 15 | git_development 16 | git_resources 17 | -------------------------------------------------------------------------------- /doc/devel/gitwash/links.inc: -------------------------------------------------------------------------------- 1 | .. compiling links file 2 | .. include:: known_projects.inc 3 | .. include:: this_project.inc 4 | .. include:: git_links.inc 5 | -------------------------------------------------------------------------------- /doc/devel/gitwash/pull_button.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/doc/devel/gitwash/pull_button.png -------------------------------------------------------------------------------- /doc/devel/gitwash/this_project.inc: -------------------------------------------------------------------------------- 1 | .. nipype 2 | .. _nipype: http://nipy.org/nipype 3 | .. _`nipype github`: http://github.com/nipy/nipype 4 | 5 | .. _`nipype mailing list`: http://mail.scipy.org/mailman/listinfo/nipy-devel 6 | -------------------------------------------------------------------------------- /doc/devel/index.rst: -------------------------------------------------------------------------------- 1 | .. _developers-guide-index: 2 | 3 | ================= 4 | Developer Guide 5 | ================= 6 | 7 | :Release: |version| 8 | :Date: |today| 9 | 10 | Since nipype is part of the NIPY_ project, we follow the same 11 | conventions documented in the `NIPY Developers Guide 12 | `_. For bleeding-edge version help see `Nightly documentation `_ 13 | 14 | .. toctree:: 15 | :maxdepth: 2 16 | 17 | writing_custom_interfaces 18 | gitwash/index 19 | architecture 20 | provenance 21 | software_using_nipype 22 | testing_nipype 23 | 24 | 25 | .. include:: ../links_names.txt 26 | -------------------------------------------------------------------------------- /doc/devel/writing_custom_interfaces.rst: -------------------------------------------------------------------------------- 1 | .. _writing_custom_interfaces: 2 | .. toctree:: 3 | :maxdepth: 2 4 | 5 | interface_specs 6 | cmd_interface_devel 7 | matlab_interface_devel 8 | python_interface_devel 9 | -------------------------------------------------------------------------------- /doc/developers.rst: -------------------------------------------------------------------------------- 1 | :orphan: 2 | 3 | .. _developers: 4 | 5 | ================== 6 | Developer's Corner 7 | ================== 8 | 9 | .. toctree:: 10 | :maxdepth: 2 11 | 12 | devel/index 13 | 14 | .. toctree:: 15 | :maxdepth: 3 16 | 17 | api/generated/nipype 18 | -------------------------------------------------------------------------------- /doc/examples.rst: -------------------------------------------------------------------------------- 1 | :orphan: 2 | 3 | .. _examples: 4 | 5 | ======================= 6 | User Guide and Examples 7 | ======================= 8 | 9 | .. admonition:: Michael Notter's User Guide 10 | 11 | Be sure to read `Michael's excellent tutorials `__. 12 | 13 | Examples 14 | ~~~~~~~~ 15 | The following examples are `literate programming `__ 16 | documents which solve specific problems using Nipype. 17 | In some cases, the same problem is solved with multiple underlying tools. 18 | 19 | .. toctree:: 20 | :maxdepth: 1 21 | :glob: 22 | 23 | users/examples/* 24 | -------------------------------------------------------------------------------- /doc/images/nipype_architecture_overview2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/doc/images/nipype_architecture_overview2.png -------------------------------------------------------------------------------- /doc/requirements.txt: -------------------------------------------------------------------------------- 1 | dipy 2 | ipython 3 | matplotlib 4 | nbsphinx 5 | sphinx-argparse 6 | sphinx>=2.1.2 7 | sphinxcontrib-apidoc 8 | sphinxcontrib-napoleon 9 | niflow-nipype1-workflows 10 | -------------------------------------------------------------------------------- /doc/searchresults.rst: -------------------------------------------------------------------------------- 1 | :orphan: 2 | 3 | .. This displays the search results from the Google Custom Search engine. 4 | Don't link to it directly. 5 | 6 | Search results 7 | ============== 8 | 9 | .. raw:: html 10 | 11 |
Loading 12 | 23 | 24 |
25 | -------------------------------------------------------------------------------- /doc/version.rst: -------------------------------------------------------------------------------- 1 | :orphan: 2 | 3 | .. _version: 4 | 5 | :Release: |version| 6 | :Date: |today| 7 | -------------------------------------------------------------------------------- /docker/files/run_builddocs.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -e 3 | set -x 4 | set -u 5 | 6 | WORKDIR=${WORK:-/work} 7 | 8 | mkdir -p ${WORKDIR}/docs 9 | make html 2>&1 | tee ${WORKDIR}/builddocs.log 10 | cp -r /src/nipype/doc/_build/html/* ${WORKDIR}/docs/ 11 | cat ${WORKDIR}/builddocs.log && if grep -q "ERROR" ${WORKDIR}/builddocs.log; then false; else true; fi 12 | -------------------------------------------------------------------------------- /docker/prune_dockerfile.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | if [ -z "$1" ]; then 4 | echo "Usage: $(basename $0) " 5 | exit 1 6 | fi 7 | 8 | # Remove empty lines, comments, and timestamp. 9 | sed -e '/\s*#.*$/d' -e '/^\s*$/d' -e '/generation_timestamp/d' "$1" 10 | -------------------------------------------------------------------------------- /examples/README.md: -------------------------------------------------------------------------------- 1 | The examples directory previously held a set of 2 | [literate programming](https://en.wikipedia.org/wiki/Literate_programming) documents that 3 | demonstrated solutions to various problems using Nipype. 4 | 5 | These examples have been moved to the 6 | [Nipype1 Examples Niflow](https://github.com/niflows/nipype1-examples). Please refer to 7 | that repository for more information, and report any issues with the examples there. 8 | -------------------------------------------------------------------------------- /nipype/COMMIT_INFO.txt: -------------------------------------------------------------------------------- 1 | # This is an ini file that may contain information about the code state 2 | [commit hash] 3 | # The line below may contain a valid hash if it has been substituted during 'git archive' 4 | archive_subst_hash=%h 5 | # This line may be modified by the install process 6 | install_hash= 7 | -------------------------------------------------------------------------------- /nipype/algorithms/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | Package contains pure python neuroimaging algorithms 5 | 6 | Examples: artifactdetect 7 | 8 | """ 9 | __docformat__ = "restructuredtext" 10 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_auto_TVTKBaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..mesh import TVTKBaseInterface 3 | 4 | 5 | def test_TVTKBaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = TVTKBaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/algorithms/tests/test_icc_anova.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from nipype.algorithms.icc import ICC_rep_anova 3 | 4 | 5 | def test_ICC_rep_anova(): 6 | # see table 2 in P. E. Shrout & Joseph L. Fleiss (1979). "Intraclass 7 | # Correlations: Uses in Assessing Rater Reliability". Psychological 8 | # Bulletin 86 (2): 420-428 9 | Y = np.array( 10 | [ 11 | [9, 2, 5, 8], 12 | [6, 1, 3, 2], 13 | [8, 4, 6, 8], 14 | [7, 1, 2, 6], 15 | [10, 5, 6, 9], 16 | [6, 2, 4, 7], 17 | ] 18 | ) 19 | 20 | icc, r_var, e_var, _, dfc, dfe = ICC_rep_anova(Y) 21 | # see table 4 22 | assert round(icc, 2) == 0.71 23 | assert dfc == 3 24 | assert dfe == 15 25 | assert np.isclose(r_var / (r_var + e_var), icc) 26 | -------------------------------------------------------------------------------- /nipype/caching/__init__.py: -------------------------------------------------------------------------------- 1 | from .memory import Memory 2 | -------------------------------------------------------------------------------- /nipype/caching/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/caching/tests/__init__.py -------------------------------------------------------------------------------- /nipype/external/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/external/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | Package contains interfaces for using existing functionality in other packages 5 | 6 | Requires Packages to be installed 7 | """ 8 | __docformat__ = "restructuredtext" 9 | 10 | from .io import DataGrabber, DataSink, SelectFiles, BIDSDataGrabber 11 | from .utility import IdentityInterface, Rename, Function, Select, Merge 12 | -------------------------------------------------------------------------------- /nipype/interfaces/afni/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | -------------------------------------------------------------------------------- /nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import AFNICommandBase 3 | 4 | 5 | def test_AFNICommandBase_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = AFNICommandBase.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/afni/tests/test_extra_Deconvolve.py: -------------------------------------------------------------------------------- 1 | """Test afni deconvolve""" 2 | 3 | from ..model import Deconvolve 4 | 5 | 6 | def test_x1dstop(): 7 | deconv = Deconvolve() 8 | deconv.inputs.out_file = "file.nii" 9 | assert "out_file" in deconv._list_outputs() 10 | deconv.inputs.x1D_stop = True 11 | assert "out_file" not in deconv._list_outputs() 12 | assert "cbucket" not in deconv._list_outputs() 13 | -------------------------------------------------------------------------------- /nipype/interfaces/ants/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | -------------------------------------------------------------------------------- /nipype/interfaces/ants/tests/test_auto_ANTSCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import ANTSCommand 3 | 4 | 5 | def test_ANTSCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | num_threads=dict( 15 | nohash=True, 16 | usedefault=True, 17 | ), 18 | ) 19 | inputs = ANTSCommand.input_spec() 20 | 21 | for key, metadata in list(input_map.items()): 22 | for metakey, value in list(metadata.items()): 23 | assert getattr(inputs.traits()[key], metakey) == value 24 | -------------------------------------------------------------------------------- /nipype/interfaces/ants/tests/test_base.py: -------------------------------------------------------------------------------- 1 | from nipype.interfaces.ants.base import Info 2 | 3 | import pytest 4 | 5 | # fmt: off 6 | ANTS_VERSIONS = [("""\ 7 | ANTs Version: 2.3.3.dev168-g29bdf 8 | Compiled: Jun 9 2020 03:44:55 9 | 10 | """, "2.3.3"), ("""\ 11 | ANTs Version: v2.3.5.post76-g28dd25c 12 | Compiled: Nov 16 2021 14:57:48 13 | 14 | """, "2.3.5"), ("""\ 15 | ANTs Version: v2.1.0.post789-g0740f 16 | Compiled: I don't still have this so not going to pretend 17 | 18 | """, "2.2.0"), 19 | ] 20 | # fmt: on 21 | 22 | 23 | @pytest.mark.parametrize("raw_info, version", ANTS_VERSIONS) 24 | def test_version_parser(raw_info, version): 25 | assert Info.parse_version(raw_info) == version 26 | -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/base/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/test_auto_BaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..core import BaseInterface 3 | 4 | 5 | def test_BaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = BaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/test_auto_CommandLine.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..core import CommandLine 3 | 4 | 5 | def test_CommandLine_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = CommandLine.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/test_auto_LibraryBaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..core import LibraryBaseInterface 3 | 4 | 5 | def test_LibraryBaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = LibraryBaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/test_auto_MpiCommandLine.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..core import MpiCommandLine 3 | 4 | 5 | def test_MpiCommandLine_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | n_procs=dict(), 15 | use_mpi=dict( 16 | usedefault=True, 17 | ), 18 | ) 19 | inputs = MpiCommandLine.input_spec() 20 | 21 | for key, metadata in list(input_map.items()): 22 | for metakey, value in list(metadata.items()): 23 | assert getattr(inputs.traits()[key], metakey) == value 24 | -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/test_auto_SEMLikeCommandLine.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..core import SEMLikeCommandLine 3 | 4 | 5 | def test_SEMLikeCommandLine_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = SEMLikeCommandLine.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/test_auto_SimpleInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..core import SimpleInterface 3 | 4 | 5 | def test_SimpleInterface_inputs(): 6 | input_map = dict() 7 | inputs = SimpleInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/base/tests/test_auto_StdOutCommandLine.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..core import StdOutCommandLine 3 | 4 | 5 | def test_StdOutCommandLine_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | out_file=dict( 15 | argstr="> %s", 16 | extensions=None, 17 | genfile=True, 18 | position=-1, 19 | ), 20 | ) 21 | inputs = StdOutCommandLine.input_spec() 22 | 23 | for key, metadata in list(input_map.items()): 24 | for metakey, value in list(metadata.items()): 25 | assert getattr(inputs.traits()[key], metakey) == value 26 | -------------------------------------------------------------------------------- /nipype/interfaces/brainsuite/__init__.py: -------------------------------------------------------------------------------- 1 | from .brainsuite import ( 2 | Bse, 3 | Bfc, 4 | Pvc, 5 | Cerebro, 6 | Cortex, 7 | Scrubmask, 8 | Tca, 9 | Dewisp, 10 | Dfs, 11 | Pialmesh, 12 | Skullfinder, 13 | Hemisplit, 14 | SVReg, 15 | BDP, 16 | ThicknessPVC, 17 | ) 18 | -------------------------------------------------------------------------------- /nipype/interfaces/brainsuite/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/brainsuite/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..brainsuite import ThicknessPVC 3 | 4 | 5 | def test_ThicknessPVC_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | subjectFilePrefix=dict( 15 | argstr="%s", 16 | mandatory=True, 17 | ), 18 | ) 19 | inputs = ThicknessPVC.input_spec() 20 | 21 | for key, metadata in list(input_map.items()): 22 | for metakey, value in list(metadata.items()): 23 | assert getattr(inputs.traits()[key], metakey) == value 24 | -------------------------------------------------------------------------------- /nipype/interfaces/camino/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | -------------------------------------------------------------------------------- /nipype/interfaces/camino2trackvis/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """Camino-Trackvis allows interoperability between Camino and TrackVis.""" 4 | from .convert import Camino2Trackvis, Trackvis2Camino 5 | -------------------------------------------------------------------------------- /nipype/interfaces/camino2trackvis/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/camino2trackvis/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/cat12/__init__.py: -------------------------------------------------------------------------------- 1 | from .preprocess import CAT12Segment, CAT12SANLMDenoising 2 | from .surface import ( 3 | ExtractAdditionalSurfaceParameters, 4 | ExtractROIBasedSurfaceMeasures, 5 | ) 6 | -------------------------------------------------------------------------------- /nipype/interfaces/cat12/base.py: -------------------------------------------------------------------------------- 1 | class Cell: 2 | def __init__(self, arg): 3 | self.arg = arg 4 | 5 | def to_string(self): 6 | if isinstance(self.arg, list): 7 | v = "\n".join([f"'{el}'" for el in self.arg]) 8 | else: 9 | v = self.arg 10 | return v 11 | 12 | 13 | class NestedCell(Cell): 14 | def __str__(self): 15 | return "{{%s}}" % self.to_string() 16 | -------------------------------------------------------------------------------- /nipype/interfaces/cat12/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/cat12/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/cmtk/__init__.py: -------------------------------------------------------------------------------- 1 | """CMP implements a full processing pipeline for creating connectomes with dMRI data.""" 2 | 3 | from .cmtk import ROIGen, CreateMatrix, CreateNodes 4 | from .nx import NetworkXMetrics, AverageNetworks 5 | from .parcellation import Parcellate 6 | from .convert import CFFConverter, MergeCNetworks 7 | from .nbs import NetworkBasedStatistic 8 | -------------------------------------------------------------------------------- /nipype/interfaces/cmtk/base.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """Base interface for cmtk""" 4 | 5 | from ..base import LibraryBaseInterface 6 | from ...utils.misc import package_check 7 | 8 | 9 | class CFFBaseInterface(LibraryBaseInterface): 10 | _pkg = "cfflib" 11 | 12 | 13 | # Originally set in convert, nbs, nx, parcellation 14 | # Set here to be imported, in case anybody depends on its presence 15 | # Remove in 2.0 16 | have_cmp = True 17 | try: 18 | package_check("cmp") 19 | except ImportError: 20 | have_cmp = False 21 | 22 | have_cfflib = True 23 | try: 24 | package_check("cfflib") 25 | except ImportError: 26 | have_cfflib = False 27 | 28 | have_cv = True 29 | try: 30 | package_check("cviewer") 31 | except ImportError: 32 | have_cv = False 33 | -------------------------------------------------------------------------------- /nipype/interfaces/cmtk/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/cmtk/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/cmtk/tests/test_auto_CFFBaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import CFFBaseInterface 3 | 4 | 5 | def test_CFFBaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = CFFBaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/diffusion_toolkit/__init__.py: -------------------------------------------------------------------------------- 1 | """Diffusion Toolkit performs data reconstruction and fiber tracking on diffusion MR images.""" 2 | 3 | from .base import Info 4 | from .postproc import SplineFilter, TrackMerge 5 | from .dti import DTIRecon, DTITracker 6 | from .odf import HARDIMat, ODFRecon, ODFTracker 7 | -------------------------------------------------------------------------------- /nipype/interfaces/diffusion_toolkit/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/diffusion_toolkit/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/dipy/__init__.py: -------------------------------------------------------------------------------- 1 | """DIPY is a computational neuroimaging tool for diffusion MRI.""" 2 | 3 | from .tracks import StreamlineTractography, TrackDensityMap 4 | from .tensors import TensorMode, DTI 5 | from .preprocess import Resample, Denoise 6 | from .reconstruction import RESTORE, EstimateResponseSH, CSD 7 | from .simulate import SimulateMultiTensor 8 | from .anisotropic_power import APMQball 9 | -------------------------------------------------------------------------------- /nipype/interfaces/dipy/registration.py: -------------------------------------------------------------------------------- 1 | from looseversion import LooseVersion 2 | from ... import logging 3 | from .base import HAVE_DIPY, dipy_version, dipy_to_nipype_interface, get_dipy_workflows 4 | 5 | IFLOGGER = logging.getLogger("nipype.interface") 6 | 7 | 8 | if HAVE_DIPY and LooseVersion(dipy_version()) >= LooseVersion("0.15"): 9 | from dipy.workflows import align 10 | 11 | l_wkflw = get_dipy_workflows(align) 12 | for name, obj in l_wkflw: 13 | new_name = name.replace("Flow", "") 14 | globals()[new_name] = dipy_to_nipype_interface(new_name, obj) 15 | del l_wkflw 16 | 17 | else: 18 | IFLOGGER.info( 19 | "We advise you to upgrade DIPY version. This upgrade will" 20 | " open access to more function" 21 | ) 22 | -------------------------------------------------------------------------------- /nipype/interfaces/dipy/setup.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | 4 | 5 | def configuration(parent_package="", top_path=None): 6 | from numpy.distutils.misc_util import Configuration 7 | 8 | config = Configuration("dipy", parent_package, top_path) 9 | 10 | # config.add_data_dir('tests') 11 | return config 12 | 13 | 14 | if __name__ == "__main__": 15 | from numpy.distutils.core import setup 16 | 17 | setup(**configuration(top_path="").todict()) 18 | -------------------------------------------------------------------------------- /nipype/interfaces/dipy/stats.py: -------------------------------------------------------------------------------- 1 | from looseversion import LooseVersion 2 | from ... import logging 3 | from .base import HAVE_DIPY, dipy_version, dipy_to_nipype_interface, get_dipy_workflows 4 | 5 | IFLOGGER = logging.getLogger("nipype.interface") 6 | 7 | if HAVE_DIPY and LooseVersion(dipy_version()) >= LooseVersion("0.16"): 8 | from dipy.workflows import stats 9 | 10 | l_wkflw = get_dipy_workflows(stats) 11 | for name, obj in l_wkflw: 12 | new_name = name.replace("Flow", "") 13 | globals()[new_name] = dipy_to_nipype_interface(new_name, obj) 14 | del l_wkflw 15 | 16 | else: 17 | IFLOGGER.info( 18 | "We advise you to upgrade DIPY version. This upgrade will" 19 | " open access to more function" 20 | ) 21 | -------------------------------------------------------------------------------- /nipype/interfaces/dipy/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/dipy/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import DipyBaseInterface 3 | 4 | 5 | def test_DipyBaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = DipyBaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/dtitk/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | DTI-TK is a spatial normalization and atlas construction toolkit for DTI. 3 | 4 | Interfaces for the `Diffusion Tensor Imaging Toolkit (DTI-TK) 5 | `_ command line tools. 6 | 7 | """ 8 | 9 | from .registration import ( 10 | Rigid, 11 | Affine, 12 | Diffeo, 13 | ComposeXfm, 14 | DiffeoSymTensor3DVol, 15 | AffSymTensor3DVol, 16 | AffScalarVol, 17 | DiffeoScalarVol, 18 | ) 19 | from .utils import ( 20 | TVAdjustVoxSp, 21 | SVAdjustVoxSp, 22 | TVResample, 23 | SVResample, 24 | TVtool, 25 | BinThresh, 26 | ) 27 | -------------------------------------------------------------------------------- /nipype/interfaces/dtitk/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | -------------------------------------------------------------------------------- /nipype/interfaces/dtitk/tests/test_auto_CommandLineDtitk.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import CommandLineDtitk 3 | 4 | 5 | def test_CommandLineDtitk_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = CommandLineDtitk.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/elastix/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """elastix is a toolbox for rigid and nonrigid registration of images.""" 4 | from .registration import Registration, ApplyWarp, AnalyzeWarp, PointsWarp 5 | from .utils import EditTransform 6 | -------------------------------------------------------------------------------- /nipype/interfaces/elastix/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/elastix/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/freesurfer/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/freesurfer/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import FSCommand 3 | 4 | 5 | def test_FSCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | subjects_dir=dict(), 15 | ) 16 | inputs = FSCommand.input_spec() 17 | 18 | for key, metadata in list(input_map.items()): 19 | for metakey, value in list(metadata.items()): 20 | assert getattr(inputs.traits()[key], metakey) == value 21 | -------------------------------------------------------------------------------- /nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import FSCommandOpenMP 3 | 4 | 5 | def test_FSCommandOpenMP_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | num_threads=dict(), 15 | subjects_dir=dict(), 16 | ) 17 | inputs = FSCommandOpenMP.input_spec() 18 | 19 | for key, metadata in list(input_map.items()): 20 | for metakey, value in list(metadata.items()): 21 | assert getattr(inputs.traits()[key], metakey) == value 22 | -------------------------------------------------------------------------------- /nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import FSScriptCommand 3 | 4 | 5 | def test_FSScriptCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | subjects_dir=dict(), 15 | ) 16 | inputs = FSScriptCommand.input_spec() 17 | 18 | for key, metadata in list(input_map.items()): 19 | for metakey, value in list(metadata.items()): 20 | assert getattr(inputs.traits()[key], metakey) == value 21 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_contrast_element.tcl: -------------------------------------------------------------------------------- 1 | # Real contrast_$ctype vector $cnum element $element 2 | set fmri(con_$ctype$cnum.$element) $val 3 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_contrast_ftest_element.tcl: -------------------------------------------------------------------------------- 1 | # F-test $cnum element $element 2 | set fmri(ftest_$ctype$cnum.$element) $val 3 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_contrast_header.tcl: -------------------------------------------------------------------------------- 1 | # Contrast & F-tests mode 2 | # real : control real EVs 3 | # orig : control original EVs 4 | set fmri(con_mode_old) orig 5 | set fmri(con_mode) orig 6 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_contrast_prolog.tcl: -------------------------------------------------------------------------------- 1 | # Display images for contrast_$ctype $cnum 2 | set fmri(conpic_$ctype.$cnum) 1 3 | 4 | # Title for contrast_$ctype $cnum 5 | set fmri(conname_$ctype.$cnum) "$cname" 6 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_contrastmask_element.tcl: -------------------------------------------------------------------------------- 1 | # Mask real contrast/F-test $c1 with real contrast/F-test $c2? 2 | set fmri(conmask${c1}_${c2}) 0 3 | 4 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_contrastmask_footer.tcl: -------------------------------------------------------------------------------- 1 | # Do contrast masking at all? 2 | set fmri(conmask1_1) 0 3 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_contrastmask_header.tcl: -------------------------------------------------------------------------------- 1 | # Contrast masking - use >0 instead of thresholding? 2 | set fmri(conmask_zerothresh_yn) 0 3 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_ev_none.tcl: -------------------------------------------------------------------------------- 1 | # EV title 2 | set fmri(evtitle$ev_num) "$ev_name" 3 | 4 | # Basic waveform shape 5 | # 0 : Square 6 | # 1 : Sinusoid 7 | # 2 : Custom (1 entry per volume) 8 | # 3 : Custom (3 column format) 9 | # 4 : Interaction 10 | # 10 : Empty (all zeros) 11 | set fmri(shape$ev_num) 2 12 | 13 | # Convolution 14 | # 0 : None 15 | # 1 : Gaussian 16 | # 2 : Gamma 17 | # 3 : Double-Gamma HRF 18 | # 4 : Gamma basis functions 19 | # 5 : Sine basis functions 20 | # 6 : FIR basis functions 21 | # 7 : Optimal/custom basis functions 22 | set fmri(convolve$ev_num) 0 23 | 24 | # Apply temporal filtering 25 | set fmri(tempfilt_yn$ev_num) $tempfilt_yn 26 | 27 | # Add temporal derivative 28 | set fmri(deriv_yn$ev_num) 0 29 | 30 | # Custom EV file 31 | set fmri(custom$ev_num) "$cond_file" 32 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_ev_ortho.tcl: -------------------------------------------------------------------------------- 1 | # Orthogonalise EV $c0 wrt EV $c1 2 | set fmri(ortho$c0.$c1) $orthogonal 3 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_fe_copes.tcl: -------------------------------------------------------------------------------- 1 | # Use lower-level cope $copeno for higher-level analysis 2 | set fmri(copeinput.${copeno}) 1 3 | 4 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_fe_ev_element.tcl: -------------------------------------------------------------------------------- 1 | # Higher-level EV value for EV 1 and input $input 2 | set fmri(evg${input}.1) 1 3 | 4 | # Group membership for input $input 5 | set fmri(groupmem.${input}) 1 6 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_fe_featdirs.tcl: -------------------------------------------------------------------------------- 1 | # 4D AVW data or FEAT directory ($runno) 2 | set feat_files($runno) "${rundir}" 3 | 4 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/model_templates/feat_nongui.tcl: -------------------------------------------------------------------------------- 1 | ########################################################## 2 | # Now options that don't appear in the GUI 3 | 4 | # Alternative example_func image (not derived from input 4D dataset) 5 | set fmri(alternative_example_func) "" 6 | 7 | # Alternative (to BETting) mask image 8 | set fmri(alternative_mask) "" 9 | 10 | # Initial structural space registration initialisation transform 11 | set fmri(init_initial_highres) "" 12 | 13 | # Structural space registration initialisation transform 14 | set fmri(init_highres) "" 15 | 16 | # Standard space registration initialisation transform 17 | set fmri(init_standard) "" 18 | 19 | # For full FEAT analysis: overwrite existing .feat output dir? 20 | set fmri(overwrite_yn) $overwrite 21 | -------------------------------------------------------------------------------- /nipype/interfaces/fsl/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/fsl/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/fsl/tests/test_auto_FSLCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import FSLCommand 3 | 4 | 5 | def test_FSLCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | output_type=dict(), 15 | ) 16 | inputs = FSLCommand.input_spec() 17 | 18 | for key, metadata in list(input_map.items()): 19 | for metakey, value in list(metadata.items()): 20 | assert getattr(inputs.traits()[key], metakey) == value 21 | -------------------------------------------------------------------------------- /nipype/interfaces/minc/testdata.py: -------------------------------------------------------------------------------- 1 | from ...testing import example_data 2 | 3 | minc2Dfile = example_data("minc_test_2D_00.mnc") 4 | minc3Dfile = example_data("minc_test_3D_00.mnc") 5 | 6 | nlp_config = example_data("minc_nlp.conf") 7 | 8 | 9 | def nonempty_minc_data(i, shape="2D"): 10 | return example_data("minc_test_%s_%.2d.mnc" % (shape, i)) 11 | -------------------------------------------------------------------------------- /nipype/interfaces/minc/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/minc/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/mipav/__init__.py: -------------------------------------------------------------------------------- 1 | """MIPAV enables quantitative analysis and visualization of multimodal medical images.""" 2 | 3 | from .developer import ( 4 | JistLaminarVolumetricLayering, 5 | JistBrainMgdmSegmentation, 6 | JistLaminarProfileGeometry, 7 | JistLaminarProfileCalculator, 8 | MedicAlgorithmN3, 9 | JistLaminarROIAveraging, 10 | MedicAlgorithmLesionToads, 11 | JistBrainMp2rageSkullStripping, 12 | JistCortexSurfaceMeshInflation, 13 | RandomVol, 14 | MedicAlgorithmImageCalculator, 15 | JistBrainMp2rageDuraEstimation, 16 | JistLaminarProfileSampling, 17 | MedicAlgorithmMipavReorient, 18 | MedicAlgorithmSPECTRE2010, 19 | JistBrainPartialVolumeFilter, 20 | JistIntensityMp2rageMasking, 21 | MedicAlgorithmThresholdToBinaryMask, 22 | ) 23 | -------------------------------------------------------------------------------- /nipype/interfaces/mipav/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/mipav/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/mixins/__init__.py: -------------------------------------------------------------------------------- 1 | from .reporting import ( 2 | ReportCapableInterface, 3 | ReportCapableInputSpec, 4 | ReportCapableOutputSpec, 5 | ) 6 | from .fixheader import CopyHeaderInputSpec, CopyHeaderInterface 7 | -------------------------------------------------------------------------------- /nipype/interfaces/mixins/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/mixins/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/mixins/tests/test_auto_CopyHeaderInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..fixheader import CopyHeaderInterface 3 | 4 | 5 | def test_CopyHeaderInterface_inputs(): 6 | input_map = dict() 7 | inputs = CopyHeaderInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/mixins/tests/test_auto_ReportCapableInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..reporting import ReportCapableInterface 3 | 4 | 5 | def test_ReportCapableInterface_inputs(): 6 | input_map = dict() 7 | inputs = ReportCapableInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/mne/__init__.py: -------------------------------------------------------------------------------- 1 | """MNE is a software for exploring, visualizing, and analyzing human neurophysiological data.""" 2 | 3 | from .base import WatershedBEM 4 | -------------------------------------------------------------------------------- /nipype/interfaces/mne/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/mne/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/mrtrix/defhdr.mat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/mrtrix/defhdr.mat -------------------------------------------------------------------------------- /nipype/interfaces/mrtrix/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/mrtrix/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/mrtrix3/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/mrtrix3/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import MRTrix3Base 3 | 4 | 5 | def test_MRTrix3Base_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = MRTrix3Base.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/niftyfit/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | NiftyFit is a software package for multi-parametric model-fitting of 4D MRI. 5 | 6 | The niftyfit module provides classes for interfacing with the `NiftyFit 7 | `__ command line tools. 8 | 9 | """ 10 | from .asl import FitAsl 11 | from .dwi import FitDwi, DwiTool 12 | from .qt1 import FitQt1 13 | -------------------------------------------------------------------------------- /nipype/interfaces/niftyfit/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/niftyfit/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/niftyfit/tests/test_auto_NiftyFitCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import NiftyFitCommand 3 | 4 | 5 | def test_NiftyFitCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = NiftyFitCommand.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/niftyreg/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | NiftyReg is an open-source software for efficient medical image registration. 5 | 6 | The niftyreg module provides classes for interfacing with the `NiftyReg 7 | `_ command line tools. 8 | 9 | """ 10 | from .base import get_custom_path 11 | from .reg import RegAladin, RegF3D 12 | from .regutils import ( 13 | RegResample, 14 | RegJacobian, 15 | RegAverage, 16 | RegTools, 17 | RegTransform, 18 | RegMeasure, 19 | ) 20 | -------------------------------------------------------------------------------- /nipype/interfaces/niftyreg/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/niftyreg/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/niftyreg/tests/test_auto_NiftyRegCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import NiftyRegCommand 3 | 4 | 5 | def test_NiftyRegCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | omp_core_val=dict( 15 | argstr="-omp %i", 16 | usedefault=True, 17 | ), 18 | ) 19 | inputs = NiftyRegCommand.input_spec() 20 | 21 | for key, metadata in list(input_map.items()): 22 | for metakey, value in list(metadata.items()): 23 | assert getattr(inputs.traits()[key], metakey) == value 24 | -------------------------------------------------------------------------------- /nipype/interfaces/niftyseg/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | The niftyseg module provides classes for interfacing with the `NIFTYSEG 5 | `_ command line tools. 6 | 7 | Top-level namespace for niftyseg. 8 | """ 9 | 10 | from .em import EM 11 | from .label_fusion import LabelFusion, CalcTopNCC 12 | from .lesions import FillLesions 13 | from .maths import UnaryMaths, BinaryMaths, BinaryMathsInteger, TupleMaths, Merge 14 | from .patchmatch import PatchMatch 15 | from .stats import UnaryStats, BinaryStats 16 | -------------------------------------------------------------------------------- /nipype/interfaces/niftyseg/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/niftyseg/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/niftyseg/tests/test_auto_NiftySegCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import NiftySegCommand 3 | 4 | 5 | def test_NiftySegCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = NiftySegCommand.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/nipy/__init__.py: -------------------------------------------------------------------------------- 1 | """NIPY is a python project for analysis of structural and functional neuroimaging data.""" 2 | 3 | from .model import FitGLM, EstimateContrast 4 | from .preprocess import ComputeMask, SpaceTimeRealigner 5 | from .utils import Similarity 6 | -------------------------------------------------------------------------------- /nipype/interfaces/nipy/base.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """Base interface for nipy""" 4 | 5 | from ..base import LibraryBaseInterface 6 | from ...utils.misc import package_check 7 | 8 | # Originally set in model, preprocess and utils 9 | # Set here to be imported, in case anybody depends on its presence 10 | # Remove in 2.0 11 | have_nipy = True 12 | try: 13 | package_check("nipy") 14 | except: 15 | have_nipy = False 16 | 17 | 18 | class NipyBaseInterface(LibraryBaseInterface): 19 | _pkg = "nipy" 20 | -------------------------------------------------------------------------------- /nipype/interfaces/nipy/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/nipy/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/nipy/tests/test_auto_NipyBaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import NipyBaseInterface 3 | 4 | 5 | def test_NipyBaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = NipyBaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/nitime/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """Nitime is a library for time-series analysis of data from neuroscience experiments.""" 4 | from .analysis import ( 5 | CoherenceAnalyzerInputSpec, 6 | CoherenceAnalyzerOutputSpec, 7 | CoherenceAnalyzer, 8 | ) 9 | -------------------------------------------------------------------------------- /nipype/interfaces/nitime/base.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """Base interface for nitime""" 4 | 5 | from ..base import LibraryBaseInterface 6 | 7 | 8 | class NitimeBaseInterface(LibraryBaseInterface): 9 | _pkg = "nitime" 10 | -------------------------------------------------------------------------------- /nipype/interfaces/nitime/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/nitime/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/nitime/tests/test_auto_NitimeBaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import NitimeBaseInterface 3 | 4 | 5 | def test_NitimeBaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = NitimeBaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/robex/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/robex/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/robex/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/robex/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/semtools/__init__.py: -------------------------------------------------------------------------------- 1 | """SEM Tools are useful tools for Structural Equation Modeling.""" 2 | 3 | from .diffusion import * 4 | from .featurecreator import GenerateCsfClippedFromClassifiedImage 5 | from .segmentation import * 6 | from .filtering import * 7 | from .brains import * 8 | from .testing import * 9 | from .utilities import * 10 | from .legacy import * 11 | from .registration import * 12 | from .converters import DWISimpleCompare, DWICompare 13 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/brains/__init__.py: -------------------------------------------------------------------------------- 1 | from .segmentation import SimilarityIndex, BRAINSTalairach, BRAINSTalairachMask 2 | from .utilities import ( 3 | HistogramMatchingFilter, 4 | GenerateEdgeMapImage, 5 | GeneratePurePlugMask, 6 | ) 7 | from .classify import BRAINSPosteriorToContinuousClass 8 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/brains/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/semtools/brains/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/semtools/diffusion/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/semtools/diffusion/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/semtools/diffusion/tractography/__init__.py: -------------------------------------------------------------------------------- 1 | from .commandlineonly import fiberstats 2 | from .fiberprocess import fiberprocess 3 | from .fibertrack import fibertrack 4 | from .ukftractography import UKFTractography 5 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/diffusion/tractography/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/semtools/diffusion/tractography/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/semtools/filtering/__init__.py: -------------------------------------------------------------------------------- 1 | from .denoising import UnbiasedNonLocalMeans 2 | from .featuredetection import ( 3 | GenerateSummedGradientImage, 4 | CannySegmentationLevelSetImageFilter, 5 | DilateImage, 6 | TextureFromNoiseImageFilter, 7 | FlippedDifference, 8 | ErodeImage, 9 | GenerateBrainClippedImage, 10 | NeighborhoodMedian, 11 | GenerateTestImage, 12 | NeighborhoodMean, 13 | HammerAttributeCreator, 14 | TextureMeasureFilter, 15 | DilateMask, 16 | DumpBinaryTrainingVectors, 17 | DistanceMaps, 18 | STAPLEAnalysis, 19 | GradientAnisotropicDiffusionImageFilter, 20 | CannyEdge, 21 | ) 22 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/filtering/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/semtools/filtering/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/semtools/generated.sh: -------------------------------------------------------------------------------- 1 | local_generate_classes.py --python_paths=/scratch/johnsonhj/src/NEP-11/NIPYPE --program_paths=/scratch/johnsonhj/src/NEP-11/bin:/usr/local/bin:/opt/ogs/bin/darwin-x64:/bin:/sbin:/usr/local/bin:/usr/bin:/usr/sbin:/usr/texbin:/Shared/sinapse/sharedopt/20120722/Darwin_i386/vv/bin:/usr/texbin:/scratch/johnsonhj/bin --output_path=/scratch/johnsonhj/src/NEP-11/BRAINSTools/AutoWorkup 2 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/legacy/__init__.py: -------------------------------------------------------------------------------- 1 | from .registration import scalartransform 2 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/legacy/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/semtools/legacy/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/semtools/registration/__init__.py: -------------------------------------------------------------------------------- 1 | from .specialized import VBRAINSDemonWarp, BRAINSDemonWarp, BRAINSTransformFromFiducials 2 | from .brainsresample import BRAINSResample 3 | from .brainsfit import BRAINSFit 4 | from .brainsresize import BRAINSResize 5 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/registration/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/semtools/registration/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/semtools/segmentation/__init__.py: -------------------------------------------------------------------------------- 1 | from .specialized import ( 2 | BRAINSCut, 3 | BRAINSROIAuto, 4 | BRAINSConstellationDetector, 5 | BRAINSCreateLabelMapFromProbabilityMaps, 6 | BinaryMaskEditorBasedOnLandmarks, 7 | BRAINSMultiSTAPLE, 8 | BRAINSABC, 9 | ESLR, 10 | ) 11 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/segmentation/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/semtools/segmentation/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/semtools/testing/__init__.py: -------------------------------------------------------------------------------- 1 | from .featuredetection import SphericalCoordinateGeneration 2 | from .landmarkscompare import LandmarksCompare 3 | from .generateaveragelmkfile import GenerateAverageLmkFile 4 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/semtools/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/semtools/utilities/__init__.py: -------------------------------------------------------------------------------- 1 | from .brains import ( 2 | BRAINSConstellationModeler, 3 | landmarksConstellationWeights, 4 | BRAINSTrimForegroundInDirection, 5 | BRAINSLmkTransform, 6 | BRAINSMush, 7 | BRAINSTransformConvert, 8 | landmarksConstellationAligner, 9 | BRAINSEyeDetector, 10 | BRAINSLinearModelerEPCA, 11 | BRAINSInitializedControlPoints, 12 | CleanUpOverlapLabels, 13 | BRAINSClipInferior, 14 | GenerateLabelMapFromProbabilityMap, 15 | BRAINSAlignMSP, 16 | BRAINSLandmarkInitializer, 17 | insertMidACPCpoint, 18 | BRAINSSnapShotWriter, 19 | JointHistogram, 20 | ShuffleVectorsModule, 21 | ImageRegionPlotter, 22 | ) 23 | -------------------------------------------------------------------------------- /nipype/interfaces/semtools/utilities/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/semtools/utilities/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/slicer/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | 3D Slicer is a platform for medical image informatics processing and visualization. 3 | 4 | For an EXPERIMENTAL implementation of an interface for the ``3dSlicer`` full framework, 5 | please check `"dynamic" Slicer `__. 6 | """ 7 | 8 | from .diffusion import * 9 | from .segmentation import * 10 | from .filtering import * 11 | from .utilities import EMSegmentTransformToNewFormat 12 | from .surface import ( 13 | MergeModels, 14 | ModelToLabelMap, 15 | GrayscaleModelMaker, 16 | ProbeVolumeWithModel, 17 | LabelMapSmoothing, 18 | ModelMaker, 19 | ) 20 | from .quantification import * 21 | from .legacy import * 22 | from .registration import * 23 | from .converters import DicomToNrrdConverter, OrientScalarVolume 24 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/base.py: -------------------------------------------------------------------------------- 1 | from ..base import SEMLikeCommandLine 2 | 3 | 4 | class SlicerCommandLine(SEMLikeCommandLine): 5 | pass 6 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/diffusion/__init__.py: -------------------------------------------------------------------------------- 1 | from .diffusion import ( 2 | ResampleDTIVolume, 3 | DWIRicianLMMSEFilter, 4 | TractographyLabelMapSeeding, 5 | DWIJointRicianLMMSEFilter, 6 | DiffusionWeightedVolumeMasking, 7 | DTIimport, 8 | DWIToDTIEstimation, 9 | DiffusionTensorScalarMeasurements, 10 | DTIexport, 11 | ) 12 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/diffusion/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/slicer/diffusion/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/slicer/filtering/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/slicer/filtering/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/slicer/legacy/__init__.py: -------------------------------------------------------------------------------- 1 | from .diffusion import * 2 | from .segmentation import OtsuThresholdSegmentation 3 | from .filtering import OtsuThresholdImageFilter, ResampleScalarVolume 4 | from .converters import BSplineToDeformationField 5 | from .registration import ( 6 | BSplineDeformableRegistration, 7 | AffineRegistration, 8 | MultiResolutionAffineRegistration, 9 | RigidRegistration, 10 | LinearRegistration, 11 | ExpertAutomatedRegistration, 12 | ) 13 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/legacy/diffusion/__init__.py: -------------------------------------------------------------------------------- 1 | from .denoising import DWIUnbiasedNonLocalMeansFilter 2 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/legacy/diffusion/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/slicer/legacy/diffusion/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/slicer/legacy/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/slicer/legacy/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/slicer/quantification/__init__.py: -------------------------------------------------------------------------------- 1 | from .changequantification import IntensityDifferenceMetric 2 | from .petstandarduptakevaluecomputation import PETStandardUptakeValueComputation 3 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/quantification/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/slicer/quantification/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/slicer/registration/__init__.py: -------------------------------------------------------------------------------- 1 | from .specialized import ( 2 | ACPCTransform, 3 | FiducialRegistration, 4 | VBRAINSDemonWarp, 5 | BRAINSDemonWarp, 6 | ) 7 | from .brainsresample import BRAINSResample 8 | from .brainsfit import BRAINSFit 9 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/registration/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/slicer/registration/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/slicer/segmentation/__init__.py: -------------------------------------------------------------------------------- 1 | from .specialized import RobustStatisticsSegmenter, EMSegmentCommandLine, BRAINSROIAuto 2 | from .simpleregiongrowingsegmentation import SimpleRegionGrowingSegmentation 3 | -------------------------------------------------------------------------------- /nipype/interfaces/slicer/segmentation/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/slicer/segmentation/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/slicer/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/slicer/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import SlicerCommandLine 3 | 4 | 5 | def test_SlicerCommandLine_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = SlicerCommandLine.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/spm/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/spm/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/spm/tests/test_auto_SPMCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import SPMCommand 3 | 4 | 5 | def test_SPMCommand_inputs(): 6 | input_map = dict( 7 | matlab_cmd=dict(), 8 | mfile=dict( 9 | usedefault=True, 10 | ), 11 | paths=dict(), 12 | use_mcr=dict(), 13 | use_v8struct=dict( 14 | min_ver="8", 15 | usedefault=True, 16 | ), 17 | ) 18 | inputs = SPMCommand.input_spec() 19 | 20 | for key, metadata in list(input_map.items()): 21 | for metakey, value in list(metadata.items()): 22 | assert getattr(inputs.traits()[key], metakey) == value 23 | -------------------------------------------------------------------------------- /nipype/interfaces/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/tests/test_auto_IOBase.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..io import IOBase 3 | 4 | 5 | def test_IOBase_inputs(): 6 | input_map = dict() 7 | inputs = IOBase.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..dcmstack import NiftiGeneratorBase 3 | 4 | 5 | def test_NiftiGeneratorBase_inputs(): 6 | input_map = dict() 7 | inputs = NiftiGeneratorBase.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/tests/test_auto_NilearnBaseInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..nilearn import NilearnBaseInterface 3 | 4 | 5 | def test_NilearnBaseInterface_inputs(): 6 | input_map = dict() 7 | inputs = NilearnBaseInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | -------------------------------------------------------------------------------- /nipype/interfaces/tests/test_auto_SQLiteSink.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..io import SQLiteSink 3 | 4 | 5 | def test_SQLiteSink_inputs(): 6 | input_map = dict( 7 | database_file=dict( 8 | extensions=None, 9 | mandatory=True, 10 | ), 11 | table_name=dict( 12 | mandatory=True, 13 | ), 14 | ) 15 | inputs = SQLiteSink.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/interfaces/utility/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | Package contains interfaces for using existing functionality in other packages 5 | 6 | Requires Packages to be installed 7 | """ 8 | 9 | from .base import IdentityInterface, Rename, Select, Split, Merge, AssertEqual 10 | from .csv import CSVReader 11 | from .wrappers import Function 12 | -------------------------------------------------------------------------------- /nipype/interfaces/utility/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/utility/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/utility/tests/test_auto_AssertEqual.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import AssertEqual 3 | 4 | 5 | def test_AssertEqual_inputs(): 6 | input_map = dict( 7 | volume1=dict( 8 | extensions=None, 9 | mandatory=True, 10 | ), 11 | volume2=dict( 12 | extensions=None, 13 | mandatory=True, 14 | ), 15 | ) 16 | inputs = AssertEqual.input_spec() 17 | 18 | for key, metadata in list(input_map.items()): 19 | for metakey, value in list(metadata.items()): 20 | assert getattr(inputs.traits()[key], metakey) == value 21 | -------------------------------------------------------------------------------- /nipype/interfaces/utility/tests/test_auto_Function.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..wrappers import Function 3 | 4 | 5 | def test_Function_inputs(): 6 | input_map = dict( 7 | function_str=dict( 8 | mandatory=True, 9 | ), 10 | ) 11 | inputs = Function.input_spec() 12 | 13 | for key, metadata in list(input_map.items()): 14 | for metakey, value in list(metadata.items()): 15 | assert getattr(inputs.traits()[key], metakey) == value 16 | 17 | 18 | def test_Function_outputs(): 19 | output_map = dict() 20 | outputs = Function.output_spec() 21 | 22 | for key, metadata in list(output_map.items()): 23 | for metakey, value in list(metadata.items()): 24 | assert getattr(outputs.traits()[key], metakey) == value 25 | -------------------------------------------------------------------------------- /nipype/interfaces/utility/tests/test_auto_IdentityInterface.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import IdentityInterface 3 | 4 | 5 | def test_IdentityInterface_inputs(): 6 | input_map = dict() 7 | inputs = IdentityInterface.input_spec() 8 | 9 | for key, metadata in list(input_map.items()): 10 | for metakey, value in list(metadata.items()): 11 | assert getattr(inputs.traits()[key], metakey) == value 12 | 13 | 14 | def test_IdentityInterface_outputs(): 15 | output_map = dict() 16 | outputs = IdentityInterface.output_spec() 17 | 18 | for key, metadata in list(output_map.items()): 19 | for metakey, value in list(metadata.items()): 20 | assert getattr(outputs.traits()[key], metakey) == value 21 | -------------------------------------------------------------------------------- /nipype/interfaces/vista/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """VistaSoft contains Matlab code to perform a variety of analysis on MRI data.""" 4 | from .vista import Vnifti2Image, VtoMat 5 | -------------------------------------------------------------------------------- /nipype/interfaces/vista/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/vista/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/workbench/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """Connectome Workbench is a visualization for neuroimaging data, esp. derived from HCP data.""" 4 | from .metric import MetricResample 5 | from .cifti import CiftiSmooth 6 | -------------------------------------------------------------------------------- /nipype/interfaces/workbench/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/interfaces/workbench/tests/__init__.py -------------------------------------------------------------------------------- /nipype/interfaces/workbench/tests/test_auto_WBCommand.py: -------------------------------------------------------------------------------- 1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT 2 | from ..base import WBCommand 3 | 4 | 5 | def test_WBCommand_inputs(): 6 | input_map = dict( 7 | args=dict( 8 | argstr="%s", 9 | ), 10 | environ=dict( 11 | nohash=True, 12 | usedefault=True, 13 | ), 14 | ) 15 | inputs = WBCommand.input_spec() 16 | 17 | for key, metadata in list(input_map.items()): 18 | for metakey, value in list(metadata.items()): 19 | assert getattr(inputs.traits()[key], metakey) == value 20 | -------------------------------------------------------------------------------- /nipype/pipeline/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | Package contains modules for generating pipelines using interfaces 5 | 6 | """ 7 | __docformat__ = "restructuredtext" 8 | from .engine import Node, MapNode, JoinNode, Workflow 9 | -------------------------------------------------------------------------------- /nipype/pipeline/engine/__init__.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 3 | # vi: set ft=python sts=4 ts=4 sw=4 et: 4 | """ 5 | Package contains modules for generating pipelines using interfaces 6 | 7 | """ 8 | 9 | __docformat__ = "restructuredtext" 10 | from .workflows import Workflow 11 | from .nodes import Node, MapNode, JoinNode 12 | from .utils import generate_expanded_graph 13 | -------------------------------------------------------------------------------- /nipype/pipeline/engine/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | -------------------------------------------------------------------------------- /nipype/pipeline/plugins/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | 4 | from .debug import DebugPlugin 5 | from .linear import LinearPlugin 6 | from .pbs import PBSPlugin 7 | from .oar import OARPlugin 8 | from .sge import SGEPlugin 9 | from .condor import CondorPlugin 10 | from .dagman import CondorDAGManPlugin 11 | from .multiproc import MultiProcPlugin 12 | from .legacymultiproc import LegacyMultiProcPlugin 13 | from .ipython import IPythonPlugin 14 | from .somaflow import SomaFlowPlugin 15 | from .pbsgraph import PBSGraphPlugin 16 | from .sgegraph import SGEGraphPlugin 17 | from .lsf import LSFPlugin 18 | from .slurm import SLURMPlugin 19 | from .slurmgraph import SLURMGraphPlugin 20 | 21 | from . import semaphore_singleton 22 | -------------------------------------------------------------------------------- /nipype/pipeline/plugins/semaphore_singleton.py: -------------------------------------------------------------------------------- 1 | import threading 2 | 3 | semaphore = threading.Semaphore(0) 4 | -------------------------------------------------------------------------------- /nipype/pipeline/plugins/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | -------------------------------------------------------------------------------- /nipype/pytest.ini: -------------------------------------------------------------------------------- 1 | [pytest] 2 | norecursedirs = .git build dist doc nipype/external tools examples src 3 | addopts = --doctest-modules 4 | doctest_optionflags = ALLOW_UNICODE NORMALIZE_WHITESPACE 5 | env = 6 | PYTHONHASHSEED=0 7 | junit_family=xunit2 8 | -------------------------------------------------------------------------------- /nipype/refs.py: -------------------------------------------------------------------------------- 1 | # Use duecredit (duecredit.org) to provide a citation to relevant work to 2 | # be cited. This does nothing, unless the user has duecredit installed, 3 | # And calls this with duecredit (as in `python -m duecredit script.py`): 4 | from .external.due import due, Doi 5 | 6 | due.cite( 7 | Doi("10.3389/fninf.2011.00013"), 8 | description="A flexible, lightweight and extensible neuroimaging data" 9 | " processing framework in Python", 10 | path="nipype", 11 | tags=["implementation"], 12 | ) 13 | 14 | due.cite( 15 | Doi("10.5281/zenodo.50186"), 16 | description="A flexible, lightweight and extensible neuroimaging data" 17 | " processing framework in Python", 18 | path="nipype", 19 | tags=["implementation"], 20 | ) 21 | -------------------------------------------------------------------------------- /nipype/scripts/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nipy/nipype/8234ec318489930fa17487cf15d210420214b00a/nipype/scripts/__init__.py 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Some of 6 | them have been copied from nipy. Any changes to these should be done 7 | upstream. 8 | 9 | * From nipy: 10 | * onetime.py 11 | * tmpdirs.py 12 | -------------------------------------------------------------------------------- /nipype/utils/__init__.py: -------------------------------------------------------------------------------- 1 | from .onetime import OneTimeProperty, setattr_on_read 2 | from .tmpdirs import TemporaryDirectory, InTemporaryDirectory 3 | -------------------------------------------------------------------------------- /nipype/utils/datetime.py: -------------------------------------------------------------------------------- 1 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- 2 | # vi: set ft=python sts=4 ts=4 sw=4 et: 3 | """ 4 | Utilities for dates and time 5 | """ 6 | 7 | from datetime import datetime as dt 8 | import sys 9 | 10 | if sys.version_info >= (3, 11): 11 | from datetime import UTC 12 | 13 | def utcnow(): 14 | """Adapter since 3.12 prior utcnow is deprecated, 15 | but not EOLed 3.8 does not have datetime.UTC""" 16 | return dt.now(UTC) 17 | 18 | else: 19 | utcnow = dt.utcnow 20 | -------------------------------------------------------------------------------- /nipype/utils/imagemanip.py: -------------------------------------------------------------------------------- 1 | """Image manipulation utilities (mostly, NiBabel manipulations).""" 2 | 3 | import nibabel as nb 4 | 5 | 6 | def copy_header(header_file, in_file, keep_dtype=True): 7 | """Copy header from a reference image onto another image.""" 8 | hdr_img = nb.load(header_file) 9 | out_img = nb.load(in_file, mmap=False) 10 | hdr = hdr_img.header.copy() 11 | if keep_dtype: 12 | hdr.set_data_dtype(out_img.get_data_dtype()) 13 | 14 | new_img = out_img.__class__(out_img.dataobj, None, hdr) 15 | if not keep_dtype: 16 | new_img.set_data_dtype(hdr_img.get_data_dtype()) 17 | 18 | new_img.to_filename(in_file) 19 | return in_file 20 | -------------------------------------------------------------------------------- /nipype/utils/spm_get_doc.m: -------------------------------------------------------------------------------- 1 | function doc = spm_get_doc(docname) 2 | % Get the documentation from SPM for the functionality named 3 | % docname. 4 | % 5 | % This will search through the spm_config() object and grab the 6 | % documentation whose name matches docname. 7 | cfgstruct = spm_flat_config(0); 8 | [rows, cols] = size(cfgstruct); 9 | docstruct.help={'None'}; 10 | % Loop over cell array and search for the docname 11 | for i = 1:cols 12 | if strcmp(cfgstruct{i}.name, docname) 13 | docstruct = cfgstruct{i}; 14 | break 15 | end 16 | end 17 | % Add a tag so we can strip off the Matlab header information and 18 | % only print out the SPM documentation. 19 | tag = 'NIPYPE\n'; 20 | doc = strcat(tag, docstruct.help{:}); 21 | end 22 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- 1 | [build-system] 2 | requires = ["setuptools >= 30.3.0"] 3 | build-backend = "setuptools.build_meta" 4 | 5 | [tool.black] 6 | skip-string-normalization = true 7 | 8 | [tool.pytest.ini_options] 9 | minversion = "6" 10 | testpaths = ["nipype"] 11 | log_cli_level = "INFO" 12 | xfail_strict = true 13 | norecursedirs = [".git"] 14 | addopts = [ 15 | "-svx", 16 | "-ra", 17 | "--strict-config", 18 | "--strict-markers", 19 | "--doctest-modules", 20 | "--cov=nipype", 21 | "--cov-report=xml", 22 | "--cov-config=pyproject.toml", 23 | ] 24 | doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS" 25 | env = "PYTHONHASHSEED=0" 26 | filterwarnings = ["ignore::DeprecationWarning"] 27 | junit_family = "xunit2" 28 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | # Auto-generated by tools/update_requirements.py 2 | click>=6.6.0 3 | networkx>=2.0 4 | nibabel>=2.1.0 5 | numpy>=1.17 6 | packaging 7 | prov>=1.5.2 8 | pydot>=1.2.3 9 | python-dateutil>=2.2 10 | rdflib>=5.0.0 11 | scipy>=0.14 12 | simplejson>=3.8.0 13 | traits>=4.6,<6.4,!=5.0 14 | filelock>=3.0.0 15 | etelemetry>=0.2.0 16 | looseversion 17 | -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [bdist_wheel] 2 | python-tag=py3 3 | -------------------------------------------------------------------------------- /tools/ci/activate.sh: -------------------------------------------------------------------------------- 1 | if [ -e virtenv/bin/activate ]; then 2 | source virtenv/bin/activate 3 | elif [ -e virtenv/Scripts/activate ]; then 4 | source virtenv/Scripts/activate 5 | else 6 | echo Cannot activate virtual environment 7 | ls -R virtenv 8 | false 9 | fi 10 | -------------------------------------------------------------------------------- /tools/ci/build_archive.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | echo "Building archive" 4 | 5 | source tools/ci/activate.sh 6 | 7 | set -eu 8 | 9 | # Required dependencies 10 | echo "INSTALL_TYPE = $INSTALL_TYPE" 11 | 12 | set -x 13 | 14 | if [ "$INSTALL_TYPE" == "sdist" ]; then 15 | python setup.py egg_info # check egg_info while we're here 16 | python setup.py sdist 17 | export ARCHIVE=$( ls dist/*.tar.gz ) 18 | elif [ "$INSTALL_TYPE" == "wheel" ]; then 19 | python setup.py bdist_wheel 20 | export ARCHIVE=$( ls dist/*.whl ) 21 | elif [ "$INSTALL_TYPE" == "archive" ]; then 22 | export ARCHIVE="package.tar.gz" 23 | git archive -o $ARCHIVE HEAD 24 | elif [ "$INSTALL_TYPE" == "pip" ]; then 25 | export ARCHIVE="." 26 | fi 27 | 28 | set +eux 29 | -------------------------------------------------------------------------------- /tools/ci/check.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | echo Running tests 4 | 5 | source tools/ci/activate.sh 6 | source tools/ci/env.sh 7 | 8 | set -eu 9 | 10 | # Required variables 11 | echo CHECK_TYPE = $CHECK_TYPE 12 | 13 | set -x 14 | 15 | if [ "${CHECK_TYPE}" == "test" ]; then 16 | pytest --capture=no --verbose --doctest-modules -c nipype/pytest.ini \ 17 | --cov-config .coveragerc --cov nipype --cov-report xml \ 18 | --junitxml=test-results.xml nipype 19 | elif [ "$CHECK_TYPE" = "specs" ]; then 20 | make specs 21 | git status -s 22 | test -z "$(git status -s)" 23 | elif [ "$CHECK_TYPE" = "style" ]; then 24 | black --check nipype setup.py 25 | else 26 | false 27 | fi 28 | 29 | set +eux 30 | 31 | echo Done running tests 32 | -------------------------------------------------------------------------------- /tools/ci/create_venv.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | echo Creating isolated virtual environment 4 | 5 | source tools/ci/env.sh 6 | 7 | set -eu 8 | 9 | # Required variables 10 | echo SETUP_REQUIRES = $SETUP_REQUIRES 11 | 12 | set -x 13 | 14 | python -m pip install --upgrade pip virtualenv 15 | virtualenv --python=python virtenv 16 | source tools/ci/activate.sh 17 | python --version 18 | python -m pip install -U $SETUP_REQUIRES 19 | which python 20 | which pip 21 | 22 | set +eux 23 | 24 | echo Done creating isolated virtual environment 25 | -------------------------------------------------------------------------------- /tools/ci/env.sh: -------------------------------------------------------------------------------- 1 | SETUP_REQUIRES="pip setuptools>=30.3.0 wheel" 2 | 3 | # Minimum requirements 4 | REQUIREMENTS="-r requirements.txt" 5 | # Minimum versions of minimum requirements 6 | MIN_REQUIREMENTS="-r min-requirements.txt" 7 | 8 | # Numpy and scipy upload nightly/weekly/intermittent wheels 9 | NIGHTLY_WHEELS="https://pypi.anaconda.org/scipy-wheels-nightly/simple" 10 | STAGING_WHEELS="https://pypi.anaconda.org/multibuild-wheels-staging/simple" 11 | PRE_PIP_FLAGS="--pre --extra-index-url $NIGHTLY_WHEELS --extra-index-url $STAGING_WHEELS" 12 | 13 | for CONF in /etc/fsl/fsl.sh /etc/afni/afni.sh; do 14 | if [ -r $CONF ]; then source $CONF; fi 15 | done 16 | 17 | FSLOUTPUTTYPE=NIFTI_GZ 18 | -------------------------------------------------------------------------------- /tools/ci/install.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | echo Installing nipype 4 | 5 | source tools/ci/activate.sh 6 | source tools/ci/env.sh 7 | 8 | set -eu 9 | 10 | # Required variables 11 | echo INSTALL_TYPE = $INSTALL_TYPE 12 | echo CHECK_TYPE = $CHECK_TYPE 13 | echo NIPYPE_EXTRAS = $NIPYPE_EXTRAS 14 | echo EXTRA_PIP_FLAGS = $EXTRA_PIP_FLAGS 15 | 16 | set -x 17 | 18 | if [ -n "$EXTRA_PIP_FLAGS" ]; then 19 | EXTRA_PIP_FLAGS=${!EXTRA_PIP_FLAGS} 20 | fi 21 | 22 | if [ "$INSTALL_TYPE" == "setup" ]; then 23 | python setup.py install 24 | else 25 | pip install $EXTRA_PIP_FLAGS $ARCHIVE 26 | fi 27 | 28 | # Basic import check 29 | python -c 'import nipype; print(nipype.__version__)' 30 | 31 | if [ "$CHECK_TYPE" == "skiptests" ]; then 32 | exit 0 33 | fi 34 | 35 | pip install $EXTRA_PIP_FLAGS "nipype[$NIPYPE_EXTRAS]" 36 | 37 | set +eux 38 | 39 | echo Done installing nipype 40 | -------------------------------------------------------------------------------- /tools/ci/install_deb_dependencies.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | echo "Installing NeuroDebian dependencies" 4 | 5 | set -eu 6 | 7 | echo "INSTALL_DEB_DEPENDENCIES = $INSTALL_DEB_DEPENDENCIES" 8 | 9 | DEPS=( 10 | fsl 11 | # afni 12 | # elastix 13 | fsl-atlases 14 | xvfb 15 | fusefat 16 | graphviz 17 | ) 18 | 19 | if $INSTALL_DEB_DEPENDENCIES; then 20 | bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh) 21 | sudo apt update 22 | sudo apt install -y -qq ${DEPS[@]} 23 | fi 24 | -------------------------------------------------------------------------------- /tools/ci/install_dependencies.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | echo Installing dependencies 4 | 5 | source tools/ci/activate.sh 6 | source tools/ci/env.sh 7 | 8 | set -eu 9 | 10 | # Required variables 11 | echo EXTRA_PIP_FLAGS = $EXTRA_PIP_FLAGS 12 | echo DEPENDS = $DEPENDS 13 | 14 | set -x 15 | 16 | if [ -n "$EXTRA_PIP_FLAGS" ]; then 17 | EXTRA_PIP_FLAGS=${!EXTRA_PIP_FLAGS} 18 | fi 19 | 20 | if [ -n "$DEPENDS" ]; then 21 | pip install ${EXTRA_PIP_FLAGS} --prefer-binary ${!DEPENDS} 22 | fi 23 | 24 | set +eux 25 | 26 | echo Done installing dependencies 27 | -------------------------------------------------------------------------------- /tools/retry_cmd.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | # 3 | # retry_cmd.sh [-n NLOOPS] [-s SLEEP] CMD 4 | # 5 | # Retry command until success or pre-specified number of failures 6 | # 7 | # 2018 Chris Markiewicz 8 | # Released into public domain 9 | 10 | NLOOPS=3 11 | TOSLEEP=5 12 | 13 | while true; do 14 | case "$1" in 15 | -n ) NLOOPS="$2"; shift 2 ;; 16 | -s ) TOSLEEP="$2"; shift 2 ;; 17 | -- ) shift; break ;; 18 | * ) break ;; 19 | esac 20 | done 21 | 22 | # Normalize whitespace in command, preserving quotes 23 | CMD="" 24 | for ARG; do 25 | CMD="$CMD \"$ARG\""; 26 | done 27 | 28 | RET=0 29 | for i in `seq $NLOOPS`; do 30 | sh -c "$CMD" 31 | RET="$?" 32 | if [ "$RET" -eq 0 ]; then break; fi 33 | if [ "$i" -ne "$NLOOPS" ]; then sleep $TOSLEEP; fi 34 | done 35 | 36 | exit $RET 37 | -------------------------------------------------------------------------------- /tools/run_examples.py: -------------------------------------------------------------------------------- 1 | import sys 2 | from textwrap import dedent 3 | 4 | 5 | if __name__ == "__main__": 6 | print( 7 | dedent( 8 | """Nipype examples have been moved to niflow-nipype1-examples. 9 | 10 | Install with: pip install niflow-nipype1-examples""" 11 | ) 12 | ) 13 | if sys.argv[1:]: 14 | print( 15 | "Run this command with: niflow-nipype1-examples " + " ".join(sys.argv[1:]) 16 | ) 17 | sys.exit(1) 18 | -------------------------------------------------------------------------------- /tools/update_mailmap.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # usage -> bash update_mailmap.sh 4 | # by default, will use the latest tag 5 | 6 | set -ux 7 | 8 | ROOT=$( git rev-parse --show-toplevel ) 9 | MAILMAP=$ROOT/.mailmap 10 | 11 | LAST=$(git describe --tags `git rev-list --tags --max-count=1`) 12 | RELEASE=${1:-$LAST} 13 | 14 | IFS=$'\n' 15 | for NAME in $(git shortlog -nse $RELEASE.. | cut -f2-); do 16 | echo $NAME 17 | done 18 | 19 | # sort and write 20 | sort $MAILMAP > .tmpmailmap 21 | cp .tmpmailmap $MAILMAP 22 | rm .tmpmailmap 23 | -------------------------------------------------------------------------------- /tools/update_requirements.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | from runpy import run_path 3 | from pathlib import Path 4 | 5 | repo_root = Path(__file__).parent.parent 6 | info_file = repo_root / "nipype" / "info.py" 7 | reqs = repo_root / "requirements.txt" 8 | 9 | info = run_path(info_file) 10 | requirements = info["REQUIRES"] 11 | 12 | script_name = Path(__file__).relative_to(repo_root) 13 | 14 | lines = [f"# Auto-generated by {script_name}", ""] 15 | 16 | # Write requirements 17 | lines[1:-1] = requirements 18 | reqs.write_text("\n".join(lines), encoding='utf-8') 19 | --------------------------------------------------------------------------------