├── .circleci
├── config.yml
├── test_py2_fmri_spm_nested_multiproc_l2.sh
├── test_py2_pytest.sh
├── test_py3_docs.sh
├── test_py3_fmri_fsl_feeds_linear_l1.sh
├── test_py3_fmri_fsl_reuse_linear_l1.sh
├── test_py3_fmri_spm_dartel_multiproc_l1.sh
├── test_py3_fmri_spm_dartel_multiproc_l2.sh
├── test_py3_fmri_spm_linear_3d.sh
├── test_py3_fmri_spm_linear_4d.sh
├── test_py3_fmri_spm_nested_multiproc_l1.sh
└── test_py3_pytest.sh
├── .coveragerc
├── .dockerignore
├── .gitattributes
├── .github
├── ISSUE_TEMPLATE.md
└── PULL_REQUEST_TEMPLATE.md
├── .gitignore
├── .mailmap
├── .travis.yml
├── .zenodo.json
├── CODE_OF_CONDUCT.md
├── CONTRIBUTING.md
├── INSTALL
├── LICENSE
├── MANIFEST.in
├── Makefile
├── README.rst
├── THANKS.rst
├── Vagrantfile
├── build_docs.py
├── codecov.yml
├── doc
├── .gitignore
├── Makefile
├── README.txt
├── _static
│ ├── nipy-logo-bg-138x120.png
│ ├── nipy.css
│ ├── nipype-banner-bg.png
│ ├── nipype.css
│ └── reggie2.png
├── _templates
│ ├── gse.html
│ ├── indexsidebar.html
│ ├── layout.html
│ ├── navbar.html
│ └── sidebar_versions.html
├── about.rst
├── api
│ └── index.rst
├── changelog
│ ├── 0.X.X-changelog
│ └── 1.X.X-changelog
├── 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
├── documentation.rst
├── images
│ ├── nipype_architecture_overview2.png
│ └── nipype_architecture_overview2.svg
├── index.rst
├── interfaces
│ ├── .gitignore
│ └── index.rst
├── links_names.txt
├── make.bat
├── quickstart.rst
├── searchresults.rst
├── sphinxext
│ ├── README.txt
│ ├── autosummary_generate.py
│ └── ipython_console_highlighting.py
├── users
│ ├── aws.rst
│ ├── caching_tutorial.rst
│ ├── cli.rst
│ ├── config_file.rst
│ ├── debug.rst
│ ├── function_interface.rst
│ ├── grabbing_and_sinking.rst
│ ├── images
│ │ ├── componentarchitecture.png
│ │ ├── gantt_chart.png
│ │ ├── proc2subj.png
│ │ ├── proc2subj2fwhm.png
│ │ ├── smoothrealignconnected.png
│ │ ├── smoothrealignunconnected.png
│ │ └── threecomponentpipe.png
│ ├── index.rst
│ ├── install.rst
│ ├── joinnode_and_itersource.rst
│ ├── mapnode_and_iterables.rst
│ ├── mipav.rst
│ ├── model_specification.rst
│ ├── neurodocker.rst
│ ├── nipypecmd.rst
│ ├── plugins.rst
│ ├── resource_sched_profiler.rst
│ ├── saving_workflows.rst
│ ├── select_files.rst
│ ├── sphinx_ext.rst
│ └── spmmcr.rst
└── version.rst
├── docker
├── files
│ ├── neurodebian.gpg
│ ├── run_builddocs.sh
│ ├── run_examples.sh
│ └── run_pytests.sh
├── generate_dockerfiles.sh
└── prune_dockerfile.sh
├── examples
├── README
├── dmri_camino_dti.py
├── dmri_connectivity.py
├── dmri_connectivity_advanced.py
├── dmri_dtk_dti.py
├── dmri_dtk_odf.py
├── dmri_fsl_dti.py
├── dmri_group_connectivity_camino.py
├── dmri_group_connectivity_mrtrix.py
├── dmri_mrtrix_dti.py
├── dmri_preprocessing.py
├── dmri_tbss_nki.py
├── fmri_ants_openfmri.py
├── fmri_freesurfer_smooth.py
├── fmri_fsl.py
├── fmri_fsl_feeds.py
├── fmri_fsl_reuse.py
├── fmri_nipy_glm.py
├── fmri_openfmri.py
├── fmri_slicer_coregistration.py
├── fmri_spm.py
├── fmri_spm_auditory.py
├── fmri_spm_dartel.py
├── fmri_spm_face.py
├── fmri_spm_nested.py
├── frontiers_paper
│ ├── smoothing_comparison.py
│ └── workflow_from_scratch.py
├── howto_caching_example.py
├── nipype_tutorial.ipynb
├── rsfmri_vol_surface_preprocessing.py
├── rsfmri_vol_surface_preprocessing_nipy.py
├── smri_ants_build_template.py
├── smri_ants_registration.py
├── smri_antsregistration_build_template.py
├── smri_cbs_skullstripping.py
├── smri_freesurfer.py
├── smri_fsreconall.py
├── tessellation_tutorial.py
├── test_spm.py
└── workshop_dartmouth_2010.py
├── 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_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
│ └── portalocker.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_MaskTool.py
│ │ │ ├── test_auto_Maskave.py
│ │ │ ├── test_auto_Means.py
│ │ │ ├── test_auto_Merge.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_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_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_ANTS.py
│ │ │ ├── test_auto_ANTSCommand.py
│ │ │ ├── test_auto_AffineInitializer.py
│ │ │ ├── test_auto_AntsJointFusion.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_ConvertScalarImageToRGB.py
│ │ │ ├── test_auto_CorticalThickness.py
│ │ │ ├── test_auto_CreateJacobianDeterminantImage.py
│ │ │ ├── test_auto_CreateTiledMosaic.py
│ │ │ ├── test_auto_DenoiseImage.py
│ │ │ ├── test_auto_GenWarpFields.py
│ │ │ ├── test_auto_JointFusion.py
│ │ │ ├── test_auto_KellyKapowski.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_WarpImageMultiTransform.py
│ │ │ ├── test_auto_WarpTimeSeriesImageMultiTransform.py
│ │ │ ├── test_auto_antsIntroduction.py
│ │ │ ├── test_auto_buildtemplateparallel.py
│ │ │ ├── test_extra_Registration.py
│ │ │ ├── test_resampling.py
│ │ │ └── test_spec_JointFusion.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
│ │ └── 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
│ ├── 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
│ │ ├── setup.py
│ │ ├── simulate.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
│ │ └── tracks.py
│ ├── dtitk
│ │ ├── __init__.py
│ │ ├── base.py
│ │ ├── registration.py
│ │ ├── tests
│ │ │ ├── __init__.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_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_affScalarVol.py
│ │ │ ├── test_auto_affScalarVolTask.py
│ │ │ ├── test_auto_affSymTensor3DVol.py
│ │ │ ├── test_auto_affSymTensor3DVolTask.py
│ │ │ ├── test_auto_diffeoScalarVol.py
│ │ │ ├── test_auto_diffeoScalarVolTask.py
│ │ │ ├── test_auto_diffeoSymTensor3DVol.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
│ │ ├── 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_ImageInfo.py
│ │ │ ├── test_auto_Jacobian.py
│ │ │ ├── test_auto_LTAConvert.py
│ │ │ ├── test_auto_Label2Annot.py
│ │ │ ├── test_auto_Label2Label.py
│ │ │ ├── test_auto_Label2Vol.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_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_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_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_Threshold.py
│ │ │ ├── test_auto_TractSkeleton.py
│ │ │ ├── test_auto_Training.py
│ │ │ ├── test_auto_TrainingSetCreator.py
│ │ │ ├── test_auto_UnaryMaths.py
│ │ │ ├── test_auto_VecReg.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
│ ├── 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
│ ├── 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_DWIExtract.py
│ │ │ ├── test_auto_EstimateFOD.py
│ │ │ ├── test_auto_FitTensor.py
│ │ │ ├── test_auto_Generate5tt.py
│ │ │ ├── test_auto_LabelConfig.py
│ │ │ ├── test_auto_LabelConvert.py
│ │ │ ├── test_auto_MRConvert.py
│ │ │ ├── test_auto_MRMath.py
│ │ │ ├── test_auto_MRTrix3Base.py
│ │ │ ├── test_auto_Mesh2PVE.py
│ │ │ ├── test_auto_ReplaceFSwithFIRST.py
│ │ │ ├── test_auto_ResponseSD.py
│ │ │ ├── test_auto_TCK2VTK.py
│ │ │ ├── test_auto_TensorMetrics.py
│ │ │ └── test_auto_Tractography.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
│ ├── 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_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_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_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_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_S3DataGrabber.py
│ │ ├── test_auto_SEMLikeCommandLine.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_extra_dcm2nii.py
│ │ ├── test_io.py
│ │ ├── test_matlab.py
│ │ └── test_nilearn.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
├── 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
│ │ ├── 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_linear.py
│ │ ├── test_multiproc.py
│ │ ├── test_multiproc_nondaemon.py
│ │ ├── test_oar.py
│ │ ├── test_pbs.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
│ └── plot_workflow.py
├── testing
│ ├── __init__.py
│ ├── data
│ │ ├── 4d_dwi.nii
│ │ ├── A.scheme
│ │ ├── A_qmat.Bdouble
│ │ ├── A_recon_params.Bdouble
│ │ ├── BrainSegmentationPrior01.nii.gz
│ │ ├── BrainSegmentationPrior02.nii.gz
│ │ ├── BrainSegmentationPrior03.nii.gz
│ │ ├── BrainSegmentationPrior04.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
│ │ ├── 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
│ │ ├── data.Bfloat
│ │ ├── db.xml
│ │ ├── degree.csv
│ │ ├── degree.mat
│ │ ├── design.con
│ │ ├── design.mat
│ │ ├── 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
│ │ ├── 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
│ │ ├── 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
│ │ ├── 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.cope1.mgz
│ │ ├── lh.cope1.nii.gz
│ │ ├── lh.hippocampus.stl
│ │ ├── lh.pial
│ │ ├── lh.pial_converted.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
│ │ ├── nodif_brain_mask.nii.gz
│ │ ├── norm.mgz
│ │ ├── output.csv
│ │ ├── 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
│ │ ├── 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.pial
│ │ ├── rh.pial_converted.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
│ │ ├── 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_dir-LR_epi.nii.gz
│ │ ├── sub-01_dir-RL_epi.nii.gz
│ │ ├── subj1.cff
│ │ ├── subj1.pck
│ │ ├── subj2.cff
│ │ ├── subj2.pck
│ │ ├── subjectDesign.con
│ │ ├── subjectDesign.mat
│ │ ├── surf.txt
│ │ ├── surf01.vtk
│ │ ├── surf1.vtk
│ │ ├── surf2.vtk
│ │ ├── targets_MASK1.nii
│ │ ├── targets_MASK2.nii
│ │ ├── tbss_dir
│ │ │ └── do_not_delete.txt
│ │ ├── tdi.mif
│ │ ├── tensor_fitted_data.Bdouble
│ │ ├── timeDesign.con
│ │ ├── timeDesign.mat
│ │ ├── timeseries.txt
│ │ ├── 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
│ │ ├── vsm.nii
│ │ ├── warpfield.nii
│ │ ├── weights.txt
│ │ ├── wm.mgz
│ │ ├── wm_mask.mif
│ │ ├── wm_undersampled.nii
│ │ └── zstat1.nii.gz
│ ├── decorators.py
│ ├── fixtures.py
│ ├── tests
│ │ └── test_utils.py
│ └── utils.py
├── tests
│ ├── __init__.py
│ └── test_nipype.py
├── utils
│ ├── README.txt
│ ├── __init__.py
│ ├── config.py
│ ├── docparse.py
│ ├── draw_gantt_chart.py
│ ├── filemanip.py
│ ├── functions.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
│ ├── tests
│ │ ├── __init__.py
│ │ ├── test_cmd.py
│ │ ├── test_config.py
│ │ ├── test_docparse.py
│ │ ├── test_filemanip.py
│ │ ├── test_functions.py
│ │ ├── test_misc.py
│ │ ├── test_nipype2boutiques.py
│ │ ├── test_provenance.py
│ │ └── use_resources
│ └── tmpdirs.py
└── workflows
│ ├── __init__.py
│ ├── data
│ ├── __init__.py
│ ├── ecc.sch
│ └── hmc.sch
│ ├── dmri
│ ├── __init__.py
│ ├── camino
│ │ ├── __init__.py
│ │ ├── connectivity_mapping.py
│ │ ├── diffusion.py
│ │ └── group_connectivity.py
│ ├── connectivity
│ │ ├── __init__.py
│ │ ├── group_connectivity.py
│ │ └── nx.py
│ ├── dipy
│ │ ├── __init__.py
│ │ └── denoise.py
│ ├── dtitk
│ │ ├── __init__.py
│ │ └── tensor_registration.py
│ ├── fsl
│ │ ├── __init__.py
│ │ ├── artifacts.py
│ │ ├── dti.py
│ │ ├── epi.py
│ │ ├── tbss.py
│ │ ├── tests
│ │ │ ├── __init__.py
│ │ │ ├── test_dti.py
│ │ │ ├── test_epi.py
│ │ │ └── test_tbss.py
│ │ └── utils.py
│ └── mrtrix
│ │ ├── __init__.py
│ │ ├── connectivity_mapping.py
│ │ ├── diffusion.py
│ │ └── group_connectivity.py
│ ├── fmri
│ ├── __init__.py
│ ├── fsl
│ │ ├── __init__.py
│ │ ├── estimate.py
│ │ ├── preprocess.py
│ │ └── tests
│ │ │ ├── __init__.py
│ │ │ └── test_preprocess.py
│ └── spm
│ │ ├── __init__.py
│ │ ├── estimate.py
│ │ ├── preprocess.py
│ │ └── tests
│ │ └── __init__.py
│ ├── graph
│ └── __init__.py
│ ├── misc
│ ├── __init__.py
│ └── utils.py
│ ├── rsfmri
│ ├── __init__.py
│ └── fsl
│ │ ├── __init__.py
│ │ ├── resting.py
│ │ └── tests
│ │ ├── __init__.py
│ │ └── test_resting.py
│ ├── smri
│ ├── __init__.py
│ ├── ants
│ │ ├── ANTSBuildTemplate.py
│ │ ├── __init__.py
│ │ └── antsRegistrationBuildTemplate.py
│ ├── freesurfer
│ │ ├── __init__.py
│ │ ├── autorecon1.py
│ │ ├── autorecon2.py
│ │ ├── autorecon3.py
│ │ ├── ba_maps.py
│ │ ├── bem.py
│ │ ├── recon.py
│ │ └── utils.py
│ └── niftyreg
│ │ ├── __init__.py
│ │ └── groupwise.py
│ └── warp
│ └── __init__.py
├── requirements.txt
├── rtd_requirements.txt
├── setup.cfg
├── setup.py
└── tools
├── README
├── apigen.py
├── build_interface_docs.py
├── build_modref_templates.py
├── checkspecs.py
├── ex2rst
├── github.py
├── gitwash_dumper.py
├── install_spm_mcr.sh
├── interfacedocgen.py
├── make_examples.py
├── retry_cmd.sh
├── run_examples.py
├── toollib.py
└── update_changes.sh
/.circleci/test_py2_fmri_spm_nested_multiproc_l2.sh:
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1 | #!/bin/bash
2 |
3 | docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e NIPYPE_NUMBER_OF_CPUS=4 -e NIPYPE_RESOURCE_MONITOR=1 "${DOCKER_IMAGE}:py27" /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
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1 | #!/bin/bash
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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}:py27" /usr/bin/run_pytests.sh
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1 | #!/bin/bash
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3 | docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /src/nipype/doc "${DOCKER_IMAGE}:py36" /usr/bin/run_builddocs.sh
4 |
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/.circleci/test_py3_fmri_fsl_feeds_linear_l1.sh:
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1 | #!/bin/bash
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3 | docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_fsl_feeds Linear /data/examples/ l1pipeline
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/.circleci/test_py3_fmri_fsl_reuse_linear_l1.sh:
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1 | #!/bin/bash
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3 | docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_fsl_reuse Linear /data/examples/ level1_workflow
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/.circleci/test_py3_fmri_spm_dartel_multiproc_l1.sh:
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1 | #!/bin/bash
2 |
3 | docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_spm_dartel MultiProc /data/examples/ level1
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1 | #!/bin/bash
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3 | docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_spm_dartel MultiProc /data/examples/ l2pipeline
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/.circleci/test_py3_fmri_spm_linear_3d.sh:
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1 | #!/bin/bash
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3 | docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow3d
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/.circleci/test_py3_fmri_spm_linear_4d.sh:
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1 | #!/bin/bash
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3 | docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d
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/.circleci/test_py3_fmri_spm_nested_multiproc_l1.sh:
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1 | #!/bin/bash
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3 | docker run --rm=false -t -v $WORKDIR:/work -v $HOME/examples:/data/examples:ro -w /work -e NIPYPE_NUMBER_OF_CPUS=4 "${DOCKER_IMAGE}:py36" /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1
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/.circleci/test_py3_pytest.sh:
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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}:py36" /usr/bin/run_pytests.sh
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/.coveragerc:
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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 | docs/**/*
26 | docs/
27 | .cache/
28 | .circle/**/*
29 | .circle/
30 | circle.yml
31 | rtd_requirements.txt
32 | Vagrantfile
33 | .travis.yml
34 | .mailmap
35 |
36 | # Previous coverage results
37 | .coverage
38 |
--------------------------------------------------------------------------------
/.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 | Please paste the output of: `python -c "import nipype; print(nipype.get_info()); print(nipype.__version__)"`
16 |
17 | ### Execution environment
18 |
19 | Choose one
20 | - Container [Tag: ???]
21 | - My python environment inside container [Base Tag: ???]
22 | - My python environment outside container
23 |
--------------------------------------------------------------------------------
/.github/PULL_REQUEST_TEMPLATE.md:
--------------------------------------------------------------------------------
1 | Pull-request guidelines (Remove this section after reading):
2 |
3 | 1. If you would like to list yourself as a Nipype contributor and your name is not mentioned please modify .zenodo.json file.
4 | 2. By submitting this request you acknowledge that your contributions are available under the Apache 2 license.
5 | 3. Use a descriptive prefix for your PR: ENH (enhancement), FIX, TST, DOC, STY, REF (refactor), WIP (Work in progress)
6 | 4. The person who accepts/merges your PR will include an update to the CHANGES file: prefix: description (URL of pull request)
7 | 5. Run `make check-before-commit` before submitting the PR.
8 |
9 | ----- REMOVE TILL HERE -----
10 |
11 | Fixes # .
12 |
13 | Changes proposed in this pull request
14 | -
15 | -
16 |
--------------------------------------------------------------------------------
/.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 |
--------------------------------------------------------------------------------
/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 build_docs.py
8 | include setup_egg.py
9 | include doc/documentation.zip
10 | include nipype/COMMIT_INFO.txt
11 |
12 | recursive-include doc *
13 | recursive-include tools *
14 |
--------------------------------------------------------------------------------
/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 |
--------------------------------------------------------------------------------
/doc/README.txt:
--------------------------------------------------------------------------------
1 | ======================
2 | Nipype Documentation
3 | ======================
4 |
5 | This directory contains the documentation for the Nipype_ project.
6 | The documentation is written in reST_ (reStructuredText) and uses
7 | Sphinx_ to render html documentation from the rst source files.
8 |
9 | A relatively recent version of Sphinx_ is required to build the
10 | documentation, at least 0.6.x.
11 |
12 | Use the ``Makefile`` to build the documentation. Common commands:
13 |
14 | Discover available make targets::
15 |
16 | make help
17 |
18 | Clean up previous build::
19 |
20 | make clean
21 |
22 | Build html documentation::
23 |
24 | make html
25 |
26 |
27 |
28 |
29 |
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/doc/_templates/navbar.html:
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1 |
2 |
9 |
10 | Home ·
11 | Quickstart ·
12 | Documentation ·
13 | About ·
14 | Nipy
15 |
16 |
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/doc/api/index.rst:
--------------------------------------------------------------------------------
1 | .. _api-index:
2 |
3 | ###
4 | API
5 | ###
6 |
7 | :Release: |version|
8 | :Date: |today|
9 |
10 | .. include:: generated/gen.rst
11 |
--------------------------------------------------------------------------------
/doc/changes.rst:
--------------------------------------------------------------------------------
1 | :tocdepth: 2
2 |
3 | .. _changes:
4 |
5 | =================
6 | Changes in Nipype
7 | =================
8 |
9 | .. include:: ../CHANGES
10 |
11 | .. include:: links_names.txt
12 |
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/doc/devel/gitwash/git_development.rst:
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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 |
17 |
--------------------------------------------------------------------------------
/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 |
18 |
19 |
--------------------------------------------------------------------------------
/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 |
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/doc/devel/gitwash/this_project.inc:
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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 |
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/doc/interfaces/.gitignore:
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1 | /generated
2 |
--------------------------------------------------------------------------------
/doc/interfaces/index.rst:
--------------------------------------------------------------------------------
1 | .. _interface-index:
2 |
3 | #########################
4 | Interfaces and Algorithms
5 | #########################
6 |
7 | :Release: |version|
8 | :Date: |today|
9 |
10 | .. include:: generated/gen.rst
11 |
--------------------------------------------------------------------------------
/doc/searchresults.rst:
--------------------------------------------------------------------------------
1 | .. This displays the search results from the Google Custom Search engine.
2 | Don't link to it directly.
3 |
4 | Search results
5 | ==============
6 |
7 | .. raw:: html
8 |
9 | Loading
10 |
21 |
22 |
23 |
--------------------------------------------------------------------------------
/doc/sphinxext/README.txt:
--------------------------------------------------------------------------------
1 | ===================
2 | Sphinx Extensions
3 | ===================
4 |
5 | We've copied these sphinx extensions over from nipy-core. Any edits
6 | should be done upstream in nipy-core, not here in nipype!
7 |
8 | These a are a few sphinx extensions we are using to build the nipy
9 | documentation. In this file we list where they each come from, since we intend
10 | to always push back upstream any modifications or improvements we make to them.
11 |
12 | * From numpy:
13 | * numpy_ext
14 |
15 | * From ipython
16 | * ipython_console_highlighting
17 |
--------------------------------------------------------------------------------
/doc/users/cli.rst:
--------------------------------------------------------------------------------
1 | .. _cli:
2 |
3 | =============================
4 | Nipype Command Line Interface
5 | =============================
6 |
7 | The Nipype Command Line Interface allows a variety of operations::
8 |
9 | $ nipypecli
10 | Usage: nipypecli [OPTIONS] COMMAND [ARGS]...
11 |
12 | Options:
13 | -h, --help Show this message and exit.
14 |
15 | Commands:
16 | convert Export nipype interfaces to other formats.
17 | crash Display Nipype crash files.
18 | run Run a Nipype Interface.
19 | search Search for tracebacks content.
20 | show Print the content of Nipype node .pklz file.
21 |
22 | These have replaced previous nipype command line tools such as
23 | `nipype_display_crash`, `nipype_crash_search`, `nipype2boutiques`,
24 | `nipype_cmd` and `nipype_display_pklz`.
25 |
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/doc/users/index.rst:
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1 | .. _users-guide-index:
2 |
3 | ============
4 | User Guide
5 | ============
6 |
7 | :Release: |version|
8 | :Date: |today|
9 |
10 | .. toctree::
11 | :maxdepth: 2
12 |
13 | install
14 | neurodocker
15 | caching_tutorial
16 |
17 | .. toctree::
18 | Nipype tutorials
19 | Porcupine graphical interface
20 |
21 | .. toctree::
22 | :maxdepth: 1
23 |
24 | plugins
25 | config_file
26 | debug
27 | cli
28 |
29 | .. toctree::
30 | :maxdepth: 1
31 |
32 | grabbing_and_sinking
33 | select_files
34 | function_interface
35 | mapnode_and_iterables
36 | joinnode_and_itersource
37 | model_specification
38 | saving_workflows
39 | spmmcr
40 | mipav
41 | nipypecmd
42 | aws
43 | resource_sched_profiler
44 | sphinx_ext
45 |
46 |
47 |
48 |
49 |
50 |
--------------------------------------------------------------------------------
/doc/users/sphinx_ext.rst:
--------------------------------------------------------------------------------
1 | .. _sphinx_ext:
2 |
3 | Sphinx extensions
4 | -----------------
5 |
6 |
7 | To help users document their *Nipype*-based code, the software is shipped
8 | with a set of extensions (currently only one) to customize the appearance
9 | and simplify the generation process.
10 |
11 | .. automodule:: nipype.sphinxext.plot_workflow
12 | :undoc-members:
13 | :noindex:
14 |
--------------------------------------------------------------------------------
/doc/version.rst:
--------------------------------------------------------------------------------
1 | .. _version:
2 |
3 | .. htmlonly::
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 |
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/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:
--------------------------------------------------------------------------------
1 | A dataset for use with these scripts can be downloaded from the nipype
2 | website. At the time of writing, it's at:
3 |
4 | http://nipype.readthedocs.io/en/0.12.0/users/pipeline_tutorial.html
5 |
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/nipype/COMMIT_INFO.txt:
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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 |
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/nipype/algorithms/__init__.py:
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1 | # -*- coding: utf-8 -*-
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 pure python neuroimaging algorithms
6 |
7 | Exaples: artifactdetect
8 |
9 | """
10 | __docformat__ = 'restructuredtext'
11 |
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/nipype/algorithms/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 |
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/nipype/algorithms/tests/test_auto_Matlab2CSV.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..misc import Matlab2CSV
4 |
5 |
6 | def test_Matlab2CSV_inputs():
7 | input_map = dict(
8 | in_file=dict(mandatory=True, ),
9 | reshape_matrix=dict(usedefault=True, ),
10 | )
11 | inputs = Matlab2CSV.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 | def test_Matlab2CSV_outputs():
17 | output_map = dict(csv_files=dict(), )
18 | outputs = Matlab2CSV.output_spec()
19 |
20 | for key, metadata in list(output_map.items()):
21 | for metakey, value in list(metadata.items()):
22 | assert getattr(outputs.traits()[key], metakey) == value
23 |
--------------------------------------------------------------------------------
/nipype/algorithms/tests/test_auto_MergeROIs.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..misc import MergeROIs
4 |
5 |
6 | def test_MergeROIs_inputs():
7 | input_map = dict(
8 | in_files=dict(),
9 | in_index=dict(),
10 | in_reference=dict(),
11 | )
12 | inputs = MergeROIs.input_spec()
13 |
14 | for key, metadata in list(input_map.items()):
15 | for metakey, value in list(metadata.items()):
16 | assert getattr(inputs.traits()[key], metakey) == value
17 | def test_MergeROIs_outputs():
18 | output_map = dict(merged_file=dict(), )
19 | outputs = MergeROIs.output_spec()
20 |
21 | for key, metadata in list(output_map.items()):
22 | for metakey, value in list(metadata.items()):
23 | assert getattr(outputs.traits()[key], metakey) == value
24 |
--------------------------------------------------------------------------------
/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..misc import NormalizeProbabilityMapSet
4 |
5 |
6 | def test_NormalizeProbabilityMapSet_inputs():
7 | input_map = dict(
8 | in_files=dict(),
9 | in_mask=dict(),
10 | )
11 | inputs = NormalizeProbabilityMapSet.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 | def test_NormalizeProbabilityMapSet_outputs():
17 | output_map = dict(out_files=dict(), )
18 | outputs = NormalizeProbabilityMapSet.output_spec()
19 |
20 | for key, metadata in list(output_map.items()):
21 | for metakey, value in list(metadata.items()):
22 | assert getattr(outputs.traits()[key], metakey) == value
23 |
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/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..mesh import TVTKBaseInterface
4 |
5 |
6 | def test_TVTKBaseInterface_inputs():
7 | input_map = dict(
8 | ignore_exception=dict(
9 | deprecated='1.0.0',
10 | nohash=True,
11 | usedefault=True,
12 | ), )
13 | inputs = TVTKBaseInterface.input_spec()
14 |
15 | for key, metadata in list(input_map.items()):
16 | for metakey, value in list(metadata.items()):
17 | assert getattr(inputs.traits()[key], metakey) == value
18 |
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/nipype/algorithms/tests/test_icc_anova.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import division
3 | import numpy as np
4 | from nipype.algorithms.icc import ICC_rep_anova
5 |
6 |
7 | def test_ICC_rep_anova():
8 | # see table 2 in P. E. Shrout & Joseph L. Fleiss (1979). "Intraclass
9 | # Correlations: Uses in Assessing Rater Reliability". Psychological
10 | # Bulletin 86 (2): 420-428
11 | Y = np.array([[9, 2, 5, 8], [6, 1, 3, 2], [8, 4, 6, 8], [7, 1, 2, 6],
12 | [10, 5, 6, 9], [6, 2, 4, 7]])
13 |
14 | icc, r_var, e_var, _, dfc, dfe = ICC_rep_anova(Y)
15 | # see table 4
16 | assert round(icc, 2) == 0.71
17 | assert dfc == 3
18 | assert dfe == 15
19 | assert np.isclose(r_var / (r_var + e_var), icc)
20 |
--------------------------------------------------------------------------------
/nipype/caching/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from .memory import Memory
3 |
--------------------------------------------------------------------------------
/nipype/caching/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/conftest.py:
--------------------------------------------------------------------------------
1 | import pytest
2 | import numpy
3 | import os
4 |
5 | DATADIR = os.path.realpath(
6 | os.path.join(os.path.dirname(__file__), 'testing/data'))
7 |
8 |
9 | @pytest.fixture(autouse=True)
10 | def add_np(doctest_namespace):
11 | doctest_namespace['np'] = numpy
12 | doctest_namespace['os'] = os
13 |
14 | doctest_namespace["datadir"] = DATADIR
15 |
16 |
17 | @pytest.fixture(autouse=True)
18 | def in_testing(request):
19 | # This seems to be a reliable way to distinguish tests from doctests
20 | if request.function is None:
21 | os.chdir(DATADIR)
22 |
--------------------------------------------------------------------------------
/nipype/external/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 interfaces for using existing functionality in other packages
6 |
7 | Requires Packages to be installed
8 | """
9 | from __future__ import (print_function, division, unicode_literals,
10 | absolute_import)
11 | __docformat__ = 'restructuredtext'
12 |
13 | from .io import DataGrabber, DataSink, SelectFiles, BIDSDataGrabber
14 | from .utility import IdentityInterface, Rename, Function, Select, Merge
15 |
--------------------------------------------------------------------------------
/nipype/interfaces/afni/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 |
--------------------------------------------------------------------------------
/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import AFNICommandBase
4 |
5 |
6 | def test_AFNICommandBase_inputs():
7 | input_map = dict(
8 | args=dict(argstr='%s', ),
9 | environ=dict(
10 | nohash=True,
11 | usedefault=True,
12 | ),
13 | ignore_exception=dict(
14 | deprecated='1.0.0',
15 | nohash=True,
16 | usedefault=True,
17 | ),
18 | terminal_output=dict(
19 | deprecated='1.0.0',
20 | nohash=True,
21 | ),
22 | )
23 | inputs = AFNICommandBase.input_spec()
24 |
25 | for key, metadata in list(input_map.items()):
26 | for metakey, value in list(metadata.items()):
27 | assert getattr(inputs.traits()[key], metakey) == value
28 |
--------------------------------------------------------------------------------
/nipype/interfaces/afni/tests/test_extra_Deconvolve.py:
--------------------------------------------------------------------------------
1 | """Test afni deconvolve"""
2 |
3 | from ..model import Deconvolve
4 |
5 | def test_x1dstop():
6 | deconv = Deconvolve()
7 | deconv.inputs.out_file = 'file.nii'
8 | assert 'out_file' in deconv._list_outputs()
9 | deconv.inputs.x1D_stop = True
10 | assert 'out_file' not in deconv._list_outputs()
11 | assert 'cbucket' not in deconv._list_outputs()
12 |
--------------------------------------------------------------------------------
/nipype/interfaces/ants/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 |
--------------------------------------------------------------------------------
/nipype/interfaces/ants/tests/test_extra_Registration.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 | from __future__ import unicode_literals
4 | from nipype.interfaces.ants import registration
5 | import os
6 | import pytest
7 |
8 |
9 | def test_ants_mand(tmpdir):
10 | tmpdir.chdir()
11 | filepath = os.path.dirname(os.path.realpath(__file__))
12 | datadir = os.path.realpath(os.path.join(filepath, '../../../testing/data'))
13 |
14 | ants = registration.ANTS()
15 | ants.inputs.transformation_model = "SyN"
16 | ants.inputs.moving_image = [os.path.join(datadir, 'resting.nii')]
17 | ants.inputs.fixed_image = [os.path.join(datadir, 'T1.nii')]
18 | ants.inputs.metric = ['MI']
19 |
20 | with pytest.raises(ValueError) as er:
21 | ants.run()
22 | assert "ANTS requires a value for input 'radius'" in str(er.value)
23 |
--------------------------------------------------------------------------------
/nipype/interfaces/base/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/base/tests/test_auto_BaseInterface.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..core import BaseInterface
4 |
5 |
6 | def test_BaseInterface_inputs():
7 | input_map = dict(
8 | ignore_exception=dict(
9 | deprecated='1.0.0',
10 | nohash=True,
11 | usedefault=True,
12 | ), )
13 | inputs = BaseInterface.input_spec()
14 |
15 | for key, metadata in list(input_map.items()):
16 | for metakey, value in list(metadata.items()):
17 | assert getattr(inputs.traits()[key], metakey) == value
18 |
--------------------------------------------------------------------------------
/nipype/interfaces/base/tests/test_auto_CommandLine.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..core import CommandLine
4 |
5 |
6 | def test_CommandLine_inputs():
7 | input_map = dict(
8 | args=dict(argstr='%s', ),
9 | environ=dict(
10 | nohash=True,
11 | usedefault=True,
12 | ),
13 | ignore_exception=dict(
14 | deprecated='1.0.0',
15 | nohash=True,
16 | usedefault=True,
17 | ),
18 | terminal_output=dict(
19 | deprecated='1.0.0',
20 | nohash=True,
21 | ),
22 | )
23 | inputs = CommandLine.input_spec()
24 |
25 | for key, metadata in list(input_map.items()):
26 | for metakey, value in list(metadata.items()):
27 | assert getattr(inputs.traits()[key], metakey) == value
28 |
--------------------------------------------------------------------------------
/nipype/interfaces/base/tests/test_auto_LibraryBaseInterface.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..core import LibraryBaseInterface
4 |
5 |
6 | def test_LibraryBaseInterface_inputs():
7 | input_map = dict(
8 | ignore_exception=dict(
9 | deprecated='1.0.0',
10 | nohash=True,
11 | usedefault=True,
12 | ), )
13 | inputs = LibraryBaseInterface.input_spec()
14 |
15 | for key, metadata in list(input_map.items()):
16 | for metakey, value in list(metadata.items()):
17 | assert getattr(inputs.traits()[key], metakey) == value
18 |
--------------------------------------------------------------------------------
/nipype/interfaces/base/tests/test_auto_SEMLikeCommandLine.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..core import SEMLikeCommandLine
4 |
5 |
6 | def test_SEMLikeCommandLine_inputs():
7 | input_map = dict(
8 | args=dict(argstr='%s', ),
9 | environ=dict(
10 | nohash=True,
11 | usedefault=True,
12 | ),
13 | ignore_exception=dict(
14 | deprecated='1.0.0',
15 | nohash=True,
16 | usedefault=True,
17 | ),
18 | terminal_output=dict(
19 | deprecated='1.0.0',
20 | nohash=True,
21 | ),
22 | )
23 | inputs = SEMLikeCommandLine.input_spec()
24 |
25 | for key, metadata in list(input_map.items()):
26 | for metakey, value in list(metadata.items()):
27 | assert getattr(inputs.traits()[key], metakey) == value
28 |
--------------------------------------------------------------------------------
/nipype/interfaces/base/tests/test_auto_SimpleInterface.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..core import SimpleInterface
4 |
5 |
6 | def test_SimpleInterface_inputs():
7 | input_map = dict(
8 | ignore_exception=dict(
9 | deprecated='1.0.0',
10 | nohash=True,
11 | usedefault=True,
12 | ), )
13 | inputs = SimpleInterface.input_spec()
14 |
15 | for key, metadata in list(input_map.items()):
16 | for metakey, value in list(metadata.items()):
17 | assert getattr(inputs.traits()[key], metakey) == value
18 |
--------------------------------------------------------------------------------
/nipype/interfaces/brainsuite/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from .brainsuite import (Bse, Bfc, Pvc, Cerebro, Cortex, Scrubmask, Tca,
3 | Dewisp, Dfs, Pialmesh, Skullfinder, Hemisplit, SVReg,
4 | BDP, ThicknessPVC)
5 |
--------------------------------------------------------------------------------
/nipype/interfaces/brainsuite/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/camino/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 |
--------------------------------------------------------------------------------
/nipype/interfaces/camino2trackvis/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 | """Camino2Trackvis top level namespace
5 | """
6 |
7 | from .convert import Camino2Trackvis, Trackvis2Camino
8 |
--------------------------------------------------------------------------------
/nipype/interfaces/camino2trackvis/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/cmtk/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from .cmtk import ROIGen, CreateMatrix, CreateNodes
3 | from .nx import NetworkXMetrics, AverageNetworks
4 | from .parcellation import Parcellate
5 | from .convert import CFFConverter, MergeCNetworks
6 | from .nbs import NetworkBasedStatistic
7 |
--------------------------------------------------------------------------------
/nipype/interfaces/cmtk/base.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 | """ Base interface for cmtk """
5 |
6 | from ..base import LibraryBaseInterface
7 | from ...utils.misc import package_check
8 |
9 |
10 | class CFFBaseInterface(LibraryBaseInterface):
11 | _pkg = 'cfflib'
12 |
13 |
14 | # Originally set in convert, nbs, nx, parcellation
15 | # Set here to be imported, in case anybody depends on its presence
16 | # Remove in 2.0
17 | have_cmp = True
18 | try:
19 | package_check('cmp')
20 | except ImportError:
21 | have_cmp = False
22 |
23 | have_cfflib = True
24 | try:
25 | package_check('cfflib')
26 | except ImportError:
27 | have_cfflib = False
28 |
29 | have_cv = True
30 | try:
31 | package_check('cviewer')
32 | except ImportError:
33 | have_cv = False
34 |
--------------------------------------------------------------------------------
/nipype/interfaces/cmtk/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/cmtk/tests/test_auto_CFFBaseInterface.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import CFFBaseInterface
4 |
5 |
6 | def test_CFFBaseInterface_inputs():
7 | input_map = dict(
8 | ignore_exception=dict(
9 | deprecated='1.0.0',
10 | nohash=True,
11 | usedefault=True,
12 | ), )
13 | inputs = CFFBaseInterface.input_spec()
14 |
15 | for key, metadata in list(input_map.items()):
16 | for metakey, value in list(metadata.items()):
17 | assert getattr(inputs.traits()[key], metakey) == value
18 |
--------------------------------------------------------------------------------
/nipype/interfaces/diffusion_toolkit/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from .base import Info
3 | from .postproc import SplineFilter, TrackMerge
4 | from .dti import DTIRecon, DTITracker
5 | from .odf import HARDIMat, ODFRecon, ODFTracker
6 |
--------------------------------------------------------------------------------
/nipype/interfaces/diffusion_toolkit/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/dipy/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from .tracks import StreamlineTractography, TrackDensityMap
3 | from .tensors import TensorMode, DTI
4 | from .preprocess import Resample, Denoise
5 | from .reconstruction import RESTORE, EstimateResponseSH, CSD
6 | from .simulate import SimulateMultiTensor
7 | from .anisotropic_power import APMQball
8 |
--------------------------------------------------------------------------------
/nipype/interfaces/dipy/setup.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 | from __future__ import (print_function, division, unicode_literals,
5 | absolute_import)
6 |
7 |
8 | def configuration(parent_package='', top_path=None):
9 | from numpy.distutils.misc_util import Configuration
10 |
11 | config = Configuration('dipy', parent_package, top_path)
12 |
13 | # config.add_data_dir('tests')
14 | return config
15 |
16 |
17 | if __name__ == '__main__':
18 | from numpy.distutils.core import setup
19 | setup(**configuration(top_path='').todict())
20 |
--------------------------------------------------------------------------------
/nipype/interfaces/dipy/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import DipyBaseInterface
4 |
5 |
6 | def test_DipyBaseInterface_inputs():
7 | input_map = dict(
8 | ignore_exception=dict(
9 | deprecated='1.0.0',
10 | nohash=True,
11 | usedefault=True,
12 | ), )
13 | inputs = DipyBaseInterface.input_spec()
14 |
15 | for key, metadata in list(input_map.items()):
16 | for metakey, value in list(metadata.items()):
17 | assert getattr(inputs.traits()[key], metakey) == value
18 |
--------------------------------------------------------------------------------
/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import DipyDiffusionInterface
4 |
5 |
6 | def test_DipyDiffusionInterface_inputs():
7 | input_map = dict(
8 | b0_thres=dict(usedefault=True, ),
9 | ignore_exception=dict(
10 | deprecated='1.0.0',
11 | nohash=True,
12 | usedefault=True,
13 | ),
14 | in_bval=dict(mandatory=True, ),
15 | in_bvec=dict(mandatory=True, ),
16 | in_file=dict(mandatory=True, ),
17 | out_prefix=dict(),
18 | )
19 | inputs = DipyDiffusionInterface.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/dtitk/__init__.py:
--------------------------------------------------------------------------------
1 | """The dtitk module provides classes for interfacing with the `Diffusion
2 | Tensor Imaging Toolkit (DTI-TK)
3 | `_ command line tools.
4 |
5 | Top-level namespace for dti-tk.
6 | """
7 |
8 | # from .base import ()
9 | from .registration import (Rigid, Affine, Diffeo,
10 | ComposeXfm, DiffeoSymTensor3DVol, AffSymTensor3DVol,
11 | AffScalarVol, DiffeoScalarVol)
12 | from .utils import (TVAdjustVoxSp, SVAdjustVoxSp, TVResample, SVResample,
13 | TVtool, BinThresh)
14 |
--------------------------------------------------------------------------------
/nipype/interfaces/dtitk/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 |
--------------------------------------------------------------------------------
/nipype/interfaces/dtitk/tests/test_auto_CommandLineDtitk.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import CommandLineDtitk
4 |
5 |
6 | def test_CommandLineDtitk_inputs():
7 | input_map = dict(
8 | args=dict(argstr='%s', ),
9 | environ=dict(
10 | nohash=True,
11 | usedefault=True,
12 | ),
13 | ignore_exception=dict(
14 | deprecated='1.0.0',
15 | nohash=True,
16 | usedefault=True,
17 | ),
18 | terminal_output=dict(
19 | deprecated='1.0.0',
20 | nohash=True,
21 | ),
22 | )
23 | inputs = CommandLineDtitk.input_spec()
24 |
25 | for key, metadata in list(input_map.items()):
26 | for metakey, value in list(metadata.items()):
27 | assert getattr(inputs.traits()[key], metakey) == value
28 |
--------------------------------------------------------------------------------
/nipype/interfaces/elastix/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | # coding: utf-8
3 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
4 | # vi: set ft=python sts=4 ts=4 sw=4 et:
5 | """Top-level namespace for elastix."""
6 |
7 | from __future__ import absolute_import
8 |
9 | from .registration import Registration, ApplyWarp, AnalyzeWarp, PointsWarp
10 | from .utils import EditTransform
11 |
--------------------------------------------------------------------------------
/nipype/interfaces/elastix/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/freesurfer/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import FSCommand
4 |
5 |
6 | def test_FSCommand_inputs():
7 | input_map = dict(
8 | args=dict(argstr='%s', ),
9 | environ=dict(
10 | nohash=True,
11 | usedefault=True,
12 | ),
13 | ignore_exception=dict(
14 | deprecated='1.0.0',
15 | nohash=True,
16 | usedefault=True,
17 | ),
18 | subjects_dir=dict(),
19 | terminal_output=dict(
20 | deprecated='1.0.0',
21 | nohash=True,
22 | ),
23 | )
24 | inputs = FSCommand.input_spec()
25 |
26 | for key, metadata in list(input_map.items()):
27 | for metakey, value in list(metadata.items()):
28 | assert getattr(inputs.traits()[key], metakey) == value
29 |
--------------------------------------------------------------------------------
/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import FSScriptCommand
4 |
5 |
6 | def test_FSScriptCommand_inputs():
7 | input_map = dict(
8 | args=dict(argstr='%s', ),
9 | environ=dict(
10 | nohash=True,
11 | usedefault=True,
12 | ),
13 | ignore_exception=dict(
14 | deprecated='1.0.0',
15 | nohash=True,
16 | usedefault=True,
17 | ),
18 | subjects_dir=dict(),
19 | terminal_output=dict(
20 | deprecated='1.0.0',
21 | nohash=True,
22 | ),
23 | )
24 | inputs = FSScriptCommand.input_spec()
25 |
26 | for key, metadata in list(input_map.items()):
27 | for metakey, value in list(metadata.items()):
28 | assert getattr(inputs.traits()[key], metakey) == value
29 |
--------------------------------------------------------------------------------
/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:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import FSLCommand
4 |
5 |
6 | def test_FSLCommand_inputs():
7 | input_map = dict(
8 | args=dict(argstr='%s', ),
9 | environ=dict(
10 | nohash=True,
11 | usedefault=True,
12 | ),
13 | ignore_exception=dict(
14 | deprecated='1.0.0',
15 | nohash=True,
16 | usedefault=True,
17 | ),
18 | output_type=dict(),
19 | terminal_output=dict(
20 | deprecated='1.0.0',
21 | nohash=True,
22 | ),
23 | )
24 | inputs = FSLCommand.input_spec()
25 |
26 | for key, metadata in list(input_map.items()):
27 | for metakey, value in list(metadata.items()):
28 | assert getattr(inputs.traits()[key], metakey) == value
29 |
--------------------------------------------------------------------------------
/nipype/interfaces/minc/testdata.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import (print_function, division, unicode_literals,
3 | absolute_import)
4 |
5 | import os
6 | from ...testing import example_data
7 |
8 | minc2Dfile = example_data('minc_test_2D_00.mnc')
9 | minc3Dfile = example_data('minc_test_3D_00.mnc')
10 |
11 | nlp_config = example_data('minc_nlp.conf')
12 |
13 |
14 | def nonempty_minc_data(i, shape='2D'):
15 | return example_data('minc_test_%s_%.2d.mnc' % (
16 | shape,
17 | i,
18 | ))
19 |
--------------------------------------------------------------------------------
/nipype/interfaces/minc/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/mipav/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import (print_function, division, unicode_literals,
3 | absolute_import)
4 | from .developer import (
5 | JistLaminarVolumetricLayering, JistBrainMgdmSegmentation,
6 | JistLaminarProfileGeometry, JistLaminarProfileCalculator, MedicAlgorithmN3,
7 | JistLaminarROIAveraging, MedicAlgorithmLesionToads,
8 | JistBrainMp2rageSkullStripping, JistCortexSurfaceMeshInflation, RandomVol,
9 | MedicAlgorithmImageCalculator, JistBrainMp2rageDuraEstimation,
10 | JistLaminarProfileSampling, MedicAlgorithmMipavReorient,
11 | MedicAlgorithmSPECTRE2010, JistBrainPartialVolumeFilter,
12 | JistIntensityMp2rageMasking, MedicAlgorithmThresholdToBinaryMask)
13 |
--------------------------------------------------------------------------------
/nipype/interfaces/mipav/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/mne/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from .base import WatershedBEM
3 |
--------------------------------------------------------------------------------
/nipype/interfaces/mne/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/mrtrix/defhdr.mat:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/satra/nipype/9333ff80d24a3b668accdebe816ee9e2cc346d72/nipype/interfaces/mrtrix/defhdr.mat
--------------------------------------------------------------------------------
/nipype/interfaces/mrtrix/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/mrtrix3/__init__.py:
--------------------------------------------------------------------------------
1 | from __future__ import absolute_import
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 | # -*- coding: utf-8 -*-
5 |
6 | from .utils import (Mesh2PVE, Generate5tt, BrainMask, TensorMetrics,
7 | ComputeTDI, TCK2VTK, MRMath, MRConvert, DWIExtract)
8 | from .preprocess import ResponseSD, ACTPrepareFSL, ReplaceFSwithFIRST
9 | from .tracking import Tractography
10 | from .reconst import FitTensor, EstimateFOD
11 | from .connectivity import LabelConfig, LabelConvert, BuildConnectome
12 |
--------------------------------------------------------------------------------
/nipype/interfaces/mrtrix3/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import MRTrix3Base
4 |
5 |
6 | def test_MRTrix3Base_inputs():
7 | input_map = dict(
8 | args=dict(argstr='%s', ),
9 | environ=dict(
10 | nohash=True,
11 | usedefault=True,
12 | ),
13 | ignore_exception=dict(
14 | deprecated='1.0.0',
15 | nohash=True,
16 | usedefault=True,
17 | ),
18 | terminal_output=dict(
19 | deprecated='1.0.0',
20 | nohash=True,
21 | ),
22 | )
23 | inputs = MRTrix3Base.input_spec()
24 |
25 | for key, metadata in list(input_map.items()):
26 | for metakey, value in list(metadata.items()):
27 | assert getattr(inputs.traits()[key], metakey) == value
28 |
--------------------------------------------------------------------------------
/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 | The niftyfit module provides classes for interfacing with the `NiftyFit`_
5 | command line tools.
6 |
7 | Top-level namespace for niftyfit.
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/satra/nipype/9333ff80d24a3b668accdebe816ee9e2cc346d72/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 __future__ import unicode_literals
3 | from ..base import NiftyFitCommand
4 |
5 |
6 | def test_NiftyFitCommand_inputs():
7 | input_map = dict(
8 | args=dict(argstr='%s', ),
9 | environ=dict(
10 | nohash=True,
11 | usedefault=True,
12 | ),
13 | ignore_exception=dict(
14 | deprecated='1.0.0',
15 | nohash=True,
16 | usedefault=True,
17 | ),
18 | terminal_output=dict(
19 | deprecated='1.0.0',
20 | nohash=True,
21 | ),
22 | )
23 | inputs = NiftyFitCommand.input_spec()
24 |
25 | for key, metadata in list(input_map.items()):
26 | for metakey, value in list(metadata.items()):
27 | assert getattr(inputs.traits()[key], metakey) == value
28 |
--------------------------------------------------------------------------------
/nipype/interfaces/niftyreg/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 | The niftyreg module provides classes for interfacing with the `NiftyReg
6 | `_ command line tools.
7 |
8 | Top-level namespace for niftyreg.
9 | """
10 |
11 | from .base import get_custom_path
12 | from .reg import RegAladin, RegF3D
13 | from .regutils import (RegResample, RegJacobian, RegAverage, RegTools,
14 | RegTransform, RegMeasure)
15 |
--------------------------------------------------------------------------------
/nipype/interfaces/niftyreg/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/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,
14 | Merge)
15 | from .patchmatch import PatchMatch
16 | from .stats import UnaryStats, BinaryStats
17 |
--------------------------------------------------------------------------------
/nipype/interfaces/niftyseg/tests/__init__.py:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/satra/nipype/9333ff80d24a3b668accdebe816ee9e2cc346d72/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 __future__ import unicode_literals
3 | from ..base import NiftySegCommand
4 |
5 |
6 | def test_NiftySegCommand_inputs():
7 | input_map = dict(
8 | args=dict(argstr='%s', ),
9 | environ=dict(
10 | nohash=True,
11 | usedefault=True,
12 | ),
13 | ignore_exception=dict(
14 | deprecated='1.0.0',
15 | nohash=True,
16 | usedefault=True,
17 | ),
18 | terminal_output=dict(
19 | deprecated='1.0.0',
20 | nohash=True,
21 | ),
22 | )
23 | inputs = NiftySegCommand.input_spec()
24 |
25 | for key, metadata in list(input_map.items()):
26 | for metakey, value in list(metadata.items()):
27 | assert getattr(inputs.traits()[key], metakey) == value
28 |
--------------------------------------------------------------------------------
/nipype/interfaces/nipy/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from .model import FitGLM, EstimateContrast
3 | from .preprocess import ComputeMask, SpaceTimeRealigner
4 | from .utils import Similarity
5 |
--------------------------------------------------------------------------------
/nipype/interfaces/nipy/base.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 | """ Base interface for nipy """
5 |
6 | from ..base import LibraryBaseInterface
7 | from ...utils.misc import package_check
8 |
9 | # Originally set in model, preprocess and utils
10 | # Set here to be imported, in case anybody depends on its presence
11 | # Remove in 2.0
12 | have_nipy = True
13 | try:
14 | package_check('nipy')
15 | except ImportError:
16 | have_nipy = False
17 |
18 |
19 | class NipyBaseInterface(LibraryBaseInterface):
20 | _pkg = 'nipy'
21 |
--------------------------------------------------------------------------------
/nipype/interfaces/nipy/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/nipy/tests/test_auto_NipyBaseInterface.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import NipyBaseInterface
4 |
5 |
6 | def test_NipyBaseInterface_inputs():
7 | input_map = dict(
8 | ignore_exception=dict(
9 | deprecated='1.0.0',
10 | nohash=True,
11 | usedefault=True,
12 | ), )
13 | inputs = NipyBaseInterface.input_spec()
14 |
15 | for key, metadata in list(input_map.items()):
16 | for metakey, value in list(metadata.items()):
17 | assert getattr(inputs.traits()[key], metakey) == value
18 |
--------------------------------------------------------------------------------
/nipype/interfaces/nitime/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 | from .analysis import (CoherenceAnalyzerInputSpec, CoherenceAnalyzerOutputSpec,
6 | CoherenceAnalyzer)
7 |
--------------------------------------------------------------------------------
/nipype/interfaces/nitime/base.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 | """ Base interface for nitime """
5 |
6 | from ..base import LibraryBaseInterface
7 |
8 |
9 | class NitimeBaseInterface(LibraryBaseInterface):
10 | _pkg = 'nitime'
11 |
--------------------------------------------------------------------------------
/nipype/interfaces/nitime/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/nitime/tests/test_auto_NitimeBaseInterface.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import NitimeBaseInterface
4 |
5 |
6 | def test_NitimeBaseInterface_inputs():
7 | input_map = dict(
8 | ignore_exception=dict(
9 | deprecated='1.0.0',
10 | nohash=True,
11 | usedefault=True,
12 | ), )
13 | inputs = NitimeBaseInterface.input_spec()
14 |
15 | for key, metadata in list(input_map.items()):
16 | for metakey, value in list(metadata.items()):
17 | assert getattr(inputs.traits()[key], metakey) == value
18 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
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 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .segmentation import SimilarityIndex, BRAINSTalairach, BRAINSTalairachMask
4 | from .utilities import (HistogramMatchingFilter, GenerateEdgeMapImage,
5 | GeneratePurePlugMask)
6 | from .classify import BRAINSPosteriorToContinuousClass
7 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/brains/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/diffusion/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .diffusion import dtiaverage, dtiestim, dtiprocess, DWIConvert
4 | from .tractography import *
5 | from .gtract import (
6 | gtractTransformToDisplacementField, gtractInvertBSplineTransform,
7 | gtractConcatDwi, gtractAverageBvalues, gtractCoregBvalues,
8 | gtractResampleAnisotropy, gtractResampleCodeImage,
9 | gtractCopyImageOrientation, gtractCreateGuideFiber, gtractAnisotropyMap,
10 | gtractClipAnisotropy, gtractResampleB0, gtractInvertRigidTransform,
11 | gtractImageConformity, compareTractInclusion, gtractFastMarchingTracking,
12 | gtractInvertDisplacementField, gtractCoRegAnatomy,
13 | gtractResampleDWIInPlace, gtractCostFastMarching, gtractFiberTracking,
14 | extractNrrdVectorIndex, gtractResampleFibers, gtractTensor)
15 | from .maxcurvature import maxcurvature
16 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/diffusion/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/diffusion/tractography/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .commandlineonly import fiberstats
4 | from .fiberprocess import fiberprocess
5 | from .fibertrack import fibertrack
6 | from .ukftractography import UKFTractography
7 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/diffusion/tractography/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/filtering/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .denoising import UnbiasedNonLocalMeans
4 | from .featuredetection import (
5 | GenerateSummedGradientImage, CannySegmentationLevelSetImageFilter,
6 | DilateImage, TextureFromNoiseImageFilter, FlippedDifference, ErodeImage,
7 | GenerateBrainClippedImage, NeighborhoodMedian, GenerateTestImage,
8 | NeighborhoodMean, HammerAttributeCreator, TextureMeasureFilter, DilateMask,
9 | DumpBinaryTrainingVectors, DistanceMaps, STAPLEAnalysis,
10 | GradientAnisotropicDiffusionImageFilter, CannyEdge)
11 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/filtering/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/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 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .registration import scalartransform
4 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/legacy/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/registration/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .specialized import (VBRAINSDemonWarp, BRAINSDemonWarp,
4 | BRAINSTransformFromFiducials)
5 | from .brainsresample import BRAINSResample
6 | from .brainsfit import BRAINSFit
7 | from .brainsresize import BRAINSResize
8 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/registration/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/segmentation/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .specialized import (
4 | BRAINSCut, BRAINSROIAuto, BRAINSConstellationDetector,
5 | BRAINSCreateLabelMapFromProbabilityMaps, BinaryMaskEditorBasedOnLandmarks,
6 | BRAINSMultiSTAPLE, BRAINSABC, ESLR)
7 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/segmentation/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/testing/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .featuredetection import SphericalCoordinateGeneration
4 | from .landmarkscompare import LandmarksCompare
5 | from .generateaveragelmkfile import GenerateAverageLmkFile
6 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/utilities/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .brains import (
4 | BRAINSConstellationModeler, landmarksConstellationWeights,
5 | BRAINSTrimForegroundInDirection, BRAINSLmkTransform, BRAINSMush,
6 | BRAINSTransformConvert, landmarksConstellationAligner, BRAINSEyeDetector,
7 | BRAINSLinearModelerEPCA, BRAINSInitializedControlPoints,
8 | CleanUpOverlapLabels, BRAINSClipInferior,
9 | GenerateLabelMapFromProbabilityMap, BRAINSAlignMSP,
10 | BRAINSLandmarkInitializer, insertMidACPCpoint, BRAINSSnapShotWriter,
11 | JointHistogram, ShuffleVectorsModule, ImageRegionPlotter)
12 |
--------------------------------------------------------------------------------
/nipype/interfaces/semtools/utilities/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/slicer/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .diffusion import *
4 | from .segmentation import *
5 | from .filtering import *
6 | from .utilities import EMSegmentTransformToNewFormat
7 | from .surface import (MergeModels, ModelToLabelMap, GrayscaleModelMaker,
8 | ProbeVolumeWithModel, LabelMapSmoothing, ModelMaker)
9 | from .quantification import *
10 | from .legacy import *
11 | from .registration import *
12 | from .converters import DicomToNrrdConverter, OrientScalarVolume
13 |
--------------------------------------------------------------------------------
/nipype/interfaces/slicer/base.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from ..base import SEMLikeCommandLine
3 |
4 |
5 | class SlicerCommandLine(SEMLikeCommandLine):
6 | pass
7 |
--------------------------------------------------------------------------------
/nipype/interfaces/slicer/diffusion/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .diffusion import (
4 | ResampleDTIVolume, DWIRicianLMMSEFilter, TractographyLabelMapSeeding,
5 | DWIJointRicianLMMSEFilter, DiffusionWeightedVolumeMasking, DTIimport,
6 | DWIToDTIEstimation, DiffusionTensorScalarMeasurements, DTIexport)
7 |
--------------------------------------------------------------------------------
/nipype/interfaces/slicer/diffusion/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/slicer/filtering/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/slicer/legacy/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .diffusion import *
4 | from .segmentation import OtsuThresholdSegmentation
5 | from .filtering import OtsuThresholdImageFilter, ResampleScalarVolume
6 | from .converters import BSplineToDeformationField
7 | from .registration import (BSplineDeformableRegistration, AffineRegistration,
8 | MultiResolutionAffineRegistration,
9 | RigidRegistration, LinearRegistration,
10 | ExpertAutomatedRegistration)
11 |
--------------------------------------------------------------------------------
/nipype/interfaces/slicer/legacy/diffusion/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .denoising import DWIUnbiasedNonLocalMeansFilter
4 |
--------------------------------------------------------------------------------
/nipype/interfaces/slicer/legacy/diffusion/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/slicer/legacy/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/slicer/quantification/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .changequantification import IntensityDifferenceMetric
4 | from .petstandarduptakevaluecomputation import PETStandardUptakeValueComputation
5 |
--------------------------------------------------------------------------------
/nipype/interfaces/slicer/quantification/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/slicer/registration/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .specialized import (ACPCTransform, FiducialRegistration,
4 | VBRAINSDemonWarp, BRAINSDemonWarp)
5 | from .brainsresample import BRAINSResample
6 | from .brainsfit import BRAINSFit
7 |
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/nipype/interfaces/slicer/registration/tests/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 |
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/nipype/interfaces/slicer/segmentation/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .specialized import (RobustStatisticsSegmenter, EMSegmentCommandLine,
4 | BRAINSROIAuto)
5 | from .simpleregiongrowingsegmentation import SimpleRegionGrowingSegmentation
6 |
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/nipype/interfaces/slicer/segmentation/tests/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 |
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/nipype/interfaces/slicer/tests/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 |
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/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import SlicerCommandLine
4 |
5 |
6 | def test_SlicerCommandLine_inputs():
7 | input_map = dict(
8 | args=dict(argstr='%s', ),
9 | environ=dict(
10 | nohash=True,
11 | usedefault=True,
12 | ),
13 | ignore_exception=dict(
14 | deprecated='1.0.0',
15 | nohash=True,
16 | usedefault=True,
17 | ),
18 | terminal_output=dict(
19 | deprecated='1.0.0',
20 | nohash=True,
21 | ),
22 | )
23 | inputs = SlicerCommandLine.input_spec()
24 |
25 | for key, metadata in list(input_map.items()):
26 | for metakey, value in list(metadata.items()):
27 | assert getattr(inputs.traits()[key], metakey) == value
28 |
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/nipype/interfaces/spm/__init__.py:
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1 | # -*- coding: utf-8 -*-
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 | """Top-level namespace for spm."""
5 |
6 | from .base import (Info, SPMCommand, logger, no_spm, scans_for_fname,
7 | scans_for_fnames)
8 | from .preprocess import (FieldMap, SliceTiming, Realign, Coregister, Normalize,
9 | Normalize12, Segment, Smooth, NewSegment, DARTEL,
10 | DARTELNorm2MNI, CreateWarped, VBMSegment)
11 | from .model import (Level1Design, EstimateModel, EstimateContrast, Threshold,
12 | OneSampleTTestDesign, TwoSampleTTestDesign,
13 | PairedTTestDesign, MultipleRegressionDesign)
14 | from .utils import (Analyze2nii, CalcCoregAffine, ApplyTransform, Reslice,
15 | ApplyInverseDeformation, ResliceToReference, DicomImport)
16 |
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/nipype/interfaces/spm/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
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/nipype/interfaces/spm/tests/test_auto_SPMCommand.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import SPMCommand
4 |
5 |
6 | def test_SPMCommand_inputs():
7 | input_map = dict(
8 | ignore_exception=dict(
9 | deprecated='1.0.0',
10 | nohash=True,
11 | usedefault=True,
12 | ),
13 | matlab_cmd=dict(),
14 | mfile=dict(usedefault=True, ),
15 | paths=dict(),
16 | use_mcr=dict(),
17 | use_v8struct=dict(
18 | min_ver='8',
19 | usedefault=True,
20 | ),
21 | )
22 | inputs = SPMCommand.input_spec()
23 |
24 | for key, metadata in list(input_map.items()):
25 | for metakey, value in list(metadata.items()):
26 | assert getattr(inputs.traits()[key], metakey) == value
27 |
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/nipype/interfaces/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
--------------------------------------------------------------------------------
/nipype/interfaces/tests/test_auto_CopyMeta.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..dcmstack import CopyMeta
4 |
5 |
6 | def test_CopyMeta_inputs():
7 | input_map = dict(
8 | dest_file=dict(mandatory=True, ),
9 | exclude_classes=dict(),
10 | include_classes=dict(),
11 | src_file=dict(mandatory=True, ),
12 | )
13 | inputs = CopyMeta.input_spec()
14 |
15 | for key, metadata in list(input_map.items()):
16 | for metakey, value in list(metadata.items()):
17 | assert getattr(inputs.traits()[key], metakey) == value
18 | def test_CopyMeta_outputs():
19 | output_map = dict(dest_file=dict(), )
20 | outputs = CopyMeta.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 |
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/nipype/interfaces/tests/test_auto_IOBase.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..io import IOBase
4 |
5 |
6 | def test_IOBase_inputs():
7 | input_map = dict(
8 | ignore_exception=dict(
9 | deprecated='1.0.0',
10 | nohash=True,
11 | usedefault=True,
12 | ), )
13 | inputs = IOBase.input_spec()
14 |
15 | for key, metadata in list(input_map.items()):
16 | for metakey, value in list(metadata.items()):
17 | assert getattr(inputs.traits()[key], metakey) == value
18 |
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/nipype/interfaces/tests/test_auto_LookupMeta.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..dcmstack import LookupMeta
4 |
5 |
6 | def test_LookupMeta_inputs():
7 | input_map = dict(
8 | in_file=dict(mandatory=True, ),
9 | meta_keys=dict(mandatory=True, ),
10 | )
11 | inputs = LookupMeta.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 | def test_LookupMeta_outputs():
17 | output_map = dict()
18 | outputs = LookupMeta.output_spec()
19 |
20 | for key, metadata in list(output_map.items()):
21 | for metakey, value in list(metadata.items()):
22 | assert getattr(outputs.traits()[key], metakey) == value
23 |
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/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..dcmstack import NiftiGeneratorBase
4 |
5 |
6 | def test_NiftiGeneratorBase_inputs():
7 | input_map = dict(
8 | ignore_exception=dict(
9 | deprecated='1.0.0',
10 | nohash=True,
11 | usedefault=True,
12 | ), )
13 | inputs = NiftiGeneratorBase.input_spec()
14 |
15 | for key, metadata in list(input_map.items()):
16 | for metakey, value in list(metadata.items()):
17 | assert getattr(inputs.traits()[key], metakey) == value
18 |
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/nipype/interfaces/tests/test_auto_NilearnBaseInterface.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..nilearn import NilearnBaseInterface
4 |
5 |
6 | def test_NilearnBaseInterface_inputs():
7 | input_map = dict(
8 | ignore_exception=dict(
9 | deprecated='1.0.0',
10 | nohash=True,
11 | usedefault=True,
12 | ), )
13 | inputs = NilearnBaseInterface.input_spec()
14 |
15 | for key, metadata in list(input_map.items()):
16 | for metakey, value in list(metadata.items()):
17 | assert getattr(inputs.traits()[key], metakey) == value
18 |
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/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import SEMLikeCommandLine
4 |
5 |
6 | def test_SEMLikeCommandLine_inputs():
7 | input_map = dict(args=dict(argstr='%s',
8 | ),
9 | environ=dict(nohash=True,
10 | usedefault=True,
11 | ),
12 | ignore_exception=dict(nohash=True,
13 | usedefault=True,
14 | ),
15 | terminal_output=dict(deprecated='1.0.0',
16 | nohash=True,
17 | ),
18 | )
19 | inputs = SEMLikeCommandLine.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 |
25 |
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/nipype/interfaces/tests/test_auto_SQLiteSink.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..io import SQLiteSink
4 |
5 |
6 | def test_SQLiteSink_inputs():
7 | input_map = dict(
8 | database_file=dict(mandatory=True, ),
9 | ignore_exception=dict(
10 | deprecated='1.0.0',
11 | nohash=True,
12 | usedefault=True,
13 | ),
14 | table_name=dict(mandatory=True, ),
15 | )
16 | inputs = SQLiteSink.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 |
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/nipype/interfaces/utility/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 interfaces for using existing functionality in other packages
6 |
7 | Requires Packages to be installed
8 | """
9 |
10 | from .base import (IdentityInterface, Rename, Select, Split, Merge,
11 | AssertEqual)
12 | from .csv import CSVReader
13 | from .wrappers import Function
14 |
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/nipype/interfaces/utility/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
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/nipype/interfaces/utility/tests/test_auto_AssertEqual.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import AssertEqual
4 |
5 |
6 | def test_AssertEqual_inputs():
7 | input_map = dict(
8 | ignore_exception=dict(
9 | deprecated='1.0.0',
10 | nohash=True,
11 | usedefault=True,
12 | ),
13 | volume1=dict(mandatory=True, ),
14 | volume2=dict(mandatory=True, ),
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 |
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/nipype/interfaces/utility/tests/test_auto_CSVReader.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..csv import CSVReader
4 |
5 |
6 | def test_CSVReader_inputs():
7 | input_map = dict(
8 | header=dict(usedefault=True, ),
9 | in_file=dict(mandatory=True, ),
10 | )
11 | inputs = CSVReader.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 | def test_CSVReader_outputs():
17 | output_map = dict()
18 | outputs = CSVReader.output_spec()
19 |
20 | for key, metadata in list(output_map.items()):
21 | for metakey, value in list(metadata.items()):
22 | assert getattr(outputs.traits()[key], metakey) == value
23 |
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/nipype/interfaces/utility/tests/test_auto_IdentityInterface.py:
--------------------------------------------------------------------------------
1 | # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2 | from __future__ import unicode_literals
3 | from ..base import IdentityInterface
4 |
5 |
6 | def test_IdentityInterface_inputs():
7 | input_map = dict()
8 | inputs = IdentityInterface.input_spec()
9 |
10 | for key, metadata in list(input_map.items()):
11 | for metakey, value in list(metadata.items()):
12 | assert getattr(inputs.traits()[key], metakey) == value
13 | def test_IdentityInterface_outputs():
14 | output_map = dict()
15 | outputs = IdentityInterface.output_spec()
16 |
17 | for key, metadata in list(output_map.items()):
18 | for metakey, value in list(metadata.items()):
19 | assert getattr(outputs.traits()[key], metakey) == value
20 |
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/nipype/interfaces/vista/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 | from .vista import (Vnifti2Image, VtoMat)
5 |
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/nipype/interfaces/vista/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 |
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/nipype/pipeline/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 | from __future__ import (print_function, division, unicode_literals,
9 | absolute_import)
10 | __docformat__ = 'restructuredtext'
11 | from .engine import Node, MapNode, JoinNode, Workflow
12 |
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/nipype/pipeline/engine/__init__.py:
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1 | #!/usr/bin/env python
2 | # -*- coding: utf-8 -*-
3 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
4 | # vi: set ft=python sts=4 ts=4 sw=4 et:
5 | """
6 | Package contains modules for generating pipelines using interfaces
7 |
8 | """
9 |
10 | from __future__ import absolute_import
11 | __docformat__ = 'restructuredtext'
12 | from .workflows import Workflow
13 | from .nodes import Node, MapNode, JoinNode
14 | from .utils import generate_expanded_graph
15 |
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/nipype/pipeline/engine/tests/__init__.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
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 |
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/nipype/pipeline/plugins/__init__.py:
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1 | # -*- coding: utf-8 -*-
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 | from __future__ import (print_function, division, unicode_literals,
5 | absolute_import)
6 |
7 | from .debug import DebugPlugin
8 | from .linear import LinearPlugin
9 | from .pbs import PBSPlugin
10 | from .oar import OARPlugin
11 | from .sge import SGEPlugin
12 | from .condor import CondorPlugin
13 | from .dagman import CondorDAGManPlugin
14 | from .multiproc import MultiProcPlugin
15 | from .ipython import IPythonPlugin
16 | from .somaflow import SomaFlowPlugin
17 | from .pbsgraph import PBSGraphPlugin
18 | from .sgegraph import SGEGraphPlugin
19 | from .lsf import LSFPlugin
20 | from .slurm import SLURMPlugin
21 | from .slurmgraph import SLURMGraphPlugin
22 |
23 | from . import semaphore_singleton
24 |
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/nipype/pipeline/plugins/semaphore_singleton.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | from __future__ import (print_function, division, unicode_literals,
3 | absolute_import)
4 | import threading
5 | semaphore = threading.Semaphore(0)
6 |
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/nipype/pipeline/plugins/tests/__init__.py:
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1 | # -*- coding: utf-8 -*-
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 |
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/nipype/pytest.ini:
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1 | [pytest]
2 | norecursedirs = .git build dist doc nipype/external tools examples src
3 | addopts = --doctest-modules -n auto
4 | doctest_optionflags = ALLOW_UNICODE NORMALIZE_WHITESPACE
5 | env =
6 | PYTHONHASHSEED=0
7 |
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/nipype/refs.py:
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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, BibTeX
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 |
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1 | #!/usr/bin/env python
2 | # -*- coding: utf-8 -*-
3 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
4 | # vi: set ft=python sts=4 ts=4 sw=4 et:
5 | from __future__ import (print_function, division, absolute_import,
6 | unicode_literals)
7 |
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1 |
2 |
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/nipype/testing/data/README:
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1 | This directory contains empty, dummy files which are meant to be used
2 | in the doctests of nipype. For verion 0.3 of nipype, we're using
3 | Traits and for input files, the code checks to confirm the assigned
4 | files actually exist. It doesn't matter what the files are, or even
5 | if they contain "real data", only that they exist. Again, these files
6 | are only meant to serve as documentation in the doctests.
7 |
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1 | fprintf(1,'Executing %s at %s:\n',mfilename,datestr(now));
2 | ver,
3 | try,
4 | if isempty(which('spm')),
5 | throw(MException('SPMCheck:NotFound','SPM not in matlab path'));
6 | end;
7 | spm_path = spm('dir');
8 | fprintf(1, 'NIPYPE %s', spm_path);
9 |
10 | ,catch ME,
11 | fprintf(2,'MATLAB code threw an exception:\n');
12 | fprintf(2,'%s\n',ME.message);
13 | if length(ME.stack) ~= 0, fprintf(2,'File:%s\nName:%s\nLine:%d\n',ME.stack.file,ME.stack.name,ME.stack.line);, end;
14 | end;
15 |
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/nipype/tests/test_nipype.py:
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1 | from .. import get_info
2 | from ..info import get_nipype_gitversion
3 | import pytest
4 |
5 |
6 | def test_nipype_info():
7 | exception_not_raised = True
8 | try:
9 | get_info()
10 | except Exception:
11 | exception_not_raised = False
12 | assert exception_not_raised
13 |
14 |
15 | @pytest.mark.skipif(not get_nipype_gitversion(),
16 | reason="not able to get version from get_nipype_gitversion")
17 | def test_git_hash():
18 | # removing the first "g" from gitversion
19 | get_nipype_gitversion()[1:] == get_info()['commit_hash']
20 |
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/nipype/utils/README.txt:
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1 | ==================
2 | Nipype Utilities
3 | ==================
4 |
5 | This directory contains various utilities used in nipype. 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 |
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/nipype/utils/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 |
4 | from .config import NUMPY_MMAP
5 | from .onetime import OneTimeProperty, setattr_on_read
6 | from .tmpdirs import TemporaryDirectory, InTemporaryDirectory
7 |
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/nipype/utils/spm_get_doc.m:
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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 |
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/nipype/utils/tests/test_nipype2boutiques.py:
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1 | # -*- coding: utf-8 -*-
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 | from future import standard_library
5 | standard_library.install_aliases()
6 |
7 | from ..nipype2boutiques import generate_boutiques_descriptor
8 |
9 |
10 | def test_generate():
11 | generate_boutiques_descriptor(module='nipype.interfaces.ants.registration',
12 | interface_name='ANTS',
13 | ignored_template_inputs=(),
14 | docker_image=None,
15 | docker_index=None,
16 | verbose=False,
17 | ignore_template_numbers=False)
18 |
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/nipype/workflows/__init__.py:
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1 | # -*- coding: utf-8 -*-
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 |
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/nipype/workflows/data/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | # coding: utf-8
3 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
4 | # vi: set ft=python sts=4 ts=4 sw=4 et:
5 | from __future__ import (print_function, division, unicode_literals,
6 | absolute_import)
7 |
8 | import os.path as op
9 |
10 |
11 | def get_flirt_schedule(name):
12 | if name == 'ecc':
13 | return op.abspath(op.join(op.dirname(__file__), 'ecc.sch'))
14 | elif name == 'hmc':
15 | return op.abspath(op.join(op.dirname(__file__), 'hmc.sch'))
16 | else:
17 | raise RuntimeError('Requested file does not exist.')
18 |
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/nipype/workflows/dmri/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | from __future__ import (print_function, division, unicode_literals,
3 | absolute_import)
4 | from . import camino, mrtrix, fsl, dipy
5 |
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/nipype/workflows/dmri/camino/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .diffusion import create_camino_dti_pipeline
4 | from .connectivity_mapping import create_connectivity_pipeline
5 | from .group_connectivity import create_group_connectivity_pipeline
6 |
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/nipype/workflows/dmri/connectivity/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .nx import (create_networkx_pipeline, create_cmats_to_csv_pipeline)
4 | from .group_connectivity import (
5 | create_merge_networks_by_group_workflow,
6 | create_merge_network_results_by_group_workflow,
7 | create_merge_group_networks_workflow,
8 | create_merge_group_network_results_workflow,
9 | create_average_networks_by_group_workflow)
10 |
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/nipype/workflows/dmri/dipy/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | # coding: utf-8
3 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
4 | # vi: set ft=python sts=4 ts=4 sw=4 et:
5 |
6 | from __future__ import absolute_import
7 | from .denoise import nlmeans_pipeline
8 |
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/nipype/workflows/dmri/dtitk/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | # coding: utf-8
3 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
4 | # vi: set ft=python sts=4 ts=4 sw=4 et:
5 |
6 | from __future__ import absolute_import
7 | from .tensor_registration import (affine_tensor_pipeline,
8 | diffeomorphic_tensor_pipeline)
9 |
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/nipype/workflows/dmri/fsl/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .dti import create_bedpostx_pipeline, bedpostx_parallel
4 |
5 | from .artifacts import (all_fmb_pipeline, all_peb_pipeline, all_fsl_pipeline,
6 | hmc_pipeline, ecc_pipeline, sdc_fmb, sdc_peb,
7 | remove_bias)
8 |
9 | from .epi import (fieldmap_correction, topup_correction,
10 | create_eddy_correct_pipeline, create_epidewarp_pipeline,
11 | create_dmri_preprocessing)
12 |
13 | from .tbss import (create_tbss_1_preproc, create_tbss_2_reg,
14 | create_tbss_3_postreg, create_tbss_4_prestats,
15 | create_tbss_all, create_tbss_non_FA)
16 |
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/nipype/workflows/dmri/fsl/tests/__init__.py:
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1 | # -*- coding: utf-8 -*-
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 |
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/nipype/workflows/dmri/mrtrix/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | from __future__ import absolute_import
3 | from .diffusion import create_mrtrix_dti_pipeline
4 | from .connectivity_mapping import create_connectivity_pipeline
5 | from .group_connectivity import (create_group_connectivity_pipeline)
6 |
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/nipype/workflows/fmri/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | from __future__ import (print_function, division, unicode_literals,
3 | absolute_import)
4 | from . import fsl, spm
5 |
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/nipype/workflows/fmri/fsl/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | from .preprocess import (create_susan_smooth, create_fsl_fs_preproc,
3 | create_parallelfeat_preproc, create_featreg_preproc,
4 | create_reg_workflow)
5 | from .estimate import create_modelfit_workflow, create_fixed_effects_flow
6 |
7 | # backwards compatibility
8 | from ...rsfmri.fsl.resting import create_resting_preproc
9 |
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/nipype/workflows/fmri/fsl/tests/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | __author__ = 'satra'
3 |
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/nipype/workflows/fmri/fsl/tests/test_preprocess.py:
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1 | __author__ = 'oliver'
2 |
3 | from ..preprocess import create_featreg_preproc, pickrun
4 |
5 |
6 | def test_pickrun():
7 | files = ['1', '2', '3', '4']
8 | assert pickrun(files, 0) == '1'
9 | assert pickrun(files, 'first') == '1'
10 | assert pickrun(files, -1) == '4'
11 | assert pickrun(files, 'last') == '4'
12 | assert pickrun(files, 'middle') == '3'
13 |
14 |
15 | def test_create_featreg_preproc():
16 | """smoke test"""
17 | wf = create_featreg_preproc(whichrun=0)
18 |
19 | # test type
20 | import nipype
21 | assert type(wf) == nipype.pipeline.engine.Workflow
22 |
23 | # test methods
24 | assert wf.get_node('extractref')
25 | assert wf._get_dot()
26 |
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/nipype/workflows/fmri/spm/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | from .preprocess import (create_spm_preproc, create_vbm_preproc,
3 | create_DARTEL_template)
4 |
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/nipype/workflows/fmri/spm/estimate.py:
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1 | # -*- coding: utf-8 -*-
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 |
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/nipype/workflows/fmri/spm/tests/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | __author__ = 'satra'
3 |
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/nipype/workflows/graph/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | from __future__ import (print_function, division, unicode_literals,
3 | absolute_import)
4 |
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/nipype/workflows/misc/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 |
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/nipype/workflows/rsfmri/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | from __future__ import (print_function, division, unicode_literals,
3 | absolute_import)
4 |
5 | from . import fsl
6 |
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/nipype/workflows/rsfmri/fsl/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | from .resting import create_resting_preproc
3 |
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/nipype/workflows/rsfmri/fsl/tests/__init__.py:
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https://raw.githubusercontent.com/satra/nipype/9333ff80d24a3b668accdebe816ee9e2cc346d72/nipype/workflows/rsfmri/fsl/tests/__init__.py
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/nipype/workflows/smri/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | from __future__ import (print_function, division, unicode_literals,
3 | absolute_import)
4 |
5 | from . import ants
6 | from . import freesurfer
7 | from . import niftyreg
8 |
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/nipype/workflows/smri/ants/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | from .ANTSBuildTemplate import ANTSTemplateBuildSingleIterationWF
3 | from .antsRegistrationBuildTemplate import antsRegistrationTemplateBuildSingleIterationWF
4 |
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/nipype/workflows/smri/freesurfer/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 | from .utils import (create_getmask_flow, create_get_stats_flow,
3 | create_tessellation_flow)
4 | from .bem import create_bem_flow
5 | from .recon import create_skullstripped_recon_flow, create_reconall_workflow
6 |
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/nipype/workflows/smri/niftyreg/__init__.py:
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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 .groupwise import (create_groupwise_average, create_nonlinear_gw_step,
5 | create_linear_gw_step)
6 |
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/nipype/workflows/warp/__init__.py:
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1 | # -*- coding: utf-8 -*-
2 |
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/requirements.txt:
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1 | numpy>=1.9.0
2 | scipy>=0.14
3 | networkx>=1.9
4 | traits>=4.6
5 | python-dateutil>=2.2
6 | nibabel>=2.1.0
7 | future>=0.16.0
8 | simplejson>=3.8.0
9 | prov==1.5.0
10 | click>=6.6.0
11 | funcsigs
12 | configparser
13 | pytest>=3.0
14 | pytest-xdist
15 | pytest-env
16 | mock
17 | pydotplus
18 | pydot>=1.2.3
19 | packaging
20 |
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/rtd_requirements.txt:
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1 | numpy>=1.9.0
2 | scipy>=0.14
3 | networkx>=1.9
4 | traits>=4.6
5 | python-dateutil>=2.2
6 | nibabel>=2.1.0
7 | future>=0.16.0
8 | simplejson>=3.8.0
9 | prov==1.5.0
10 | funcsigs
11 | configparser
12 | pytest>=3.0
13 | mock
14 | pydotplus
15 | pydot>=1.2.3
16 | psutil
17 | matplotlib
18 | packaging
19 | numpydoc
20 |
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/setup.cfg:
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1 | [bdist_wheel]
2 | universal=1
3 |
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/tools/README:
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1 | ==============
2 | Nipype Tools
3 | ==============
4 |
5 | This directory contains various tools used by the nipype developers.
6 | Only install tools here that are unique to the nipype project. Any
7 | tools shared with our parent project, nipy, should go in the
8 | nipy/tools directory.
9 |
10 | Exceptions
11 | ----------
12 |
13 | * apigen.py: This is not importable from nipy, so I copied it.
14 | * build_modref_templates.py: This was copied and modified to work with nipype.
15 |
16 |
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/tools/retry_cmd.sh:
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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 |
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