Index

A

ABoverlap (class in nipype.interfaces.afni.utils) ACompCor (class in nipype.algorithms.confounds) ACPCTransform (class in nipype.interfaces.slicer.registration.specialized) ActivationCount (class in nipype.algorithms.stats) ACTPrepareFSL (class in nipype.interfaces.mrtrix3.preprocess) add_class_to_package() (in module nipype.interfaces.slicer.generate_classes) add_dicts_by_key() (in module nipype.interfaces.cmtk.nx) add_directive_header() (nipype.sphinxext.documenter.NipypeClassDocumenter method) add_edge_data() (in module nipype.interfaces.cmtk.nx) add_node_data() (in module nipype.interfaces.cmtk.nx) add_nodes() (nipype.pipeline.engine.workflows.Workflow method) add_options() (in module nipype.utils.nipype_cmd) add_results() (nipype.utils.provenance.ProvStore method) add_startup_job() (nipype.pipeline.plugins.sge.QstatSubstitute method) add_traits() (in module nipype.interfaces.io) AddCSVColumn (class in nipype.algorithms.misc) AddCSVRow (class in nipype.algorithms.misc) AddNoise (class in nipype.algorithms.misc) AddScalarVolumes (class in nipype.interfaces.slicer.filtering.arithmetic) AddXFormToHeader (class in nipype.interfaces.freesurfer.utils) Affine (class in nipype.interfaces.dtitk.registration) AffineInitializer (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.utils) AffineRegistration (class in nipype.interfaces.slicer.legacy.registration) AffineTask (class in nipype.interfaces.dtitk.registration) AffScalarVol (class in nipype.interfaces.dtitk.registration) affScalarVolTask (class in nipype.interfaces.dtitk.registration) AffSymTensor3DVol (class in nipype.interfaces.dtitk.registration) affSymTensor3DVolTask (class in nipype.interfaces.dtitk.registration) AFNICommand (class in nipype.interfaces.afni.base) AFNICommandBase (class in nipype.interfaces.afni.base) AFNIPythonCommand (class in nipype.interfaces.afni.base) AFNItoNIFTI (class in nipype.interfaces.afni.utils) aggregate_filename() (in module nipype.interfaces.minc.base) aggregate_outputs() (nipype.interfaces.afni.preprocess.ClipLevel method) (nipype.interfaces.afni.preprocess.Seg method) (nipype.interfaces.afni.utils.Autobox method) (nipype.interfaces.afni.utils.BrickStat method) (nipype.interfaces.ants.MeasureImageSimilarity method) (nipype.interfaces.ants.registration.MeasureImageSimilarity method) (nipype.interfaces.base.core.BaseInterface method) (nipype.interfaces.base.core.Interface method) (nipype.interfaces.freesurfer.preprocess.SegmentCC method) (nipype.interfaces.freesurfer.utils.ImageInfo method) (nipype.interfaces.fsl.model.SmoothEstimate method) (nipype.interfaces.fsl.preprocess.FLIRT method) (nipype.interfaces.fsl.utils.ImageStats method) (nipype.interfaces.niftyseg.label_fusion.CalcTopNCC method) (nipype.interfaces.spm.model.Threshold method) (nipype.interfaces.spm.model.ThresholdStatistics method)

AI (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.utils) AlignEpiAnatPy (class in nipype.interfaces.afni.preprocess) Allineate (class in nipype.interfaces.afni.preprocess) always_run (nipype.interfaces.base.core.Interface property) Analyze2nii (class in nipype.interfaces.spm.utils) AnalyzeHeader (class in nipype.interfaces.camino.convert) AnalyzeWarp (class in nipype.interfaces.elastix.registration) ANTS (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.registration) ANTSCommand (class in nipype.interfaces.ants.base) antsIntroduction (class in nipype.interfaces.ants.legacy) AntsJointFusion (in module nipype.interfaces.ants) (in module nipype.interfaces.ants.segmentation) Aparc2Aseg (class in nipype.interfaces.freesurfer.utils) Apas2Aseg (class in nipype.interfaces.freesurfer.utils) APMQball (class in nipype.interfaces.dipy.anisotropic_power) ApplyDeformations (class in nipype.interfaces.spm.preprocess) ApplyInverseDeformation (class in nipype.interfaces.spm.utils) ApplyMask (class in nipype.interfaces.freesurfer.utils) (class in nipype.interfaces.fsl.maths) ApplyTOPUP (class in nipype.interfaces.fsl.epi) ApplyTransform (class in nipype.interfaces.spm.utils) ApplyTransforms (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.resampling) ApplyTransformsToPoints (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.resampling) ApplyVDM (class in nipype.interfaces.spm.preprocess) ApplyVolTransform (class in nipype.interfaces.freesurfer.preprocess) ApplyWarp (class in nipype.interfaces.elastix.registration) (class in nipype.interfaces.fsl.preprocess) ApplyXFM (class in nipype.interfaces.fsl.preprocess) AR1Image (class in nipype.interfaces.fsl.maths) ArtifactDetect (class in nipype.algorithms.rapidart) AssertEqual (class in nipype.interfaces.utility.base) Atropos (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.segmentation) Autobox (class in nipype.interfaces.afni.utils) Automask (class in nipype.interfaces.afni.preprocess) AutoTcorrelate (class in nipype.interfaces.afni.preprocess) AutoTLRC (class in nipype.interfaces.afni.preprocess) Average (class in nipype.interfaces.minc.minc) average_networks() (in module nipype.interfaces.cmtk.nx) AverageAffineTransform (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.utils) AverageImages (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.utils) AverageNetworks (class in nipype.interfaces.cmtk.nx) AvScale (class in nipype.interfaces.fsl.utils) Axialize (class in nipype.interfaces.afni.utils)

B

B0Calc (class in nipype.interfaces.fsl.possum) Bandpass (class in nipype.interfaces.afni.preprocess) base_dir (nipype.pipeline.engine.base.EngineBase attribute) BaseInterface (class in nipype.interfaces.base.core) BasePath (class in nipype.interfaces.base.traits_extension) BaseTraitedSpec (class in nipype.interfaces.base.specs) BBox (class in nipype.interfaces.minc.minc) BBRegister (class in nipype.interfaces.freesurfer.preprocess) BDP (class in nipype.interfaces.brainsuite.brainsuite) Beast (class in nipype.interfaces.minc.minc) BEDPOSTX (in module nipype.interfaces.fsl.dti) BEDPOSTX5 (class in nipype.interfaces.fsl.dti) BestLinReg (class in nipype.interfaces.minc.minc) BET (class in nipype.interfaces.fsl.preprocess) Bfc (class in nipype.interfaces.brainsuite.brainsuite) bids_gen_info() (in module nipype.algorithms.modelgen) BIDSDataGrabber (class in nipype.interfaces.io) BIDSDataGrabberInputSpec (class in nipype.interfaces.io) BigAverage (class in nipype.interfaces.minc.minc) Binarize (class in nipype.interfaces.freesurfer.model) BinaryMaskEditorBasedOnLandmarks (class in nipype.interfaces.semtools.segmentation.specialized) BinaryMaths (class in nipype.interfaces.fsl.maths) (class in nipype.interfaces.niftyseg.maths) BinaryMathsInteger (class in nipype.interfaces.niftyseg.maths) BinaryStats (class in nipype.interfaces.niftyseg.stats) BinThresh (class in nipype.interfaces.dtitk.utils) BinThreshTask (class in nipype.interfaces.dtitk.utils) Blob (class in nipype.interfaces.minc.minc) Blur (class in nipype.interfaces.minc.minc) BlurInMask (class in nipype.interfaces.afni.preprocess) BlurToFWHM (class in nipype.interfaces.afni.preprocess) BrainExtraction (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.segmentation) BrainMask (class in nipype.interfaces.mrtrix3.utils) BRAINSABC (class in nipype.interfaces.semtools.segmentation.specialized) BRAINSAlignMSP (class in nipype.interfaces.semtools.utilities.brains) BRAINSClipInferior (class in nipype.interfaces.semtools.utilities.brains)

BRAINSConstellationDetector (class in nipype.interfaces.semtools.segmentation.specialized) BRAINSConstellationModeler (class in nipype.interfaces.semtools.utilities.brains) BRAINSCreateLabelMapFromProbabilityMaps (class in nipype.interfaces.semtools.segmentation.specialized) BRAINSCut (class in nipype.interfaces.semtools.segmentation.specialized) BRAINSDemonWarp (class in nipype.interfaces.semtools.registration.specialized) (class in nipype.interfaces.slicer.registration.specialized) BRAINSEyeDetector (class in nipype.interfaces.semtools.utilities.brains) BRAINSFit (class in nipype.interfaces.semtools.registration.brainsfit) (class in nipype.interfaces.slicer.registration.brainsfit) BRAINSInitializedControlPoints (class in nipype.interfaces.semtools.utilities.brains) BRAINSLandmarkInitializer (class in nipype.interfaces.semtools.utilities.brains) BRAINSLinearModelerEPCA (class in nipype.interfaces.semtools.utilities.brains) BRAINSLmkTransform (class in nipype.interfaces.semtools.utilities.brains) BRAINSMultiSTAPLE (class in nipype.interfaces.semtools.segmentation.specialized) BRAINSMush (class in nipype.interfaces.semtools.utilities.brains) BRAINSPosteriorToContinuousClass (class in nipype.interfaces.semtools.brains.classify) BRAINSResample (class in nipype.interfaces.semtools.registration.brainsresample) (class in nipype.interfaces.slicer.registration.brainsresample) BRAINSResize (class in nipype.interfaces.semtools.registration.brainsresize) BRAINSROIAuto (class in nipype.interfaces.semtools.segmentation.specialized) (class in nipype.interfaces.slicer.segmentation.specialized) BRAINSSnapShotWriter (class in nipype.interfaces.semtools.utilities.brains) BRAINSTalairach (class in nipype.interfaces.semtools.brains.segmentation) BRAINSTalairachMask (class in nipype.interfaces.semtools.brains.segmentation) BRAINSTransformConvert (class in nipype.interfaces.semtools.utilities.brains) BRAINSTransformFromFiducials (class in nipype.interfaces.semtools.registration.specialized) BRAINSTrimForegroundInDirection (class in nipype.interfaces.semtools.utilities.brains) BrickStat (class in nipype.interfaces.afni.utils) Bru2 (class in nipype.interfaces.bru2nii) Bse (class in nipype.interfaces.brainsuite.brainsuite) BSplineDeformableRegistration (class in nipype.interfaces.slicer.legacy.registration) BSplineToDeformationField (class in nipype.interfaces.slicer.legacy.converters) Bucket (class in nipype.interfaces.afni.utils) build_doc() (in module nipype.utils.docparse) BuildConnectome (class in nipype.interfaces.mrtrix3.connectivity) buildtemplateparallel (class in nipype.interfaces.ants.legacy) Bunch (class in nipype.interfaces.base.support)

C

C3d (class in nipype.interfaces.c3) C3dAffineTool (class in nipype.interfaces.c3) cache() (nipype.caching.memory.Memory method), [1] CALabel (class in nipype.interfaces.freesurfer.preprocess) Calc (class in nipype.interfaces.afni.utils) (class in nipype.interfaces.minc.minc) calc_moments() (in module nipype.algorithms.misc) CalcCoregAffine (class in nipype.interfaces.spm.utils) CalcTopNCC (class in nipype.interfaces.niftyseg.label_fusion) calculate_resource_timeseries() (in module nipype.utils.draw_gantt_chart) CalculateMedian (class in nipype.algorithms.misc) CalculateNormalizedMoments (class in nipype.algorithms.misc) Camino2Trackvis (class in nipype.interfaces.camino2trackvis.convert) can_resume (nipype.interfaces.base.core.Interface property) CannyEdge (class in nipype.interfaces.semtools.filtering.featuredetection) CannySegmentationLevelSetImageFilter (class in nipype.interfaces.semtools.filtering.featuredetection) canonicalize_env() (in module nipype.utils.filemanip) CANormalize (class in nipype.interfaces.freesurfer.preprocess) capture_provenance() (in module nipype.interfaces.io) CARegister (class in nipype.interfaces.freesurfer.preprocess) CastScalarVolume (class in nipype.interfaces.slicer.filtering.arithmetic) Cat (class in nipype.interfaces.afni.utils) CAT12SANLMDenoising (class in nipype.interfaces.cat12.preprocess) CAT12Segment (class in nipype.interfaces.cat12.preprocess) CatMatvec (class in nipype.interfaces.afni.utils) Cell (class in nipype.interfaces.cat12.base) Cell2Str (class in nipype.interfaces.cat12.preprocess) (class in nipype.interfaces.cat12.surface) CenterMass (class in nipype.interfaces.afni.utils) Cerebro (class in nipype.interfaces.brainsuite.brainsuite) CFFBaseInterface (class in nipype.interfaces.cmtk.base) CFFConverter (class in nipype.interfaces.cmtk.convert) ChangeDataType (class in nipype.interfaces.fsl.maths) check_depends() (in module nipype.utils.filemanip) check_forhash() (in module nipype.utils.filemanip) check_fsl() (in module nipype.interfaces.fsl.base) check_latest_version() (in module nipype) check_minc() (in module nipype.interfaces.minc.base) check_version() (nipype.interfaces.niftyreg.base.NiftyRegCommand method) CheckerBoardFilter (class in nipype.interfaces.slicer.filtering.checkerboardfilter) CheckTalairachAlignment (class in nipype.interfaces.freesurfer.utils) CiftiSmooth (class in nipype.interfaces.workbench.cifti) clamp() (nipype.utils.ram_estimator.RamEstimator static method) Classifier (class in nipype.interfaces.fsl.fix) clean_working_directory() (in module nipype.pipeline.engine.utils) Cleaner (class in nipype.interfaces.fsl.fix) cleanup() (nipype.utils.tmpdirs.TemporaryDirectory method) CleanUpOverlapLabels (class in nipype.interfaces.semtools.utilities.brains) clear_previous_runs() (nipype.caching.memory.Memory method), [1], [2] clear_runs_since() (nipype.caching.memory.Memory method) ClipLevel (class in nipype.interfaces.afni.preprocess) clone() (nipype.pipeline.engine.base.EngineBase method) (nipype.pipeline.engine.workflows.Workflow method) Cluster (class in nipype.interfaces.fsl.model) cmat() (in module nipype.interfaces.cmtk.cmtk) cmd (nipype.interfaces.afni.base.AFNIPythonCommand property) (nipype.interfaces.base.core.CommandLine property) (nipype.interfaces.fsl.fix.Classifier attribute) (nipype.interfaces.fsl.fix.Cleaner attribute) (nipype.interfaces.fsl.fix.FeatureExtractor attribute) (nipype.interfaces.fsl.fix.Training attribute) cmdline (nipype.interfaces.base.core.CommandLine property) (nipype.interfaces.base.core.MpiCommandLine property) (nipype.interfaces.freesurfer.preprocess.DICOMConvert property) (nipype.interfaces.freesurfer.preprocess.ReconAll property) (nipype.interfaces.minc.minc.Blur property) (nipype.interfaces.niftyreg.regutils.RegAverage property) CoherenceAnalyzer (class in nipype.interfaces.nitime.analysis) combine_mask_files() (in module nipype.algorithms.confounds) CommandLine (class in nipype.interfaces.base.core) CommandLineDtitk (class in nipype.interfaces.dtitk.base) compareTractInclusion (class in nipype.interfaces.semtools.diffusion.gtract) CompCor (class in nipype.algorithms.confounds) Complex (class in nipype.interfaces.fsl.utils) ComposeMultiTransform (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.utils) ComposeXfm (class in nipype.interfaces.dtitk.registration) ComposeXfmTask (class in nipype.interfaces.dtitk.registration) CompositeTransformUtil (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.registration) compute_dict_measures() (in module nipype.interfaces.cmtk.nx)

compute_dvars() (in module nipype.algorithms.confounds) compute_edge_measures() (in module nipype.interfaces.cmtk.nx) compute_network_measures() (in module nipype.interfaces.cmtk.nx) compute_node_measures() (in module nipype.interfaces.cmtk.nx) compute_noise_components() (in module nipype.algorithms.confounds) compute_singlevalued_measures() (in module nipype.interfaces.cmtk.nx) ComputeDVARS (class in nipype.algorithms.confounds) ComputeEigensystem (class in nipype.interfaces.camino.dti) ComputeFractionalAnisotropy (class in nipype.interfaces.camino.dti) ComputeMask (class in nipype.interfaces.nipy.preprocess) ComputeMeanDiffusivity (class in nipype.interfaces.camino.dti) ComputeMeshWarp (class in nipype.algorithms.mesh) ComputeTDI (class in nipype.interfaces.mrtrix3.utils) ComputeTensorTrace (class in nipype.interfaces.camino.dti) concat_files() (in module nipype.interfaces.mrtrix.tensors) Concatenate (class in nipype.interfaces.freesurfer.model) ConcatenateLTA (class in nipype.interfaces.freesurfer.preprocess) CondorDAGManPlugin (class in nipype.pipeline.plugins.dagman) CondorPlugin (class in nipype.pipeline.plugins.condor) Config (class in nipype.sphinxext.apidoc) configuration() (in module nipype.interfaces.dipy.setup) configure_input_data() (in module nipype.interfaces.vtkbase) Conmat (class in nipype.interfaces.camino.connectivity) connect() (nipype.pipeline.engine.workflows.Workflow method) ConstrainedSphericalDeconvolution (class in nipype.interfaces.mrtrix.tensors) (class in nipype.interfaces.mrtrix3.reconst) container_to_string() (in module nipype.utils.misc) contains_doctest() (in module nipype.sphinxext.plot_workflow) Contrast (class in nipype.interfaces.freesurfer.utils) ContrastMgr (class in nipype.interfaces.fsl.model) Convert (class in nipype.interfaces.minc.minc) convert_to_traits_type() (in module nipype.interfaces.dipy.base) ConvertDset (class in nipype.interfaces.afni.utils) ConvertScalarImageToRGB (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.visualization) ConvertWarp (class in nipype.interfaces.fsl.utils) ConvertXFM (class in nipype.interfaces.fsl.utils) Copy (class in nipype.interfaces.afni.utils) (class in nipype.interfaces.minc.minc) copy2subjdir() (in module nipype.interfaces.freesurfer.utils) copy_header() (in module nipype.utils.imagemanip) copyfile() (in module nipype.utils.filemanip) copyfiles() (in module nipype.utils.filemanip) CopyGeom (class in nipype.interfaces.fsl.utils) CopyHeaderInterface (class in nipype.interfaces.mixins.fixheader) CopyMeta (class in nipype.interfaces.dcmstack) copytree() (in module nipype.interfaces.io) Coregister (class in nipype.interfaces.spm.preprocess) Cortex (class in nipype.interfaces.brainsuite.brainsuite) CorticalThickness (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.segmentation) cosine_filter() (in module nipype.algorithms.confounds) count_iterables() (in module nipype.pipeline.engine.utils) crash2txt() (in module nipype.utils.filemanip) crawl_code_struct() (in module nipype.interfaces.slicer.generate_classes) create_allpoints_cmat() (in module nipype.interfaces.cmtk.cmtk) create_annot_label() (in module nipype.interfaces.cmtk.parcellation) create_endpoints_array() (in module nipype.interfaces.cmtk.cmtk) create_event_dict() (in module nipype.utils.draw_gantt_chart) create_function_from_source() (in module nipype.utils.functions) create_interface_specs() (in module nipype.interfaces.dipy.base) create_nodes() (in module nipype.interfaces.cmtk.cmtk) create_pyscript() (in module nipype.pipeline.plugins.tools) create_roi() (in module nipype.interfaces.cmtk.parcellation) create_wm_mask() (in module nipype.interfaces.cmtk.parcellation) CreateJacobianDeterminantImage (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.utils) CreateMatrix (class in nipype.interfaces.cmtk.cmtk) CreateNifti (class in nipype.algorithms.misc) CreateNodes (class in nipype.interfaces.cmtk.cmtk) createoutputdirs() (in module nipype.interfaces.freesurfer.utils) CreateTiledMosaic (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.visualization) CreateWarped (class in nipype.interfaces.spm.preprocess) crop_and_move_datasets() (in module nipype.interfaces.cmtk.parcellation) CSD (class in nipype.interfaces.dipy.reconstruction) CSVReader (class in nipype.interfaces.utility.csv) Curvature (class in nipype.interfaces.freesurfer.utils) CurvatureAnisotropicDiffusion (class in nipype.interfaces.slicer.filtering.denoising) CurvatureStats (class in nipype.interfaces.freesurfer.utils) cwd (nipype.utils.config.NipypeConfig property)

D

daemon (nipype.pipeline.plugins.legacymultiproc.NonDaemonMixin property) DARTEL (class in nipype.interfaces.spm.preprocess) DARTELNorm2MNI (class in nipype.interfaces.spm.preprocess) DataFinder (class in nipype.interfaces.io) DataGrabber (class in nipype.interfaces.io) DataSink (class in nipype.interfaces.io) datefmt (nipype.utils.logger.Logging attribute) Dcm2nii (class in nipype.interfaces.dcm2nii) Dcm2niix (class in nipype.interfaces.dcm2nii) DcmStack (class in nipype.interfaces.dcmstack) DebugPlugin (class in nipype.pipeline.plugins.debug) Deconvolve (class in nipype.interfaces.afni.model) DEF_SAMPLING_STRATEGY (nipype.interfaces.ants.Registration attribute) (nipype.interfaces.ants.registration.Registration attribute) default_submit_template (nipype.pipeline.plugins.dagman.CondorDAGManPlugin attribute) DegreeCentrality (class in nipype.interfaces.afni.preprocess) Denoise (class in nipype.interfaces.dipy.preprocess) DenoiseImage (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.segmentation) Despike (class in nipype.interfaces.afni.preprocess) Detrend (class in nipype.interfaces.afni.preprocess) Dewisp (class in nipype.interfaces.brainsuite.brainsuite) Dfs (class in nipype.interfaces.brainsuite.brainsuite) DICOMConvert (class in nipype.interfaces.freesurfer.preprocess) DicomImport (class in nipype.interfaces.spm.utils) DicomToNrrdConverter (class in nipype.interfaces.slicer.converters) dict_diff() (in module nipype.utils.misc) dictcopy() (nipype.interfaces.base.support.Bunch method) Diffeo (class in nipype.interfaces.dtitk.registration) DiffeoScalarVol (class in nipype.interfaces.dtitk.registration) diffeoScalarVolTask (class in nipype.interfaces.dtitk.registration) DiffeoSymTensor3DVol (class in nipype.interfaces.dtitk.registration) diffeoSymTensor3DVolTask (class in nipype.interfaces.dtitk.registration) DiffeoTask (class in nipype.interfaces.dtitk.registration) DiffusionTensorScalarMeasurements (class in nipype.interfaces.slicer.diffusion.diffusion) DiffusionTensorStreamlineTrack (class in nipype.interfaces.mrtrix.tracking) DiffusionWeightedVolumeMasking (class in nipype.interfaces.slicer.diffusion.diffusion) DilateImage (class in nipype.interfaces.fsl.maths) (class in nipype.interfaces.semtools.filtering.featuredetection) DilateMask (class in nipype.interfaces.semtools.filtering.featuredetection) dipy_to_nipype_interface() (in module nipype.interfaces.dipy.base) dipy_version() (in module nipype.interfaces.dipy.base) DipyBaseInterface (class in nipype.interfaces.dipy.base) DipyDiffusionInterface (class in nipype.interfaces.dipy.base) Directions2Amplitude (class in nipype.interfaces.mrtrix.tensors)

Directory (class in nipype.interfaces.base.traits_extension) disable_file_logging() (nipype.utils.logger.Logging method) disable_resource_monitor() (nipype.utils.config.NipypeConfig method) disconnect() (nipype.pipeline.engine.workflows.Workflow method) dist_is_editable() (in module nipype.utils.filemanip) Distance (class in nipype.algorithms.metrics) (class in nipype.algorithms.misc) DistanceMap (class in nipype.interfaces.fsl.dti) DistanceMaps (class in nipype.interfaces.semtools.filtering.featuredetection) DistributedPluginBase (class in nipype.pipeline.plugins.base) Dot (class in nipype.interfaces.afni.utils) draw_lines() (in module nipype.utils.draw_gantt_chart) draw_nodes() (in module nipype.utils.draw_gantt_chart) draw_resource_bar() (in module nipype.utils.draw_gantt_chart) DT2NIfTI (class in nipype.interfaces.camino.convert) DTI (class in nipype.interfaces.dipy.tensors) dtiaverage (class in nipype.interfaces.semtools.diffusion.diffusion) dtiestim (class in nipype.interfaces.semtools.diffusion.diffusion) DTIexport (class in nipype.interfaces.slicer.diffusion.diffusion) DTIFit (class in nipype.interfaces.camino.dti) (class in nipype.interfaces.fsl.dti) DTIimport (class in nipype.interfaces.slicer.diffusion.diffusion) dtiprocess (class in nipype.interfaces.semtools.diffusion.diffusion) DTIRecon (class in nipype.interfaces.diffusion_toolkit.dti) DTITKRenameMixin (class in nipype.interfaces.dtitk.base) DTITracker (class in nipype.interfaces.diffusion_toolkit.dti) DTLUTGen (class in nipype.interfaces.camino.dti) DTMetric (class in nipype.interfaces.camino.dti) DualRegression (class in nipype.interfaces.fsl.model) Dump (class in nipype.interfaces.minc.minc) DumpBinaryTrainingVectors (class in nipype.interfaces.semtools.filtering.featuredetection) DWI2SphericalHarmonicsImage (class in nipype.interfaces.mrtrix.tensors) DWI2Tensor (class in nipype.interfaces.mrtrix.preprocess) DWIBiasCorrect (class in nipype.interfaces.mrtrix3.preprocess) DWICompare (class in nipype.interfaces.semtools.converters) DWIConvert (class in nipype.interfaces.semtools.diffusion.diffusion) DWIDenoise (class in nipype.interfaces.mrtrix3.preprocess) DWIExtract (class in nipype.interfaces.mrtrix3.utils) DWIJointRicianLMMSEFilter (class in nipype.interfaces.slicer.diffusion.diffusion) DWIPreproc (class in nipype.interfaces.mrtrix3.preprocess) DWIRicianLMMSEFilter (class in nipype.interfaces.slicer.diffusion.diffusion) DWISimpleCompare (class in nipype.interfaces.semtools.converters) DWIToDTIEstimation (class in nipype.interfaces.slicer.diffusion.diffusion) DwiTool (class in nipype.interfaces.niftyfit.dwi) DWIUnbiasedNonLocalMeansFilter (class in nipype.interfaces.slicer.legacy.diffusion.denoising) DynamicTraitedSpec (class in nipype.interfaces.base.specs)

E

ECM (class in nipype.interfaces.afni.preprocess) Eddy (class in nipype.interfaces.fsl.epi) EddyCorrect (class in nipype.interfaces.fsl.epi) EddyQuad (class in nipype.interfaces.fsl.epi) Edge3 (class in nipype.interfaces.afni.utils) EditTransform (class in nipype.interfaces.elastix.utils) EditWMwithAseg (class in nipype.interfaces.freesurfer.preprocess) EM (class in nipype.interfaces.niftyseg.em) emptydirs() (in module nipype.utils.filemanip) EMRegister (class in nipype.interfaces.freesurfer.registration) EMSegmentCommandLine (class in nipype.interfaces.slicer.segmentation.specialized) EMSegmentTransformToNewFormat (class in nipype.interfaces.slicer.utilities) enable_debug_mode() (nipype.utils.config.NipypeConfig method) enable_file_logging() (nipype.utils.logger.Logging method) enable_provenance() (nipype.utils.config.NipypeConfig method) enable_resource_monitor() (nipype.utils.config.NipypeConfig method) EngineBase (class in nipype.pipeline.engine.base) ensure_list() (in module nipype.utils.filemanip) EPIDeWarp (class in nipype.interfaces.fsl.epi) EpiReg (class in nipype.interfaces.fsl.epi) Erode (class in nipype.interfaces.mrtrix.preprocess) ErodeImage (class in nipype.interfaces.fsl.maths) (class in nipype.interfaces.semtools.filtering.featuredetection) ErrorMap (class in nipype.algorithms.metrics) ESLR (class in nipype.interfaces.semtools.segmentation.specialized)

EstimateContrast (class in nipype.interfaces.nipy.model) (class in nipype.interfaces.spm.model) EstimateFOD (class in nipype.interfaces.mrtrix3.reconst) EstimateModel (class in nipype.interfaces.spm.model) EstimateResponseForSH (class in nipype.interfaces.mrtrix.tensors) EstimateResponseSH (class in nipype.interfaces.dipy.reconstruction) EulerNumber (class in nipype.interfaces.freesurfer.utils) Eval (class in nipype.interfaces.afni.utils) evaluate_connect_function() (in module nipype.pipeline.engine.utils) execute_task() (in module nipype.pipeline.plugins.ipython) exists (nipype.interfaces.base.traits_extension.BasePath attribute) exists() (nipype.interfaces.niftyreg.base.NiftyRegCommand method) expand_iterables() (in module nipype.pipeline.engine.utils) ExpertAutomatedRegistration (class in nipype.interfaces.slicer.legacy.registration) export() (nipype.pipeline.engine.workflows.Workflow method) export_graph() (in module nipype.pipeline.engine.utils) ExportFile (class in nipype.interfaces.io) Extract (class in nipype.interfaces.minc.minc) extract() (in module nipype.interfaces.cmtk.parcellation) ExtractAdditionalSurfaceParameters (class in nipype.interfaces.cat12.surface) ExtractMainComponent (class in nipype.interfaces.freesurfer.utils) extractNrrdVectorIndex (class in nipype.interfaces.semtools.diffusion.gtract) ExtractROI (class in nipype.interfaces.fsl.utils) ExtractROIBasedSurfaceMeasures (class in nipype.interfaces.cat12.surface) ExtractSkeleton (class in nipype.interfaces.slicer.filtering.extractskeleton)

F

FactorialDesign (class in nipype.interfaces.spm.model) fallback_svd() (in module nipype.algorithms.confounds) FAST (class in nipype.interfaces.fsl.preprocess) fcsv_to_hdf5 (class in nipype.interfaces.semtools.utilities.brains) FEAT (class in nipype.interfaces.fsl.model) FEATModel (class in nipype.interfaces.fsl.model) FEATRegister (class in nipype.interfaces.fsl.model) FeatureExtractor (class in nipype.interfaces.fsl.fix) fiberprocess (class in nipype.interfaces.semtools.diffusion.tractography.fiberprocess) fiberstats (class in nipype.interfaces.semtools.diffusion.tractography.commandlineonly) fibertrack (class in nipype.interfaces.semtools.diffusion.tractography.fibertrack) FiducialRegistration (class in nipype.interfaces.slicer.registration.specialized) FieldMap (class in nipype.interfaces.spm.preprocess) File (class in nipype.interfaces.base.traits_extension) filemap (nipype.interfaces.freesurfer.preprocess.MRIConvert attribute) (nipype.interfaces.fsl.model.Cluster attribute) (nipype.interfaces.fsl.preprocess.FNIRT attribute) filename() (nipype.sphinxext.plot_workflow.ImageFile method) filename_to_list() (in module nipype.utils.filemanip) filenames() (nipype.sphinxext.plot_workflow.ImageFile method) fileno() (nipype.utils.subprocess.Stream method) fill_in_missing_output_path() (in module nipype.utils.nipype2boutiques) FillLesions (class in nipype.interfaces.niftyseg.lesions) FILMGLS (class in nipype.interfaces.fsl.model) FilterRegressor (class in nipype.interfaces.fsl.utils) FilterTracks (class in nipype.interfaces.mrtrix.tracking) Fim (class in nipype.interfaces.afni.preprocess) final_argument_whitespace (nipype.sphinxext.plot_workflow.WorkflowDirective attribute) find_indices() (in module nipype.utils.misc) FindCenterOfBrain (class in nipype.interfaces.semtools.utilities.brains) FindShPeaks (class in nipype.interfaces.mrtrix.tensors) FindTheBiggest (class in nipype.interfaces.fsl.dti) FIRST (class in nipype.interfaces.fsl.preprocess) FitAsl (class in nipype.interfaces.niftyfit.asl) FitDwi (class in nipype.interfaces.niftyfit.dwi) FitGLM (class in nipype.interfaces.nipy.model) FitMSParams (class in nipype.interfaces.freesurfer.preprocess) FitQt1 (class in nipype.interfaces.niftyfit.qt1) FitTensor (class in nipype.interfaces.mrtrix3.reconst) fix_keys_for_gexf() (in module nipype.interfaces.cmtk.nx)

FixTopology (class in nipype.interfaces.freesurfer.utils) FLAMEO (class in nipype.interfaces.fsl.model) flatten() (in module nipype.utils.misc) FlippedDifference (class in nipype.interfaces.semtools.filtering.featuredetection) FLIRT (class in nipype.interfaces.fsl.preprocess) fltcols() (in module nipype.utils.matlabtools) fmt (nipype.utils.logger.Logging attribute) fname (nipype.utils.profiler.ResourceMonitor property) (nipype.utils.profiler.ResourceMonitorMock property) fname_presuffix() (in module nipype.utils.filemanip) fnames_presuffix() (in module nipype.utils.filemanip) FNIRT (class in nipype.interfaces.fsl.preprocess) force_run (nipype.interfaces.freesurfer.preprocess.ReconAll attribute) force_to_valid_python_variable_name() (in module nipype.interfaces.slicer.generate_classes) format_dot() (in module nipype.pipeline.engine.utils) format_help() (in module nipype.interfaces.base.support) format_node() (in module nipype.pipeline.engine.utils) format_params() (in module nipype.utils.docparse) format_template() (in module nipype.sphinxext.plot_workflow) Fourier (class in nipype.interfaces.afni.preprocess) FramewiseDisplacement (class in nipype.algorithms.confounds) free_display() (in module nipype.utils.config) FreeSurferSource (class in nipype.interfaces.io) FSCommand (class in nipype.interfaces.freesurfer.base) FSCommandOpenMP (class in nipype.interfaces.freesurfer.base) FSL2MRTrix (class in nipype.interfaces.mrtrix.tensors) FSL2Scheme (class in nipype.interfaces.camino.convert) FSLCommand (class in nipype.interfaces.fsl.base) FSLXCommand (class in nipype.interfaces.fsl.dti) FSScriptCommand (class in nipype.interfaces.freesurfer.base) FSSurfaceCommand (class in nipype.interfaces.freesurfer.base) ftypes (nipype.interfaces.afni.base.Info attribute) (nipype.interfaces.fsl.base.Info attribute) FUGUE (class in nipype.interfaces.fsl.preprocess) fullname (nipype.pipeline.engine.base.EngineBase property) func_is_3d() (in module nipype.interfaces.spm.base) Function (class in nipype.interfaces.utility.wrappers) FuseSegmentations (class in nipype.interfaces.freesurfer.longitudinal) FuzzyOverlap (class in nipype.algorithms.metrics) (class in nipype.algorithms.misc) FWHMx (class in nipype.interfaces.afni.utils)

G

GaussianBlurImageFilter (class in nipype.interfaces.slicer.filtering.denoising) GCOR (class in nipype.interfaces.afni.utils) gen_filename_from_param() (in module nipype.interfaces.slicer.generate_classes) gen_info() (in module nipype.algorithms.modelgen) gen_noise() (nipype.algorithms.misc.AddNoise method) Generate5tt (class in nipype.interfaces.mrtrix3.utils) Generate5tt2gmwmi (class in nipype.interfaces.mrtrix3.utils) generate_all_classes() (in module nipype.interfaces.slicer.generate_classes) generate_boutiques_descriptor() (in module nipype.utils.nipype2boutiques) generate_class() (in module nipype.interfaces.slicer.generate_classes) generate_custom_inputs() (in module nipype.utils.nipype2boutiques) generate_expanded_graph() (in module nipype.pipeline.engine.utils) generate_gantt_chart() (in module nipype.utils.draw_gantt_chart) generate_tool_outputs() (in module nipype.utils.nipype2boutiques) GenerateAverageLmkFile (class in nipype.interfaces.semtools.testing.generateaveragelmkfile) GenerateBrainClippedImage (class in nipype.interfaces.semtools.filtering.featuredetection) GenerateCsfClippedFromClassifiedImage (class in nipype.interfaces.semtools.featurecreator) GenerateDirections (class in nipype.interfaces.mrtrix.tensors) GenerateEdgeMapImage (class in nipype.interfaces.semtools.brains.utilities) GenerateLabelMapFromProbabilityMap (class in nipype.interfaces.semtools.utilities.brains) GeneratePurePlugMask (class in nipype.interfaces.semtools.brains.utilities) GenerateSummedGradientImage (class in nipype.interfaces.semtools.filtering.featuredetection) GenerateTestImage (class in nipype.interfaces.semtools.filtering.featuredetection) GenerateWhiteMatterMask (class in nipype.interfaces.mrtrix.preprocess) Gennlxfm (class in nipype.interfaces.minc.minc) GenWarpFields (class in nipype.interfaces.ants.legacy) get() (nipype.interfaces.base.specs.BaseTraitedSpec method) (nipype.interfaces.base.support.Bunch method) (nipype.interfaces.base.traits_extension.OutputMultiObject method) (nipype.utils.config.NipypeConfig method) get_all_files() (in module nipype.pipeline.engine.utils) get_attr_id() (in module nipype.utils.provenance) get_boutiques_groups() (in module nipype.utils.nipype2boutiques) get_boutiques_input() (in module nipype.utils.nipype2boutiques) get_boutiques_output() (in module nipype.utils.nipype2boutiques) get_boutiques_output_from_inp() (in module nipype.utils.nipype2boutiques) get_command_line_flag() (in module nipype.utils.nipype2boutiques) get_connectivity_matrix() (in module nipype.interfaces.cmtk.cmtk) get_custom_path() (in module nipype.interfaces.niftyreg.base) get_data() (nipype.utils.config.NipypeConfig method) get_data_dims() (in module nipype.interfaces.mrtrix.convert) get_default_args() (in module nipype.interfaces.dipy.base) get_dependencies() (in module nipype.utils.filemanip) get_description_from_spec() (in module nipype.utils.nipype2boutiques) get_dipy_workflows() (in module nipype.interfaces.dipy.base) get_display() (nipype.utils.config.NipypeConfig method) get_doc() (in module nipype.utils.docparse) get_filecopy_info() (in module nipype.interfaces.base.specs) get_first_3dfile() (in module nipype.interfaces.spm.base) get_hashval() (in module nipype.utils.provenance) (nipype.interfaces.base.specs.BaseTraitedSpec method) get_id() (in module nipype.utils.provenance) get_info() (in module nipype) get_levels() (in module nipype.pipeline.engine.utils) get_matlab_command() (in module nipype.interfaces.matlab) get_max_resources_used() (in module nipype.utils.profiler) get_node() (nipype.pipeline.engine.workflows.Workflow method) get_output() (nipype.pipeline.engine.nodes.Node method) get_params_from_doc() (in module nipype.utils.docparse)

get_print_name() (in module nipype.pipeline.engine.utils) get_r_command() (in module nipype.interfaces.r) get_related_files() (in module nipype.utils.filemanip) get_rois_crossed() (in module nipype.interfaces.cmtk.cmtk) get_staple_args() (nipype.interfaces.niftyseg.label_fusion.LabelFusion method) get_steps_args() (nipype.interfaces.niftyseg.label_fusion.LabelFusion method) get_subnodes() (nipype.pipeline.engine.nodes.MapNode method) get_system_total_memory_gb() (in module nipype.utils.profiler) get_trait_desc() (in module nipype.interfaces.base.support) get_traitsfree() (nipype.interfaces.base.specs.BaseTraitedSpec method) get_url() (in module nipype.sphinxext.gh) get_version() (nipype.interfaces.niftyseg.base.NiftySegCommand method) get_vox_dims() (in module nipype.interfaces.mrtrix.convert) get_wf_formats() (in module nipype.sphinxext.plot_workflow) getboolean() (nipype.utils.config.NipypeConfig method) getFileName() (in module nipype.interfaces.brainsuite.brainsuite) getinfo() (nipype.interfaces.spm.base.Info class method) getLevelName() (nipype.utils.logger.Logging method) getLogger() (nipype.utils.logger.Logging method) getsource() (in module nipype.utils.functions) GLM (class in nipype.interfaces.fsl.model) GLMFit (class in nipype.interfaces.freesurfer.model) gpu_count() (in module nipype.utils.gpu_count) grab_doc() (in module nipype.utils.docparse) (in module nipype.utils.spm_docs) grab_xml() (in module nipype.interfaces.slicer.generate_classes) GradientAnisotropicDiffusion (class in nipype.interfaces.slicer.filtering.denoising) GradientAnisotropicDiffusionImageFilter (class in nipype.interfaces.semtools.filtering.featuredetection) GraphError GraphPluginBase (class in nipype.pipeline.plugins.base) GrayscaleFillHoleImageFilter (class in nipype.interfaces.slicer.filtering.morphology) GrayscaleGrindPeakImageFilter (class in nipype.interfaces.slicer.filtering.morphology) GrayscaleModelMaker (class in nipype.interfaces.slicer.surface) GroupAndStack (class in nipype.interfaces.dcmstack) GTMPVC (class in nipype.interfaces.freesurfer.petsurfer) GTMSeg (class in nipype.interfaces.freesurfer.petsurfer) gtractAnisotropyMap (class in nipype.interfaces.semtools.diffusion.gtract) gtractAverageBvalues (class in nipype.interfaces.semtools.diffusion.gtract) gtractClipAnisotropy (class in nipype.interfaces.semtools.diffusion.gtract) gtractConcatDwi (class in nipype.interfaces.semtools.diffusion.gtract) gtractCopyImageOrientation (class in nipype.interfaces.semtools.diffusion.gtract) gtractCoRegAnatomy (class in nipype.interfaces.semtools.diffusion.gtract) gtractCoregBvalues (class in nipype.interfaces.semtools.diffusion.gtract) gtractCostFastMarching (class in nipype.interfaces.semtools.diffusion.gtract) gtractCreateGuideFiber (class in nipype.interfaces.semtools.diffusion.gtract) gtractFastMarchingTracking (class in nipype.interfaces.semtools.diffusion.gtract) gtractFiberTracking (class in nipype.interfaces.semtools.diffusion.gtract) gtractImageConformity (class in nipype.interfaces.semtools.diffusion.gtract) gtractInvertBSplineTransform (class in nipype.interfaces.semtools.diffusion.gtract) gtractInvertDisplacementField (class in nipype.interfaces.semtools.diffusion.gtract) gtractInvertRigidTransform (class in nipype.interfaces.semtools.diffusion.gtract) gtractResampleAnisotropy (class in nipype.interfaces.semtools.diffusion.gtract) gtractResampleB0 (class in nipype.interfaces.semtools.diffusion.gtract) gtractResampleCodeImage (class in nipype.interfaces.semtools.diffusion.gtract) gtractResampleDWIInPlace (class in nipype.interfaces.semtools.diffusion.gtract) gtractResampleFibers (class in nipype.interfaces.semtools.diffusion.gtract) gtractTensor (class in nipype.interfaces.semtools.diffusion.gtract) gtractTransformToDisplacementField (class in nipype.interfaces.semtools.diffusion.gtract) Gunzip (class in nipype.algorithms.misc) Gzip (class in nipype.algorithms.misc)

H

HammerAttributeCreator (class in nipype.interfaces.semtools.filtering.featuredetection) HARDIMat (class in nipype.interfaces.diffusion_toolkit.odf) has_content (nipype.sphinxext.plot_workflow.WorkflowDirective attribute) has_metadata() (in module nipype.interfaces.base.traits_extension) (nipype.interfaces.base.specs.BaseTraitedSpec method) has_option() (nipype.utils.config.NipypeConfig method) hash_exists() (nipype.pipeline.engine.nodes.Node method) hash_infile() (in module nipype.utils.filemanip)

hash_rename() (in module nipype.utils.filemanip) hash_timestamp() (in module nipype.utils.filemanip) help() (nipype.interfaces.base.core.Interface class method) (nipype.pipeline.engine.nodes.Node method) Hemisplit (class in nipype.interfaces.brainsuite.brainsuite) Hist (class in nipype.interfaces.afni.preprocess) HistogramMatching (class in nipype.interfaces.slicer.filtering.histogrammatching) HistogramMatchingFilter (class in nipype.interfaces.semtools.brains.utilities) human_order_sorted() (in module nipype.utils.misc)

I

ICA_AROMA (class in nipype.interfaces.fsl.aroma) ICC (class in nipype.algorithms.icc) ICC_projection_matrix() (in module nipype.algorithms.icc) ICC_rep_anova() (in module nipype.algorithms.icc) IdentityInterface (class in nipype.interfaces.utility.base) Image2Voxel (class in nipype.interfaces.camino.convert) ImageFile (class in nipype.interfaces.base.traits_extension) (class in nipype.sphinxext.plot_workflow) ImageFileSPM (class in nipype.interfaces.spm.base) ImageInfo (class in nipype.interfaces.freesurfer.utils) ImageLabelCombine (class in nipype.interfaces.slicer.filtering.imagelabelcombine) ImageMath (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.utils) ImageMaths (class in nipype.interfaces.fsl.utils) ImageMeants (class in nipype.interfaces.fsl.utils) ImageRegionPlotter (class in nipype.interfaces.semtools.utilities.brains) ImageStats (class in nipype.interfaces.camino.utils) (class in nipype.interfaces.fsl.utils) IMG_ZIP_FMT (in module nipype.interfaces.base.traits_extension) imports (nipype.interfaces.base.core.LibraryBaseInterface attribute) (nipype.interfaces.cmtk.parcellation.Parcellate attribute) indirectory() (in module nipype.utils.filemanip) Info (class in nipype.interfaces.afni.base) (class in nipype.interfaces.ants.base) (class in nipype.interfaces.dcm2nii) (class in nipype.interfaces.diffusion_toolkit.base) (class in nipype.interfaces.freesurfer.base) (class in nipype.interfaces.fsl.base) (class in nipype.interfaces.minc.base) (class in nipype.interfaces.mrtrix3.base) (class in nipype.interfaces.niftyreg.base) (class in nipype.interfaces.spm.base) (class in nipype.interfaces.workbench.base) info_regexp() (nipype.interfaces.freesurfer.utils.ImageInfo method) info_text (nipype.interfaces.base.traits_extension.BasePath property) input_spec (nipype.interfaces.base.core.Interface attribute) (nipype.interfaces.io.BIDSDataGrabber attribute) (nipype.interfaces.utility.base.IdentityInterface attribute) (nipype.interfaces.utility.base.Rename attribute)

InputMultiObject (class in nipype.interfaces.base.traits_extension) InputMultiPath (in module nipype.interfaces.base.traits_extension) inputs (nipype.pipeline.engine.base.EngineBase property) (nipype.pipeline.engine.nodes.JoinNode property) (nipype.pipeline.engine.nodes.MapNode property) (nipype.pipeline.engine.nodes.Node property) (nipype.pipeline.engine.workflows.Workflow property) insert_doc() (in module nipype.utils.docparse) insertMidACPCpoint (class in nipype.interfaces.semtools.utilities.brains) InTemporaryDirectory (class in nipype.utils.tmpdirs) IntensityDifferenceMetric (class in nipype.interfaces.slicer.quantification.changequantification) intensitymap_file_basename() (nipype.interfaces.fsl.preprocess.FNIRT class method) Interface (class in nipype.interfaces.base.core) interface (nipype.pipeline.engine.nodes.Node property) InterfaceDocstring (class in nipype.sphinxext.apidoc.docstring) InterfaceResult (class in nipype.interfaces.base.support) InvWarp (class in nipype.interfaces.fsl.utils) IOBase (class in nipype.interfaces.io) IPythonPlugin (class in nipype.pipeline.plugins.ipython) is_cached() (nipype.pipeline.engine.nodes.Node method) is_container() (in module nipype.utils.misc) is_gpu_node() (nipype.pipeline.engine.nodes.Node method) is_initializing() (nipype.pipeline.plugins.sge.QJobInfo method) is_job_pending() (nipype.pipeline.plugins.sge.QstatSubstitute method) is_job_state_pending() (nipype.pipeline.plugins.sge.QJobInfo method) is_outlier() (in module nipype.algorithms.confounds) is_pending() (nipype.pipeline.plugins.sge.QJobInfo method) is_running() (nipype.pipeline.plugins.sge.QJobInfo method) is_zombie() (nipype.pipeline.plugins.sge.QJobInfo method) isdefined() (in module nipype.interfaces.base.traits_extension) IsotropicSmooth (class in nipype.interfaces.fsl.maths) items() (nipype.interfaces.base.specs.BaseTraitedSpec method) (nipype.interfaces.base.support.Bunch method) iteritems() (nipype.interfaces.base.support.Bunch method) itername (nipype.pipeline.engine.base.EngineBase property)

J

Jacobian (class in nipype.interfaces.freesurfer.utils) JistBrainMgdmSegmentation (class in nipype.interfaces.mipav.developer) JistBrainMp2rageDuraEstimation (class in nipype.interfaces.mipav.developer) JistBrainMp2rageSkullStripping (class in nipype.interfaces.mipav.developer) JistBrainPartialVolumeFilter (class in nipype.interfaces.mipav.developer) JistCortexSurfaceMeshInflation (class in nipype.interfaces.mipav.developer) JistIntensityMp2rageMasking (class in nipype.interfaces.mipav.developer) JistLaminarProfileCalculator (class in nipype.interfaces.mipav.developer) JistLaminarProfileGeometry (class in nipype.interfaces.mipav.developer) JistLaminarProfileSampling (class in nipype.interfaces.mipav.developer) JistLaminarROIAveraging (class in nipype.interfaces.mipav.developer)

JistLaminarVolumetricLayering (class in nipype.interfaces.mipav.developer) jobname (nipype.interfaces.spm.base.SPMCommand property) jobtype (nipype.interfaces.spm.base.SPMCommand property) joinfield (nipype.pipeline.engine.nodes.JoinNode attribute) JoinNode (class in nipype.pipeline.engine.nodes) joinsource (nipype.pipeline.engine.nodes.JoinNode property) JointFusion (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.segmentation) JointHistogram (class in nipype.interfaces.semtools.utilities.brains) JSONFileGrabber (class in nipype.interfaces.io) JSONFileSink (class in nipype.interfaces.io)

K

KellyKapowski (class in nipype.interfaces.ants.segmentation)

keywords (nipype.interfaces.nipy.preprocess.SpaceTimeRealigner attribute)

L

L2Model (class in nipype.interfaces.fsl.model) l_outputs() (in module nipype.interfaces.brainsuite.brainsuite) Label2Annot (class in nipype.interfaces.freesurfer.model) Label2Label (class in nipype.interfaces.freesurfer.model) Label2Vol (class in nipype.interfaces.freesurfer.model) LabelConfig (class in nipype.interfaces.mrtrix3.connectivity) LabelConvert (class in nipype.interfaces.mrtrix3.connectivity) LabelFusion (class in nipype.interfaces.niftyseg.label_fusion) LabelGeometry (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.utils) LabelMapSmoothing (class in nipype.interfaces.slicer.surface) LandmarksCompare (class in nipype.interfaces.semtools.testing.landmarkscompare) landmarksConstellationAligner (class in nipype.interfaces.semtools.utilities.brains) landmarksConstellationWeights (class in nipype.interfaces.semtools.utilities.brains) LaplacianThickness (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.segmentation) LegacyMultiProcPlugin (class in nipype.pipeline.plugins.legacymultiproc) length() (in module nipype.interfaces.cmtk.cmtk) Level1Design (class in nipype.interfaces.fsl.model) (class in nipype.interfaces.spm.model) LFCD (class in nipype.interfaces.afni.preprocess) LibraryBaseInterface (class in nipype.interfaces.base.core) LinearPlugin (class in nipype.pipeline.plugins.linear) LinearRegistration (class in nipype.interfaces.slicer.legacy.registration)

LinRecon (class in nipype.interfaces.camino.odf) list_node_names() (nipype.pipeline.engine.workflows.Workflow method) list_to_filename() (in module nipype.utils.filemanip) listClasses() (in module nipype.utils.nipype_cmd) load() (nipype.pipeline.engine.base.EngineBase static method) load_inputs_from_json() (nipype.interfaces.base.core.BaseInterface method) load_json() (in module nipype.utils.filemanip) load_resultfile() (in module nipype.pipeline.engine.utils) load_spm_mat() (in module nipype.utils.filemanip) load_template() (in module nipype.interfaces.fsl.model) loadcrash() (in module nipype.utils.filemanip) loadpkl() (in module nipype.utils.filemanip) LocalBistat (class in nipype.interfaces.afni.utils) Localstat (class in nipype.interfaces.afni.utils) log_nodes_cb() (in module nipype.utils.profiler) log_to_dict() (in module nipype.utils.draw_gantt_chart) Logan (class in nipype.interfaces.freesurfer.petsurfer) logdebug_dict_differences() (nipype.utils.logger.Logging method) Logging (class in nipype.utils.logger) LookupMeta (class in nipype.interfaces.dcmstack) looseversion() (nipype.interfaces.freesurfer.base.Info class method) (nipype.interfaces.mrtrix3.base.Info class method) LSFPlugin (class in nipype.pipeline.plugins.lsf) LTAConvert (class in nipype.interfaces.freesurfer.utils)

M

main() (in module nipype.utils.nipype_cmd) make_key_func() (in module nipype.interfaces.dcmstack) MakeAverageSubject (class in nipype.interfaces.freesurfer.utils) MakeDyadicVectors (class in nipype.interfaces.fsl.dti) makefmtlist() (in module nipype.algorithms.misc) MakeSurfaces (class in nipype.interfaces.freesurfer.utils) maketypelist() (in module nipype.algorithms.misc) MapNode (class in nipype.pipeline.engine.nodes) mark_wf_labels() (in module nipype.sphinxext.plot_workflow) Maskave (class in nipype.interfaces.afni.preprocess) MaskFilter (class in nipype.interfaces.mrtrix3.utils) MaskScalarVolume (class in nipype.interfaces.slicer.filtering.arithmetic) MaskTool (class in nipype.interfaces.afni.utils) Math (class in nipype.interfaces.minc.minc) MathsCommand (class in nipype.interfaces.fsl.maths) (class in nipype.interfaces.niftyseg.maths) Matlab2CSV (class in nipype.algorithms.misc) MatlabCommand (class in nipype.interfaces.matlab) maxcurvature (class in nipype.interfaces.semtools.diffusion.maxcurvature) MaxImage (class in nipype.interfaces.fsl.maths) MaxnImage (class in nipype.interfaces.fsl.maths) MCFLIRT (class in nipype.interfaces.fsl.preprocess) MeanImage (class in nipype.interfaces.fsl.maths) Means (class in nipype.interfaces.afni.preprocess) MeasureImageSimilarity (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.registration) MedianFilter3D (class in nipype.interfaces.mrtrix.preprocess) MedianImage (class in nipype.interfaces.fsl.maths) MedianImageFilter (class in nipype.interfaces.slicer.filtering.denoising) MedicAlgorithmImageCalculator (class in nipype.interfaces.mipav.developer) MedicAlgorithmLesionToads (class in nipype.interfaces.mipav.developer) MedicAlgorithmMipavReorient (class in nipype.interfaces.mipav.developer) MedicAlgorithmN3 (class in nipype.interfaces.mipav.developer) MedicAlgorithmSPECTRE2010 (class in nipype.interfaces.mipav.developer) MedicAlgorithmThresholdToBinaryMask (class in nipype.interfaces.mipav.developer) MELODIC (class in nipype.interfaces.fsl.model) mem_gb (nipype.pipeline.engine.nodes.Node property) mem_gb_runtime (nipype.pipeline.engine.nodes.Node property) Memory (class in nipype.caching.memory) Merge (class in nipype.interfaces.afni.utils) (class in nipype.interfaces.fsl.utils) (class in nipype.interfaces.niftyseg.maths) (class in nipype.interfaces.utility.base) merge_bundles() (in module nipype.pipeline.engine.utils) merge_csvs() (in module nipype.algorithms.misc) merge_dict() (in module nipype.pipeline.engine.utils) merge_rois() (in module nipype.algorithms.misc) MergeCNetworks (class in nipype.interfaces.cmtk.convert) MergeCSVFiles (class in nipype.algorithms.misc) MergeModels (class in nipype.interfaces.slicer.surface) MergeNifti (class in nipype.interfaces.dcmstack) MergeROIs (class in nipype.algorithms.misc) MESD (class in nipype.interfaces.camino.odf) Mesh2PVE (class in nipype.interfaces.mrtrix3.utils) MeshFix (class in nipype.interfaces.meshfix) MeshWarpMaths (class in nipype.algorithms.mesh) MetricResample (class in nipype.interfaces.workbench.metric) MinImage (class in nipype.interfaces.fsl.maths) mkdir_p() (in module nipype.utils.config) mlab_tempfile() (in module nipype.utils.matlabtools) MNIBiasCorrection (class in nipype.interfaces.freesurfer.preprocess) ModelFit (class in nipype.interfaces.camino.dti) ModelMaker (class in nipype.interfaces.slicer.surface) ModelToLabelMap (class in nipype.interfaces.slicer.surface) modify_paths() (in module nipype.pipeline.engine.utils) ModifyAffine (class in nipype.algorithms.misc) module nipype nipype.algorithms nipype.algorithms.confounds nipype.algorithms.icc nipype.algorithms.mesh nipype.algorithms.metrics nipype.algorithms.misc nipype.algorithms.modelgen nipype.algorithms.rapidart nipype.algorithms.stats nipype.caching nipype.caching.memory nipype.interfaces nipype.interfaces.afni nipype.interfaces.afni.base nipype.interfaces.afni.model nipype.interfaces.afni.preprocess nipype.interfaces.afni.svm nipype.interfaces.afni.utils nipype.interfaces.ants nipype.interfaces.ants.base nipype.interfaces.ants.legacy nipype.interfaces.ants.registration nipype.interfaces.ants.resampling nipype.interfaces.ants.segmentation nipype.interfaces.ants.utils nipype.interfaces.ants.visualization nipype.interfaces.base nipype.interfaces.base.core nipype.interfaces.base.specs nipype.interfaces.base.support nipype.interfaces.base.traits_extension nipype.interfaces.brainsuite nipype.interfaces.brainsuite.brainsuite nipype.interfaces.bru2nii nipype.interfaces.c3 nipype.interfaces.camino nipype.interfaces.camino.calib nipype.interfaces.camino.connectivity nipype.interfaces.camino.convert nipype.interfaces.camino.dti nipype.interfaces.camino.odf nipype.interfaces.camino.utils nipype.interfaces.camino2trackvis nipype.interfaces.camino2trackvis.convert nipype.interfaces.cat12 nipype.interfaces.cat12.base nipype.interfaces.cat12.preprocess nipype.interfaces.cat12.surface nipype.interfaces.cmtk nipype.interfaces.cmtk.base nipype.interfaces.cmtk.cmtk nipype.interfaces.cmtk.convert nipype.interfaces.cmtk.nbs nipype.interfaces.cmtk.nx nipype.interfaces.cmtk.parcellation nipype.interfaces.dcm2nii nipype.interfaces.dcmstack nipype.interfaces.diffusion_toolkit nipype.interfaces.diffusion_toolkit.base nipype.interfaces.diffusion_toolkit.dti nipype.interfaces.diffusion_toolkit.odf nipype.interfaces.diffusion_toolkit.postproc nipype.interfaces.dipy nipype.interfaces.dipy.anisotropic_power nipype.interfaces.dipy.base nipype.interfaces.dipy.preprocess nipype.interfaces.dipy.reconstruction nipype.interfaces.dipy.registration nipype.interfaces.dipy.setup nipype.interfaces.dipy.simulate nipype.interfaces.dipy.stats nipype.interfaces.dipy.tensors nipype.interfaces.dipy.tracks nipype.interfaces.dtitk nipype.interfaces.dtitk.base nipype.interfaces.dtitk.registration nipype.interfaces.dtitk.utils nipype.interfaces.dynamic_slicer nipype.interfaces.elastix nipype.interfaces.elastix.base nipype.interfaces.elastix.registration nipype.interfaces.elastix.utils nipype.interfaces.freesurfer nipype.interfaces.freesurfer.base nipype.interfaces.freesurfer.longitudinal nipype.interfaces.freesurfer.model nipype.interfaces.freesurfer.petsurfer nipype.interfaces.freesurfer.preprocess nipype.interfaces.freesurfer.registration nipype.interfaces.freesurfer.utils nipype.interfaces.fsl nipype.interfaces.fsl.aroma nipype.interfaces.fsl.base nipype.interfaces.fsl.dti nipype.interfaces.fsl.epi nipype.interfaces.fsl.fix nipype.interfaces.fsl.maths nipype.interfaces.fsl.model nipype.interfaces.fsl.possum nipype.interfaces.fsl.preprocess nipype.interfaces.fsl.utils nipype.interfaces.image nipype.interfaces.io nipype.interfaces.matlab nipype.interfaces.meshfix nipype.interfaces.minc nipype.interfaces.minc.base nipype.interfaces.minc.minc nipype.interfaces.minc.testdata nipype.interfaces.mipav nipype.interfaces.mipav.developer nipype.interfaces.mipav.generate_classes nipype.interfaces.mixins nipype.interfaces.mixins.fixheader nipype.interfaces.mixins.reporting nipype.interfaces.mne nipype.interfaces.mne.base nipype.interfaces.mrtrix nipype.interfaces.mrtrix.convert nipype.interfaces.mrtrix.preprocess nipype.interfaces.mrtrix.tensors nipype.interfaces.mrtrix.tracking nipype.interfaces.mrtrix3 nipype.interfaces.mrtrix3.base nipype.interfaces.mrtrix3.connectivity nipype.interfaces.mrtrix3.preprocess nipype.interfaces.mrtrix3.reconst nipype.interfaces.mrtrix3.tracking nipype.interfaces.mrtrix3.utils nipype.interfaces.niftyfit nipype.interfaces.niftyfit.asl nipype.interfaces.niftyfit.base nipype.interfaces.niftyfit.dwi nipype.interfaces.niftyfit.qt1 nipype.interfaces.niftyreg nipype.interfaces.niftyreg.base nipype.interfaces.niftyreg.reg nipype.interfaces.niftyreg.regutils nipype.interfaces.niftyseg nipype.interfaces.niftyseg.base nipype.interfaces.niftyseg.em nipype.interfaces.niftyseg.label_fusion nipype.interfaces.niftyseg.lesions nipype.interfaces.niftyseg.maths nipype.interfaces.niftyseg.patchmatch nipype.interfaces.niftyseg.stats nipype.interfaces.nilearn nipype.interfaces.nipy nipype.interfaces.nipy.base nipype.interfaces.nipy.model nipype.interfaces.nipy.preprocess nipype.interfaces.nipy.utils nipype.interfaces.nitime nipype.interfaces.nitime.analysis nipype.interfaces.nitime.base nipype.interfaces.petpvc nipype.interfaces.quickshear nipype.interfaces.r nipype.interfaces.robex nipype.interfaces.robex.preprocess nipype.interfaces.semtools nipype.interfaces.semtools.brains nipype.interfaces.semtools.brains.classify nipype.interfaces.semtools.brains.segmentation nipype.interfaces.semtools.brains.utilities nipype.interfaces.semtools.converters nipype.interfaces.semtools.diffusion nipype.interfaces.semtools.diffusion.diffusion nipype.interfaces.semtools.diffusion.gtract nipype.interfaces.semtools.diffusion.maxcurvature nipype.interfaces.semtools.diffusion.tractography nipype.interfaces.semtools.diffusion.tractography.commandlineonly nipype.interfaces.semtools.diffusion.tractography.fiberprocess nipype.interfaces.semtools.diffusion.tractography.fibertrack nipype.interfaces.semtools.diffusion.tractography.ukftractography nipype.interfaces.semtools.featurecreator nipype.interfaces.semtools.filtering nipype.interfaces.semtools.filtering.denoising nipype.interfaces.semtools.filtering.featuredetection nipype.interfaces.semtools.legacy nipype.interfaces.semtools.legacy.registration nipype.interfaces.semtools.registration nipype.interfaces.semtools.registration.brainsfit nipype.interfaces.semtools.registration.brainsresample nipype.interfaces.semtools.registration.brainsresize nipype.interfaces.semtools.registration.specialized nipype.interfaces.semtools.segmentation nipype.interfaces.semtools.segmentation.specialized nipype.interfaces.semtools.testing nipype.interfaces.semtools.testing.featuredetection nipype.interfaces.semtools.testing.generateaveragelmkfile nipype.interfaces.semtools.testing.landmarkscompare nipype.interfaces.semtools.utilities nipype.interfaces.semtools.utilities.brains nipype.interfaces.slicer nipype.interfaces.slicer.base nipype.interfaces.slicer.converters nipype.interfaces.slicer.diffusion nipype.interfaces.slicer.diffusion.diffusion nipype.interfaces.slicer.filtering nipype.interfaces.slicer.filtering.arithmetic nipype.interfaces.slicer.filtering.checkerboardfilter nipype.interfaces.slicer.filtering.denoising nipype.interfaces.slicer.filtering.extractskeleton nipype.interfaces.slicer.filtering.histogrammatching nipype.interfaces.slicer.filtering.imagelabelcombine nipype.interfaces.slicer.filtering.morphology nipype.interfaces.slicer.filtering.n4itkbiasfieldcorrection nipype.interfaces.slicer.filtering.resamplescalarvectordwivolume nipype.interfaces.slicer.filtering.thresholdscalarvolume nipype.interfaces.slicer.filtering.votingbinaryholefillingimagefilter nipype.interfaces.slicer.generate_classes nipype.interfaces.slicer.legacy nipype.interfaces.slicer.legacy.converters nipype.interfaces.slicer.legacy.diffusion nipype.interfaces.slicer.legacy.diffusion.denoising nipype.interfaces.slicer.legacy.filtering nipype.interfaces.slicer.legacy.registration nipype.interfaces.slicer.legacy.segmentation nipype.interfaces.slicer.quantification nipype.interfaces.slicer.quantification.changequantification nipype.interfaces.slicer.quantification.petstandarduptakevaluecomputation nipype.interfaces.slicer.registration nipype.interfaces.slicer.registration.brainsfit nipype.interfaces.slicer.registration.brainsresample nipype.interfaces.slicer.registration.specialized nipype.interfaces.slicer.segmentation nipype.interfaces.slicer.segmentation.simpleregiongrowingsegmentation nipype.interfaces.slicer.segmentation.specialized nipype.interfaces.slicer.surface nipype.interfaces.slicer.utilities nipype.interfaces.spm nipype.interfaces.spm.base nipype.interfaces.spm.model nipype.interfaces.spm.preprocess nipype.interfaces.spm.utils nipype.interfaces.utility nipype.interfaces.utility.base nipype.interfaces.utility.csv nipype.interfaces.utility.wrappers nipype.interfaces.vista nipype.interfaces.vista.vista nipype.interfaces.vtkbase nipype.interfaces.workbench nipype.interfaces.workbench.base nipype.interfaces.workbench.cifti nipype.interfaces.workbench.metric nipype.pipeline nipype.pipeline.engine nipype.pipeline.engine.base nipype.pipeline.engine.nodes nipype.pipeline.engine.utils nipype.pipeline.engine.workflows nipype.pipeline.plugins nipype.pipeline.plugins.base nipype.pipeline.plugins.condor nipype.pipeline.plugins.dagman nipype.pipeline.plugins.debug nipype.pipeline.plugins.ipython nipype.pipeline.plugins.legacymultiproc nipype.pipeline.plugins.linear nipype.pipeline.plugins.lsf nipype.pipeline.plugins.multiproc nipype.pipeline.plugins.oar nipype.pipeline.plugins.pbs nipype.pipeline.plugins.pbsgraph nipype.pipeline.plugins.semaphore_singleton nipype.pipeline.plugins.sge nipype.pipeline.plugins.sgegraph nipype.pipeline.plugins.slurm nipype.pipeline.plugins.slurmgraph nipype.pipeline.plugins.somaflow nipype.pipeline.plugins.tools nipype.sphinxext nipype.sphinxext.apidoc nipype.sphinxext.apidoc.docstring nipype.sphinxext.documenter nipype.sphinxext.gh nipype.sphinxext.plot_workflow nipype.utils nipype.utils.config nipype.utils.datetime nipype.utils.docparse nipype.utils.draw_gantt_chart nipype.utils.filemanip nipype.utils.functions nipype.utils.gpu_count nipype.utils.imagemanip nipype.utils.logger nipype.utils.matlabtools nipype.utils.misc nipype.utils.nipype2boutiques nipype.utils.nipype_cmd nipype.utils.onetime nipype.utils.profiler nipype.utils.provenance nipype.utils.ram_estimator nipype.utils.spm_docs nipype.utils.subprocess nipype.utils.tmpdirs

MotionOutliers (class in nipype.interfaces.fsl.utils) MpiCommandLine (class in nipype.interfaces.base.core) MPRtoMNI305 (class in nipype.interfaces.freesurfer.registration) MRCat (class in nipype.interfaces.mrtrix3.utils) MRConvert (class in nipype.interfaces.mrtrix.preprocess) (class in nipype.interfaces.mrtrix3.utils) MRDeGibbs (class in nipype.interfaces.mrtrix3.preprocess) MRIConvert (class in nipype.interfaces.freesurfer.preprocess) MRICoreg (class in nipype.interfaces.freesurfer.registration) MRIFill (class in nipype.interfaces.freesurfer.utils) MRIMarchingCubes (class in nipype.interfaces.freesurfer.utils) MRIPretess (class in nipype.interfaces.freesurfer.utils) MRIsCALabel (class in nipype.interfaces.freesurfer.preprocess) MRIsCalc (class in nipype.interfaces.freesurfer.utils) MRIsCombine (class in nipype.interfaces.freesurfer.utils) MRIsConvert (class in nipype.interfaces.freesurfer.utils) MRIsExpand (class in nipype.interfaces.freesurfer.utils) MRIsInflate (class in nipype.interfaces.freesurfer.utils) MRISPreproc (class in nipype.interfaces.freesurfer.model) MRISPreprocReconAll (class in nipype.interfaces.freesurfer.model) MRITessellate (class in nipype.interfaces.freesurfer.utils) MRMath (class in nipype.interfaces.mrtrix3.utils) MRMultiply (class in nipype.interfaces.mrtrix.preprocess) MRResize (class in nipype.interfaces.mrtrix3.utils) MRTM1 (class in nipype.interfaces.freesurfer.petsurfer) MRTM2 (class in nipype.interfaces.freesurfer.petsurfer) MRTransform (class in nipype.interfaces.mrtrix.preprocess) (class in nipype.interfaces.mrtrix3.utils) MRTrix2TrackVis (class in nipype.interfaces.mrtrix.convert) MRTrix3Base (class in nipype.interfaces.mrtrix3.base) MRTrixInfo (class in nipype.interfaces.mrtrix.preprocess) MRTrixViewer (class in nipype.interfaces.mrtrix.preprocess) MS_LDA (class in nipype.interfaces.freesurfer.model) MTNormalise (class in nipype.interfaces.mrtrix3.utils) MultiChannelNewSegment (class in nipype.interfaces.spm.preprocess) MultiImageMaths (class in nipype.interfaces.fsl.maths) MultiObject (class in nipype.interfaces.base.traits_extension) MultipleRegressDesign (class in nipype.interfaces.fsl.model) MultipleRegressionDesign (class in nipype.interfaces.spm.model) MultiplyImages (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.utils) MultiplyScalarVolumes (class in nipype.interfaces.slicer.filtering.arithmetic) MultiProcPlugin (class in nipype.pipeline.plugins.multiproc) MultiResolutionAffineRegistration (class in nipype.interfaces.slicer.legacy.registration) MySQLSink (class in nipype.interfaces.io)

N

N4BiasFieldCorrection (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.segmentation) N4ITKBiasFieldCorrection (class in nipype.interfaces.slicer.filtering.n4itkbiasfieldcorrection) n_procs (nipype.pipeline.engine.nodes.Node property) name (nipype.pipeline.engine.base.EngineBase property) name() (nipype.interfaces.spm.base.Info class method) needed_outputs (nipype.pipeline.engine.nodes.Node property) NeighborhoodMean (class in nipype.interfaces.semtools.filtering.featuredetection) NeighborhoodMedian (class in nipype.interfaces.semtools.filtering.featuredetection) NestedCell (class in nipype.interfaces.cat12.base) NetCorr (class in nipype.interfaces.afni.preprocess) NetworkBasedStatistic (class in nipype.interfaces.cmtk.nbs) NetworkXMetrics (class in nipype.interfaces.cmtk.nx) NewSegment (class in nipype.interfaces.spm.preprocess) NIfTIDT2Camino (class in nipype.interfaces.camino.convert) NiftiGeneratorBase (class in nipype.interfaces.dcmstack) NiftyFitCommand (class in nipype.interfaces.niftyfit.base) NiftyRegCommand (class in nipype.interfaces.niftyreg.base) NiftySegCommand (class in nipype.interfaces.niftyseg.base) NilearnBaseInterface (class in nipype.interfaces.nilearn) NipyBaseInterface (class in nipype.interfaces.nipy.base) nipype module nipype.algorithms module nipype.algorithms.confounds module nipype.algorithms.icc module nipype.algorithms.mesh module nipype.algorithms.metrics module nipype.algorithms.misc module nipype.algorithms.modelgen module nipype.algorithms.rapidart module nipype.algorithms.stats module nipype.caching module nipype.caching.memory module nipype.interfaces module nipype.interfaces.afni module nipype.interfaces.afni.base module nipype.interfaces.afni.model module nipype.interfaces.afni.preprocess module nipype.interfaces.afni.svm module nipype.interfaces.afni.utils module nipype.interfaces.ants module nipype.interfaces.ants.base module nipype.interfaces.ants.legacy module nipype.interfaces.ants.registration module nipype.interfaces.ants.resampling module nipype.interfaces.ants.segmentation module nipype.interfaces.ants.utils module nipype.interfaces.ants.visualization module nipype.interfaces.base module nipype.interfaces.base.core module nipype.interfaces.base.specs module nipype.interfaces.base.support module nipype.interfaces.base.traits_extension module nipype.interfaces.brainsuite module nipype.interfaces.brainsuite.brainsuite module nipype.interfaces.bru2nii module nipype.interfaces.c3 module nipype.interfaces.camino module nipype.interfaces.camino.calib module nipype.interfaces.camino.connectivity module nipype.interfaces.camino.convert module nipype.interfaces.camino.dti module nipype.interfaces.camino.odf module nipype.interfaces.camino.utils module nipype.interfaces.camino2trackvis module nipype.interfaces.camino2trackvis.convert module nipype.interfaces.cat12 module nipype.interfaces.cat12.base module nipype.interfaces.cat12.preprocess module nipype.interfaces.cat12.surface module nipype.interfaces.cmtk module nipype.interfaces.cmtk.base module nipype.interfaces.cmtk.cmtk module nipype.interfaces.cmtk.convert module nipype.interfaces.cmtk.nbs module nipype.interfaces.cmtk.nx module nipype.interfaces.cmtk.parcellation module nipype.interfaces.dcm2nii module nipype.interfaces.dcmstack module nipype.interfaces.diffusion_toolkit module nipype.interfaces.diffusion_toolkit.base module nipype.interfaces.diffusion_toolkit.dti module nipype.interfaces.diffusion_toolkit.odf module nipype.interfaces.diffusion_toolkit.postproc module nipype.interfaces.dipy module nipype.interfaces.dipy.anisotropic_power module nipype.interfaces.dipy.base module nipype.interfaces.dipy.preprocess module nipype.interfaces.dipy.reconstruction module nipype.interfaces.dipy.registration module nipype.interfaces.dipy.setup module nipype.interfaces.dipy.simulate module nipype.interfaces.dipy.stats module nipype.interfaces.dipy.tensors module nipype.interfaces.dipy.tracks module nipype.interfaces.dtitk module nipype.interfaces.dtitk.base module nipype.interfaces.dtitk.registration module nipype.interfaces.dtitk.utils module nipype.interfaces.dynamic_slicer module nipype.interfaces.elastix module nipype.interfaces.elastix.base module nipype.interfaces.elastix.registration module nipype.interfaces.elastix.utils module nipype.interfaces.freesurfer module nipype.interfaces.freesurfer.base module nipype.interfaces.freesurfer.longitudinal module nipype.interfaces.freesurfer.model module nipype.interfaces.freesurfer.petsurfer module nipype.interfaces.freesurfer.preprocess module nipype.interfaces.freesurfer.registration module nipype.interfaces.freesurfer.utils module nipype.interfaces.fsl module nipype.interfaces.fsl.aroma module nipype.interfaces.fsl.base module nipype.interfaces.fsl.dti module nipype.interfaces.fsl.epi module nipype.interfaces.fsl.fix module nipype.interfaces.fsl.maths module nipype.interfaces.fsl.model module nipype.interfaces.fsl.possum module nipype.interfaces.fsl.preprocess module nipype.interfaces.fsl.utils module nipype.interfaces.image module nipype.interfaces.io module nipype.interfaces.matlab module nipype.interfaces.meshfix module nipype.interfaces.minc module nipype.interfaces.minc.base module nipype.interfaces.minc.minc module nipype.interfaces.minc.testdata module nipype.interfaces.mipav module nipype.interfaces.mipav.developer module nipype.interfaces.mipav.generate_classes module nipype.interfaces.mixins module nipype.interfaces.mixins.fixheader module nipype.interfaces.mixins.reporting module nipype.interfaces.mne module nipype.interfaces.mne.base module nipype.interfaces.mrtrix module nipype.interfaces.mrtrix.convert module nipype.interfaces.mrtrix.preprocess module nipype.interfaces.mrtrix.tensors module nipype.interfaces.mrtrix.tracking module nipype.interfaces.mrtrix3 module nipype.interfaces.mrtrix3.base module nipype.interfaces.mrtrix3.connectivity module nipype.interfaces.mrtrix3.preprocess module nipype.interfaces.mrtrix3.reconst module nipype.interfaces.mrtrix3.tracking module nipype.interfaces.mrtrix3.utils module nipype.interfaces.niftyfit module nipype.interfaces.niftyfit.asl module nipype.interfaces.niftyfit.base module nipype.interfaces.niftyfit.dwi module nipype.interfaces.niftyfit.qt1 module nipype.interfaces.niftyreg module nipype.interfaces.niftyreg.base module nipype.interfaces.niftyreg.reg module nipype.interfaces.niftyreg.regutils module nipype.interfaces.niftyseg module nipype.interfaces.niftyseg.base module nipype.interfaces.niftyseg.em module nipype.interfaces.niftyseg.label_fusion module nipype.interfaces.niftyseg.lesions module nipype.interfaces.niftyseg.maths module nipype.interfaces.niftyseg.patchmatch module nipype.interfaces.niftyseg.stats module nipype.interfaces.nilearn module nipype.interfaces.nipy module nipype.interfaces.nipy.base module nipype.interfaces.nipy.model module nipype.interfaces.nipy.preprocess module nipype.interfaces.nipy.utils module nipype.interfaces.nitime module nipype.interfaces.nitime.analysis module nipype.interfaces.nitime.base module nipype.interfaces.petpvc module

nipype.interfaces.quickshear module nipype.interfaces.r module nipype.interfaces.robex module nipype.interfaces.robex.preprocess module nipype.interfaces.semtools module nipype.interfaces.semtools.brains module nipype.interfaces.semtools.brains.classify module nipype.interfaces.semtools.brains.segmentation module nipype.interfaces.semtools.brains.utilities module nipype.interfaces.semtools.converters module nipype.interfaces.semtools.diffusion module nipype.interfaces.semtools.diffusion.diffusion module nipype.interfaces.semtools.diffusion.gtract module nipype.interfaces.semtools.diffusion.maxcurvature module nipype.interfaces.semtools.diffusion.tractography module nipype.interfaces.semtools.diffusion.tractography.commandlineonly module nipype.interfaces.semtools.diffusion.tractography.fiberprocess module nipype.interfaces.semtools.diffusion.tractography.fibertrack module nipype.interfaces.semtools.diffusion.tractography.ukftractography module nipype.interfaces.semtools.featurecreator module nipype.interfaces.semtools.filtering module nipype.interfaces.semtools.filtering.denoising module nipype.interfaces.semtools.filtering.featuredetection module nipype.interfaces.semtools.legacy module nipype.interfaces.semtools.legacy.registration module nipype.interfaces.semtools.registration module nipype.interfaces.semtools.registration.brainsfit module nipype.interfaces.semtools.registration.brainsresample module nipype.interfaces.semtools.registration.brainsresize module nipype.interfaces.semtools.registration.specialized module nipype.interfaces.semtools.segmentation module nipype.interfaces.semtools.segmentation.specialized module nipype.interfaces.semtools.testing module nipype.interfaces.semtools.testing.featuredetection module nipype.interfaces.semtools.testing.generateaveragelmkfile module nipype.interfaces.semtools.testing.landmarkscompare module nipype.interfaces.semtools.utilities module nipype.interfaces.semtools.utilities.brains module nipype.interfaces.slicer module nipype.interfaces.slicer.base module nipype.interfaces.slicer.converters module nipype.interfaces.slicer.diffusion module nipype.interfaces.slicer.diffusion.diffusion module nipype.interfaces.slicer.filtering module nipype.interfaces.slicer.filtering.arithmetic module nipype.interfaces.slicer.filtering.checkerboardfilter module nipype.interfaces.slicer.filtering.denoising module nipype.interfaces.slicer.filtering.extractskeleton module nipype.interfaces.slicer.filtering.histogrammatching module nipype.interfaces.slicer.filtering.imagelabelcombine module nipype.interfaces.slicer.filtering.morphology module nipype.interfaces.slicer.filtering.n4itkbiasfieldcorrection module nipype.interfaces.slicer.filtering.resamplescalarvectordwivolume module nipype.interfaces.slicer.filtering.thresholdscalarvolume module nipype.interfaces.slicer.filtering.votingbinaryholefillingimagefilter module nipype.interfaces.slicer.generate_classes module nipype.interfaces.slicer.legacy module nipype.interfaces.slicer.legacy.converters module nipype.interfaces.slicer.legacy.diffusion module nipype.interfaces.slicer.legacy.diffusion.denoising module nipype.interfaces.slicer.legacy.filtering module nipype.interfaces.slicer.legacy.registration module nipype.interfaces.slicer.legacy.segmentation module nipype.interfaces.slicer.quantification module nipype.interfaces.slicer.quantification.changequantification module nipype.interfaces.slicer.quantification.petstandarduptakevaluecomputation module nipype.interfaces.slicer.registration module nipype.interfaces.slicer.registration.brainsfit module nipype.interfaces.slicer.registration.brainsresample module nipype.interfaces.slicer.registration.specialized module nipype.interfaces.slicer.segmentation module nipype.interfaces.slicer.segmentation.simpleregiongrowingsegmentation module nipype.interfaces.slicer.segmentation.specialized module nipype.interfaces.slicer.surface module nipype.interfaces.slicer.utilities module nipype.interfaces.spm module nipype.interfaces.spm.base module nipype.interfaces.spm.model module nipype.interfaces.spm.preprocess module nipype.interfaces.spm.utils module nipype.interfaces.utility module nipype.interfaces.utility.base module nipype.interfaces.utility.csv module nipype.interfaces.utility.wrappers module nipype.interfaces.vista module nipype.interfaces.vista.vista module nipype.interfaces.vtkbase module nipype.interfaces.workbench module nipype.interfaces.workbench.base module nipype.interfaces.workbench.cifti module nipype.interfaces.workbench.metric module nipype.pipeline module nipype.pipeline.engine module nipype.pipeline.engine.base module nipype.pipeline.engine.nodes module nipype.pipeline.engine.utils module nipype.pipeline.engine.workflows module nipype.pipeline.plugins module nipype.pipeline.plugins.base module nipype.pipeline.plugins.condor module nipype.pipeline.plugins.dagman module nipype.pipeline.plugins.debug module nipype.pipeline.plugins.ipython module nipype.pipeline.plugins.legacymultiproc module nipype.pipeline.plugins.linear module nipype.pipeline.plugins.lsf module nipype.pipeline.plugins.multiproc module nipype.pipeline.plugins.oar module nipype.pipeline.plugins.pbs module nipype.pipeline.plugins.pbsgraph module nipype.pipeline.plugins.semaphore_singleton module nipype.pipeline.plugins.sge module nipype.pipeline.plugins.sgegraph module nipype.pipeline.plugins.slurm module nipype.pipeline.plugins.slurmgraph module nipype.pipeline.plugins.somaflow module nipype.pipeline.plugins.tools module nipype.sphinxext module nipype.sphinxext.apidoc module nipype.sphinxext.apidoc.docstring module nipype.sphinxext.documenter module nipype.sphinxext.gh module nipype.sphinxext.plot_workflow module nipype.utils module nipype.utils.config module nipype.utils.datetime module nipype.utils.docparse module nipype.utils.draw_gantt_chart module nipype.utils.filemanip module nipype.utils.functions module nipype.utils.gpu_count module nipype.utils.imagemanip module nipype.utils.logger module nipype.utils.matlabtools module nipype.utils.misc module nipype.utils.nipype2boutiques module nipype.utils.nipype_cmd module nipype.utils.onetime module nipype.utils.profiler module nipype.utils.provenance module nipype.utils.ram_estimator module nipype.utils.spm_docs module nipype.utils.subprocess module nipype.utils.tmpdirs module NipypeClassDocumenter (class in nipype.sphinxext.documenter) NipypeConfig (class in nipype.utils.config) NipypeDocstring (class in nipype.sphinxext.apidoc.docstring) NipypeInterfaceError NipypeTester (class in nipype) NitimeBaseInterface (class in nipype.interfaces.nitime.base) nlmeans_proxy() (in module nipype.interfaces.dipy.preprocess) NlpFit (class in nipype.interfaces.minc.minc) no_afni() (in module nipype.interfaces.afni.base) no_dipy() (in module nipype.interfaces.dipy.base) no_freesurfer() (in module nipype.interfaces.freesurfer.base) no_fsl() (in module nipype.interfaces.fsl.base) no_fsl_course_data() (in module nipype.interfaces.fsl.base) no_minc() (in module nipype.interfaces.minc.base) no_spm() (in module nipype.interfaces.spm.base) no_tvtk() (in module nipype.interfaces.vtkbase) no_vtk() (in module nipype.interfaces.vtkbase) Node (class in nipype.pipeline.engine.nodes) node_completed_status() (in module nipype.pipeline.plugins.sgegraph) (in module nipype.pipeline.plugins.slurmgraph) NodeExecutionError nodelist_runner() (in module nipype.pipeline.engine.utils) NonDaemonForkContext (class in nipype.pipeline.plugins.legacymultiproc) NonDaemonForkProcess (class in nipype.pipeline.plugins.legacymultiproc) NonDaemonForkServerContext (class in nipype.pipeline.plugins.legacymultiproc) NonDaemonForkServerProcess (class in nipype.pipeline.plugins.legacymultiproc) NonDaemonMixin (class in nipype.pipeline.plugins.legacymultiproc) NonDaemonPool (class in nipype.pipeline.plugins.legacymultiproc) NonDaemonSpawnContext (class in nipype.pipeline.plugins.legacymultiproc) NonDaemonSpawnProcess (class in nipype.pipeline.plugins.legacymultiproc) nonempty_minc_data() (in module nipype.interfaces.minc.testdata) NonSteadyStateDetector (class in nipype.algorithms.confounds) Norm (class in nipype.interfaces.minc.minc) Normalize (class in nipype.interfaces.freesurfer.preprocess) (class in nipype.interfaces.spm.preprocess) Normalize12 (class in nipype.interfaces.spm.preprocess) normalize_filenames() (nipype.interfaces.freesurfer.utils.MRIsCombine method) (nipype.interfaces.freesurfer.utils.MRIsExpand method) normalize_mc_params() (in module nipype.utils.misc) normalize_tpms() (in module nipype.algorithms.misc) NormalizeProbabilityMapSet (class in nipype.algorithms.misc) Notes (class in nipype.interfaces.afni.utils) ntwks_to_matrices() (in module nipype.interfaces.cmtk.nbs) num_subnodes() (nipype.pipeline.engine.nodes.MapNode method) num_threads (nipype.interfaces.afni.base.AFNICommand property) NwarpAdjust (class in nipype.interfaces.afni.utils) NwarpApply (class in nipype.interfaces.afni.utils) NwarpCat (class in nipype.interfaces.afni.utils)

O

OARPlugin (class in nipype.pipeline.plugins.oar) ODFRecon (class in nipype.interfaces.diffusion_toolkit.odf) ODFTracker (class in nipype.interfaces.diffusion_toolkit.odf) on_cifs() (in module nipype.utils.filemanip) OneDToolPy (class in nipype.interfaces.afni.utils) OneSampleTTest (class in nipype.interfaces.freesurfer.model) OneSampleTTestDesign (class in nipype.interfaces.spm.model) OneTimeProperty (class in nipype.utils.onetime) option_spec (nipype.sphinxext.plot_workflow.WorkflowDirective attribute) optional_arguments (nipype.sphinxext.plot_workflow.WorkflowDirective attribute) OrientScalarVolume (class in nipype.interfaces.slicer.converters) orth() (in module nipype.algorithms.modelgen) OtsuThresholdImageFilter (class in nipype.interfaces.slicer.legacy.filtering) OtsuThresholdSegmentation (class in nipype.interfaces.slicer.legacy.segmentation) out_of_date() (in module nipype.sphinxext.plot_workflow) OutlierCount (class in nipype.interfaces.afni.preprocess) output_dir() (nipype.pipeline.engine.nodes.Node method) output_spec (nipype.interfaces.base.core.Interface attribute) (nipype.interfaces.dcmstack.LookupMeta attribute) (nipype.interfaces.dynamic_slicer.SlicerCommandLine attribute) (nipype.interfaces.io.BIDSDataGrabber attribute) (nipype.interfaces.io.DataFinder attribute) (nipype.interfaces.io.DataGrabber attribute) (nipype.interfaces.io.JSONFileGrabber attribute) (nipype.interfaces.io.S3DataGrabber attribute) (nipype.interfaces.io.SelectFiles attribute) (nipype.interfaces.io.SSHDataGrabber attribute) (nipype.interfaces.io.XNATSource attribute) (nipype.interfaces.utility.base.IdentityInterface attribute) (nipype.interfaces.utility.base.Split attribute) (nipype.interfaces.utility.csv.CSVReader attribute) (nipype.interfaces.utility.wrappers.Function attribute)

output_type() (nipype.interfaces.fsl.base.Info class method) output_type_to_ext() (nipype.interfaces.afni.base.Info class method) (nipype.interfaces.fsl.base.Info class method) OutputMultiObject (class in nipype.interfaces.base.traits_extension) OutputMultiPath (in module nipype.interfaces.base.traits_extension) outputs (nipype.pipeline.engine.base.EngineBase property) (nipype.pipeline.engine.nodes.MapNode property) (nipype.pipeline.engine.nodes.Node property) (nipype.pipeline.engine.workflows.Workflow property) outputtype() (nipype.interfaces.afni.base.Info class method) Overlap (class in nipype.algorithms.metrics) (class in nipype.algorithms.misc) Overlay (class in nipype.interfaces.fsl.utils)

P

P2PDistance (class in nipype.algorithms.mesh) package_check() (in module nipype.utils.misc) package_version (nipype.interfaces.base.specs.BaseTraitedSpec attribute) PackageInfo (class in nipype.interfaces.base.core) Paint (class in nipype.interfaces.freesurfer.registration) PairedTTestDesign (class in nipype.interfaces.spm.model) Parcellate (class in nipype.interfaces.cmtk.parcellation) ParcellationStats (class in nipype.interfaces.freesurfer.utils) parse_params() (in module nipype.interfaces.slicer.generate_classes) parse_values() (in module nipype.interfaces.slicer.generate_classes) parse_version() (nipype.interfaces.afni.base.Info static method) (nipype.interfaces.ants.base.Info static method) (nipype.interfaces.base.core.PackageInfo static method) (nipype.interfaces.dcm2nii.Info static method) (nipype.interfaces.freesurfer.base.Info static method) (nipype.interfaces.fsl.base.Info static method) (nipype.interfaces.mrtrix3.base.Info static method) (nipype.interfaces.niftyreg.base.Info static method) (nipype.interfaces.workbench.base.Info static method) ParseDICOMDir (class in nipype.interfaces.freesurfer.preprocess) PatchMatch (class in nipype.interfaces.niftyseg.patchmatch) path() (nipype.interfaces.spm.base.Info class method) PBSGraphPlugin (class in nipype.pipeline.plugins.pbsgraph) PBSPlugin (class in nipype.pipeline.plugins.pbs) PercentileImage (class in nipype.interfaces.fsl.maths) PETPVC (class in nipype.interfaces.petpvc) PETStandardUptakeValueComputation (class in nipype.interfaces.slicer.quantification.petstandarduptakevaluecomputation) Pialmesh (class in nipype.interfaces.brainsuite.brainsuite) PickAtlas (class in nipype.algorithms.misc)

PicoPDFs (class in nipype.interfaces.camino.dti) Pik (class in nipype.interfaces.minc.minc) PipeFunc (class in nipype.caching.memory) plot_confound() (in module nipype.algorithms.confounds) PlotMotionParams (class in nipype.interfaces.fsl.utils) PlotTimeSeries (class in nipype.interfaces.fsl.utils) PluginBase (class in nipype.pipeline.plugins.base) PointsWarp (class in nipype.interfaces.elastix.registration) PowerSpectrum (class in nipype.interfaces.fsl.utils) PRELUDE (class in nipype.interfaces.fsl.preprocess) PrepareFieldmap (class in nipype.interfaces.fsl.epi) print_dictionary() (nipype.pipeline.plugins.sge.QstatSubstitute method) priority (nipype.sphinxext.documenter.NipypeClassDocumenter attribute) ProbabilisticSphericallyDeconvolutedStreamlineTrack (class in nipype.interfaces.mrtrix.tracking) ProbeVolumeWithModel (class in nipype.interfaces.slicer.surface) ProbTrackX (class in nipype.interfaces.fsl.dti) ProbTrackX2 (class in nipype.interfaces.fsl.dti) Process (nipype.pipeline.plugins.legacymultiproc.NonDaemonForkContext attribute) (nipype.pipeline.plugins.legacymultiproc.NonDaemonForkServerContext attribute) (nipype.pipeline.plugins.legacymultiproc.NonDaemonSpawnContext attribute) process_initializer() (in module nipype.pipeline.plugins.legacymultiproc) (in module nipype.pipeline.plugins.multiproc) ProcStreamlines (class in nipype.interfaces.camino.convert) ProgressPercentage (class in nipype.interfaces.io) ProjThresh (class in nipype.interfaces.fsl.dti) prov_encode() (in module nipype.utils.provenance) ProvStore (class in nipype.utils.provenance) push_file() (in module nipype.interfaces.io) push_provenance() (in module nipype.interfaces.io) Pvc (class in nipype.interfaces.brainsuite.brainsuite)

Q

QBallMX (class in nipype.interfaces.camino.odf) QJobInfo (class in nipype.pipeline.plugins.sge) QstatSubstitute (class in nipype.pipeline.plugins.sge) qsub_sanitize_job_name() (in module nipype.pipeline.plugins.sge)

QualityIndex (class in nipype.interfaces.afni.preprocess) Quickshear (class in nipype.interfaces.quickshear) quote_id() (in module nipype.interfaces.io) Qwarp (class in nipype.interfaces.afni.preprocess) QwarpPlusMinus (class in nipype.interfaces.afni.preprocess)

R

raise_exception() (nipype.interfaces.base.core.CommandLine method) RamEstimator (class in nipype.utils.ram_estimator) Randomise (class in nipype.interfaces.fsl.model) RandomVol (class in nipype.interfaces.mipav.developer) RCommand (class in nipype.interfaces.r) read() (nipype.utils.subprocess.Stream method) read_log() (in module nipype.caching.memory) read_mrtrix_header() (in module nipype.interfaces.mrtrix.convert) read_mrtrix_streamlines() (in module nipype.interfaces.mrtrix.convert) read_mrtrix_tracks() (in module nipype.interfaces.mrtrix.convert) read_stream() (in module nipype.utils.filemanip) read_unknown_ntwk() (in module nipype.interfaces.cmtk.nx) Realign (class in nipype.interfaces.spm.preprocess) RealignUnwarp (class in nipype.interfaces.spm.preprocess) rebase_path_traits() (in module nipype.interfaces.base.traits_extension) ReconAll (class in nipype.interfaces.freesurfer.preprocess) Refit (class in nipype.interfaces.afni.utils) RegAladin (class in nipype.interfaces.niftyreg.reg) RegAverage (class in nipype.interfaces.niftyreg.regutils) RegF3D (class in nipype.interfaces.niftyreg.reg) Register (class in nipype.interfaces.freesurfer.registration) RegisterAVItoTalairach (class in nipype.interfaces.freesurfer.registration) Registration (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.registration) (class in nipype.interfaces.elastix.registration) RegistrationSynQuick (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.registration) RegJacobian (class in nipype.interfaces.niftyreg.regutils) RegMeasure (class in nipype.interfaces.niftyreg.regutils) RegResample (class in nipype.interfaces.niftyreg.regutils) regress_poly() (in module nipype.algorithms.confounds) RegTools (class in nipype.interfaces.niftyreg.regutils) RegTransform (class in nipype.interfaces.niftyreg.regutils) ReHo (class in nipype.interfaces.afni.utils) RelabelHypointensities (class in nipype.interfaces.freesurfer.utils) relpath() (in module nipype.utils.filemanip) Remlfit (class in nipype.interfaces.afni.model) remove_all_edges() (in module nipype.interfaces.cmtk.nx) remove_coding() (in module nipype.sphinxext.plot_workflow) remove_identical_paths() (in module nipype.algorithms.misc) remove_nodes() (nipype.pipeline.engine.workflows.Workflow method) RemoveIntersection (class in nipype.interfaces.freesurfer.utils) RemoveNeck (class in nipype.interfaces.freesurfer.utils) Rename (class in nipype.interfaces.utility.base) RenameInputSpec (class in nipype.interfaces.utility.base) render_figures() (in module nipype.sphinxext.plot_workflow) reorder_cmd_line_args() (in module nipype.utils.nipype2boutiques) Reorient (class in nipype.interfaces.image) Reorient2Std (class in nipype.interfaces.fsl.utils) replace_opts() (in module nipype.utils.docparse) replaceext() (in module nipype.algorithms.misc) ReplaceFSwithFIRST (class in nipype.interfaces.mrtrix3.preprocess) report_crash() (in module nipype.pipeline.plugins.tools) report_nodes_not_run() (in module nipype.pipeline.plugins.tools) ReportCapableInterface (class in nipype.interfaces.mixins.reporting) required_arguments (nipype.sphinxext.plot_workflow.WorkflowDirective attribute) Resample (class in nipype.interfaces.afni.utils) (class in nipype.interfaces.dipy.preprocess) (class in nipype.interfaces.freesurfer.preprocess) (class in nipype.interfaces.minc.minc) resample_proxy() (in module nipype.interfaces.dipy.preprocess) ResampleDTIVolume (class in nipype.interfaces.slicer.diffusion.diffusion) ResampleImageBySpacing (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.utils)

ResampleScalarVectorDWIVolume (class in nipype.interfaces.slicer.filtering.resamplescalarvectordwivolume) ResampleScalarVolume (class in nipype.interfaces.slicer.legacy.filtering) Rescale (class in nipype.interfaces.image) Reshape (class in nipype.interfaces.minc.minc) Reslice (class in nipype.interfaces.spm.utils) ResliceToReference (class in nipype.interfaces.spm.utils) resolve (nipype.interfaces.base.traits_extension.BasePath attribute) resolve_path_traits() (in module nipype.interfaces.base.traits_extension) resource_monitor (nipype.interfaces.base.core.BaseInterface attribute) (nipype.utils.config.NipypeConfig property) ResourceMonitor (class in nipype.utils.profiler) ResourceMonitorMock (class in nipype.utils.profiler) ResponseSD (class in nipype.interfaces.mrtrix3.preprocess) RESTORE (class in nipype.interfaces.dipy.reconstruction) result (nipype.pipeline.engine.nodes.Node property) Retroicor (class in nipype.interfaces.afni.preprocess) reverse_opt_map() (in module nipype.utils.docparse) rgetcwd() (in module nipype.utils.misc) Rigid (class in nipype.interfaces.dtitk.registration) RigidRegistration (class in nipype.interfaces.slicer.legacy.registration) RigidTask (class in nipype.interfaces.dtitk.registration) rm_all_but() (in module nipype.caching.memory) RobexSegment (class in nipype.interfaces.robex.preprocess) RobustFOV (class in nipype.interfaces.fsl.utils) RobustRegister (class in nipype.interfaces.freesurfer.preprocess) RobustStatisticsSegmenter (class in nipype.interfaces.slicer.segmentation.specialized) RobustTemplate (class in nipype.interfaces.freesurfer.longitudinal) ROIGen (class in nipype.interfaces.cmtk.cmtk) ROIStats (class in nipype.interfaces.afni.preprocess) run() (nipype.interfaces.base.core.BaseInterface method) (nipype.interfaces.base.core.Interface method) (nipype.interfaces.freesurfer.base.FSCommand method) (nipype.interfaces.freesurfer.base.FSCommandOpenMP method) (nipype.interfaces.freesurfer.model.Label2Annot method) (nipype.interfaces.freesurfer.model.Label2Label method) (nipype.interfaces.freesurfer.model.MRISPreprocReconAll method) (nipype.interfaces.freesurfer.model.SegStatsReconAll method) (nipype.interfaces.freesurfer.preprocess.MRIsCALabel method) (nipype.interfaces.freesurfer.preprocess.SegmentCC method) (nipype.interfaces.freesurfer.utils.Aparc2Aseg method) (nipype.interfaces.freesurfer.utils.Contrast method) (nipype.interfaces.freesurfer.utils.CurvatureStats method) (nipype.interfaces.freesurfer.utils.FixTopology method) (nipype.interfaces.freesurfer.utils.MakeSurfaces method) (nipype.interfaces.freesurfer.utils.ParcellationStats method) (nipype.interfaces.freesurfer.utils.VolumeMask method) (nipype.pipeline.engine.nodes.Node method) (nipype.pipeline.engine.workflows.Workflow method) (nipype.pipeline.plugins.base.DistributedPluginBase method) (nipype.pipeline.plugins.base.GraphPluginBase method) (nipype.pipeline.plugins.base.PluginBase method) (nipype.pipeline.plugins.debug.DebugPlugin method) (nipype.pipeline.plugins.ipython.IPythonPlugin method) (nipype.pipeline.plugins.linear.LinearPlugin method) (nipype.sphinxext.plot_workflow.WorkflowDirective method) (nipype.utils.profiler.ResourceMonitor method) run_code() (in module nipype.sphinxext.plot_workflow) run_command() (in module nipype.utils.subprocess) run_instance() (in module nipype.utils.nipype_cmd) run_node() (in module nipype.pipeline.plugins.legacymultiproc) (in module nipype.pipeline.plugins.multiproc) runtime (nipype.interfaces.base.support.RuntimeContext property) RuntimeContext (class in nipype.interfaces.base.support)

S

S3DataGrabber (class in nipype.interfaces.io) s3tolocal() (nipype.interfaces.io.S3DataGrabber method) safe_encode() (in module nipype.utils.provenance) SampleToSurface (class in nipype.interfaces.freesurfer.utils) sanitize_path_comp() (in module nipype.interfaces.dcmstack) save() (nipype.pipeline.engine.base.EngineBase method) save_data() (nipype.utils.config.NipypeConfig method) save_fibers() (in module nipype.interfaces.cmtk.cmtk) save_hashfile() (in module nipype.pipeline.engine.utils) save_inputs_to_json() (nipype.interfaces.base.core.BaseInterface method) save_json() (in module nipype.utils.filemanip) save_resultfile() (in module nipype.pipeline.engine.utils) savepkl() (in module nipype.utils.filemanip) scalartransform (class in nipype.interfaces.semtools.legacy.registration) scale_timings() (in module nipype.algorithms.modelgen) scans_for_fname() (in module nipype.interfaces.spm.base) scans_for_fnames() (in module nipype.interfaces.spm.base) Scrubmask (class in nipype.interfaces.brainsuite.brainsuite) search_files() (in module nipype.interfaces.dcm2nii) Seg (class in nipype.interfaces.afni.preprocess) Segment (class in nipype.interfaces.spm.preprocess) SegmentCC (class in nipype.interfaces.freesurfer.preprocess) SegmentWM (class in nipype.interfaces.freesurfer.preprocess) SegStats (class in nipype.interfaces.freesurfer.model) SegStatsReconAll (class in nipype.interfaces.freesurfer.model) Select (class in nipype.interfaces.utility.base) SelectFiles (class in nipype.interfaces.io) SEMLikeCommandLine (class in nipype.interfaces.base.core) set() (nipype.interfaces.base.support.Bunch method) (nipype.interfaces.base.traits_extension.OutputMultiObject method) (nipype.utils.config.NipypeConfig method) set_default_config() (nipype.utils.config.NipypeConfig method) set_default_matlab_cmd() (nipype.interfaces.matlab.MatlabCommand class method) set_default_mfile() (nipype.interfaces.matlab.MatlabCommand class method) set_default_num_threads() (nipype.interfaces.ants.base.ANTSCommand class method) set_default_output_type() (nipype.interfaces.afni.base.AFNICommand class method) (nipype.interfaces.fsl.base.FSLCommand class method) set_default_paths() (nipype.interfaces.matlab.MatlabCommand class method) set_default_r_cmd() (nipype.interfaces.r.RCommand method) set_default_rfile() (nipype.interfaces.r.RCommand method) set_default_subjects_dir() (nipype.interfaces.freesurfer.base.FSCommand class method) set_default_terminal_output() (nipype.interfaces.base.core.CommandLine class method) set_input() (nipype.pipeline.engine.nodes.MapNode method) (nipype.pipeline.engine.nodes.Node method) set_log_dir() (nipype.utils.config.NipypeConfig method) set_mlab_paths() (nipype.interfaces.spm.base.SPMCommand class method) set_state() (nipype.pipeline.plugins.sge.QJobInfo method) setattr_on_read() (in module nipype.utils.onetime) setup() (in module nipype.sphinxext.apidoc) (in module nipype.sphinxext.documenter) (in module nipype.sphinxext.plot_workflow) SFLUTGen (class in nipype.interfaces.camino.calib) SFPeaks (class in nipype.interfaces.camino.odf) SFPICOCalibData (class in nipype.interfaces.camino.calib) sge_debug_print() (in module nipype.pipeline.plugins.sge) SGEGraphPlugin (class in nipype.pipeline.plugins.sgegraph) SGELikeBatchManagerBase (class in nipype.pipeline.plugins.base) SGEPlugin (class in nipype.pipeline.plugins.sge) SH2Amp (class in nipype.interfaces.mrtrix3.utils) SHConv (class in nipype.interfaces.mrtrix3.utils) Shredder (class in nipype.interfaces.camino.convert) ShuffleVectorsModule (class in nipype.interfaces.semtools.utilities.brains) SigLoss (class in nipype.interfaces.fsl.epi) (class in nipype.interfaces.fsl.utils) SignalExtraction (class in nipype.interfaces.nilearn) silentrm() (in module nipype.utils.filemanip) Similarity (class in nipype.algorithms.metrics) (class in nipype.interfaces.nipy.utils) SimilarityIndex (class in nipype.interfaces.semtools.brains.segmentation) SimpleInterface (class in nipype.interfaces.base.core) SimpleRegionGrowingSegmentation (class in nipype.interfaces.slicer.segmentation.simpleregiongrowingsegmentation) SimpleThreshold (class in nipype.algorithms.misc) simplify_list() (in module nipype.utils.filemanip)

SimulateMultiTensor (class in nipype.interfaces.dipy.simulate) Skullfinder (class in nipype.interfaces.brainsuite.brainsuite) SkullStrip (class in nipype.interfaces.afni.preprocess) Slice (class in nipype.interfaces.fsl.utils) Slicer (class in nipype.interfaces.fsl.utils) SlicerCommandLine (class in nipype.interfaces.dynamic_slicer) (class in nipype.interfaces.slicer.base) SliceTimer (class in nipype.interfaces.fsl.preprocess) SliceTiming (class in nipype.interfaces.spm.preprocess) SLURMGraphPlugin (class in nipype.pipeline.plugins.slurmgraph) SLURMPlugin (class in nipype.pipeline.plugins.slurm) SMM (class in nipype.interfaces.fsl.model) Smooth (class in nipype.interfaces.freesurfer.preprocess) (class in nipype.interfaces.fsl.utils) (class in nipype.interfaces.spm.preprocess) SmoothEstimate (class in nipype.interfaces.fsl.model) SmoothTessellation (class in nipype.interfaces.freesurfer.utils) SomaFlowPlugin (class in nipype.pipeline.plugins.somaflow) SpaceTimeRealigner (class in nipype.interfaces.nipy.preprocess) SpatialFilter (class in nipype.interfaces.fsl.maths) SpecifyModel (class in nipype.algorithms.modelgen) SpecifySparseModel (class in nipype.algorithms.modelgen) SpecifySPMModel (class in nipype.algorithms.modelgen) Sphere (class in nipype.interfaces.freesurfer.utils) SphericalAverage (class in nipype.interfaces.freesurfer.model) SphericalCoordinateGeneration (class in nipype.interfaces.semtools.testing.featuredetection) SphericallyDeconvolutedStreamlineTrack (class in nipype.interfaces.mrtrix.tracking) SplineFilter (class in nipype.interfaces.diffusion_toolkit.postproc) Split (class in nipype.interfaces.fsl.utils) (class in nipype.interfaces.utility.base) split_filename() (in module nipype.utils.filemanip) split_rois() (in module nipype.algorithms.misc) SplitNifti (class in nipype.interfaces.dcmstack) SplitROIs (class in nipype.algorithms.misc) spm_hrf() (in module nipype.algorithms.modelgen) SPMCommand (class in nipype.interfaces.spm.base) SQLiteSink (class in nipype.interfaces.io) SSHDataGrabber (class in nipype.interfaces.io) standard_image() (nipype.interfaces.afni.base.Info static method) (nipype.interfaces.fsl.base.Info static method) STAPLEAnalysis (class in nipype.interfaces.semtools.filtering.featuredetection) start() (nipype.utils.profiler.ResourceMonitorMock method) StatsCommand (class in nipype.interfaces.niftyseg.stats) StdImage (class in nipype.interfaces.fsl.maths) StdOutCommandLine (class in nipype.interfaces.base.core) StimulusCorrelation (class in nipype.algorithms.rapidart) stop() (nipype.utils.profiler.ResourceMonitor method) (nipype.utils.profiler.ResourceMonitorMock method) stop_display() (nipype.utils.config.NipypeConfig method) Str (class in nipype.interfaces.base.traits_extension) str2bool() (in module nipype.utils.misc) Stream (class in nipype.utils.subprocess) StreamlineTrack (class in nipype.interfaces.mrtrix.tracking) StreamlineTractography (class in nipype.interfaces.dipy.tracks) strip_temp() (in module nipype.pipeline.engine.utils) subjectsdir() (nipype.interfaces.freesurfer.base.Info class method) SubtractScalarVolumes (class in nipype.interfaces.slicer.filtering.arithmetic) Surface2VolTransform (class in nipype.interfaces.freesurfer.utils) SurfaceSmooth (class in nipype.interfaces.freesurfer.utils) SurfaceSnapshots (class in nipype.interfaces.freesurfer.utils) SurfaceTransform (class in nipype.interfaces.freesurfer.utils) SUSAN (class in nipype.interfaces.fsl.preprocess) SVAdjustVoxSp (class in nipype.interfaces.dtitk.utils) SVAdjustVoxSpTask (class in nipype.interfaces.dtitk.utils) SVMTest (class in nipype.interfaces.afni.svm) SVMTrain (class in nipype.interfaces.afni.svm) SVReg (class in nipype.interfaces.brainsuite.brainsuite) SVResample (class in nipype.interfaces.dtitk.utils) SVResampleTask (class in nipype.interfaces.dtitk.utils) SwapDimensions (class in nipype.interfaces.fsl.utils) synchronize_iterables() (in module nipype.pipeline.engine.utils) Synthesize (class in nipype.interfaces.afni.model) SynthesizeFLASH (class in nipype.interfaces.freesurfer.preprocess)

T

TalairachAVI (class in nipype.interfaces.freesurfer.utils) TalairachQC (class in nipype.interfaces.freesurfer.utils) Tca (class in nipype.interfaces.brainsuite.brainsuite) TCat (class in nipype.interfaces.afni.utils) TCatSubBrick (class in nipype.interfaces.afni.utils) TCK2VTK (class in nipype.interfaces.mrtrix3.utils) TCompCor (class in nipype.algorithms.confounds) TCorr1D (class in nipype.interfaces.afni.preprocess) TCorrelate (class in nipype.interfaces.afni.preprocess) TCorrMap (class in nipype.interfaces.afni.preprocess) TemporalFilter (class in nipype.interfaces.fsl.maths) TemporaryDirectory (class in nipype.utils.tmpdirs) Tensor2ApparentDiffusion (class in nipype.interfaces.mrtrix.preprocess) Tensor2FractionalAnisotropy (class in nipype.interfaces.mrtrix.preprocess) Tensor2Vector (class in nipype.interfaces.mrtrix.preprocess) TensorMetrics (class in nipype.interfaces.mrtrix3.utils) TensorMode (class in nipype.interfaces.dipy.tensors) terminal_output (nipype.interfaces.base.core.CommandLine property) Text2Vest (class in nipype.interfaces.fsl.utils) TextureFromNoiseImageFilter (class in nipype.interfaces.semtools.filtering.featuredetection) TextureMeasureFilter (class in nipype.interfaces.semtools.filtering.featuredetection) ThicknessPVC (class in nipype.interfaces.brainsuite.brainsuite) Threshold (class in nipype.interfaces.fsl.maths) (class in nipype.interfaces.mrtrix.preprocess) (class in nipype.interfaces.spm.model) ThresholdImage (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.utils) ThresholdScalarVolume (class in nipype.interfaces.slicer.filtering.thresholdscalarvolume) ThresholdStatistics (class in nipype.interfaces.spm.model) Tkregister2 (class in nipype.interfaces.freesurfer.utils) TNorm (class in nipype.interfaces.afni.preprocess) To3D (class in nipype.interfaces.afni.utils) to_string() (nipype.interfaces.cat12.base.Cell method) ToEcat (class in nipype.interfaces.minc.minc) topological_sort() (in module nipype.pipeline.engine.utils) TOPUP (class in nipype.interfaces.fsl.epi) ToRaw (class in nipype.interfaces.minc.minc) TProject (class in nipype.interfaces.afni.preprocess)

Track (class in nipype.interfaces.camino.dti) TrackBallStick (class in nipype.interfaces.camino.dti) TrackBayesDirac (class in nipype.interfaces.camino.dti) TrackBedpostxDeter (class in nipype.interfaces.camino.dti) TrackBedpostxProba (class in nipype.interfaces.camino.dti) TrackBootstrap (class in nipype.interfaces.camino.dti) TrackDensityMap (class in nipype.interfaces.dipy.tracks) TrackDT (class in nipype.interfaces.camino.dti) TrackMerge (class in nipype.interfaces.diffusion_toolkit.postproc) TrackPICo (class in nipype.interfaces.camino.dti) Tracks2Prob (class in nipype.interfaces.mrtrix.tracking) Trackvis2Camino (class in nipype.interfaces.camino2trackvis.convert) Tractography (class in nipype.interfaces.mrtrix3.tracking) TractographyLabelMapSeeding (class in nipype.interfaces.slicer.diffusion.diffusion) TractShredder (class in nipype.interfaces.camino.convert) TractSkeleton (class in nipype.interfaces.fsl.dti) Training (class in nipype.interfaces.fsl.fix) TrainingSetCreator (class in nipype.interfaces.fsl.fix) trait_get() (nipype.interfaces.base.specs.BaseTraitedSpec method) transform_to_affine() (in module nipype.interfaces.mrtrix.convert) TransformFSLConvert (class in nipype.interfaces.mrtrix3.utils) Trim (class in nipype.interfaces.nipy.preprocess) trim() (in module nipype.utils.misc) TShift (class in nipype.interfaces.afni.preprocess) TSmooth (class in nipype.interfaces.afni.preprocess) TSNR (class in nipype.algorithms.confounds) (class in nipype.algorithms.misc) TStat (class in nipype.interfaces.afni.utils) Tuple (class in nipype.interfaces.base.traits_extension) TupleMaths (class in nipype.interfaces.niftyseg.maths) TVAdjustOriginTask (class in nipype.interfaces.dtitk.utils) TVAdjustVoxSp (class in nipype.interfaces.dtitk.utils) TVAdjustVoxSpTask (class in nipype.interfaces.dtitk.utils) TVResample (class in nipype.interfaces.dtitk.utils) TVResampleTask (class in nipype.interfaces.dtitk.utils) TVTKBaseInterface (class in nipype.algorithms.mesh) TVtool (class in nipype.interfaces.dtitk.utils) TVtoolTask (class in nipype.interfaces.dtitk.utils) TwoSampleTTestDesign (class in nipype.interfaces.spm.model)

U

UKFTractography (class in nipype.interfaces.semtools.diffusion.tractography.ukftractography) UnaryMaths (class in nipype.interfaces.fsl.maths) (class in nipype.interfaces.niftyseg.maths) UnaryStats (class in nipype.interfaces.niftyseg.stats) UnbiasedNonLocalMeans (class in nipype.interfaces.semtools.filtering.denoising) Undump (class in nipype.interfaces.afni.utils) unescape_doctest() (in module nipype.sphinxext.plot_workflow) unflatten() (in module nipype.utils.misc) Unifize (class in nipype.interfaces.afni.utils)

UnpackSDICOMDir (class in nipype.interfaces.freesurfer.preprocess) unquote_id() (in module nipype.interfaces.io) update() (nipype.interfaces.base.support.Bunch method) (nipype.pipeline.engine.nodes.Node method) update_config() (nipype.utils.config.NipypeConfig method) update_info() (nipype.pipeline.plugins.sge.QJobInfo method) update_logging() (nipype.utils.logger.Logging method) update_matplotlib() (nipype.utils.config.NipypeConfig method) utcnow() (in module nipype.utils.datetime)

V

validate() (nipype.interfaces.base.traits_extension.BasePath method) (nipype.interfaces.base.traits_extension.File method) (nipype.interfaces.base.traits_extension.MultiObject method) (nipype.interfaces.base.traits_extension.Tuple method) VBMSegment (class in nipype.interfaces.spm.preprocess) VBRAINSDemonWarp (class in nipype.interfaces.semtools.registration.specialized) (class in nipype.interfaces.slicer.registration.specialized) VecReg (class in nipype.interfaces.fsl.dti) version (nipype.interfaces.ants.base.ANTSCommand property) (nipype.interfaces.base.core.BaseInterface property) (nipype.interfaces.base.core.Interface property) (nipype.interfaces.base.core.LibraryBaseInterface property) (nipype.interfaces.base.support.InterfaceResult property) (nipype.interfaces.dcm2nii.Dcm2niix property) (nipype.interfaces.freesurfer.base.FSCommand property) (nipype.interfaces.freesurfer.preprocess.ReconAll property) (nipype.interfaces.fsl.base.FSLCommand property) (nipype.interfaces.mrtrix3.base.MRTrix3Base property) (nipype.interfaces.niftyreg.base.NiftyRegCommand property) (nipype.interfaces.spm.base.SPMCommand property) (nipype.interfaces.workbench.base.WBCommand property) version() (nipype.interfaces.base.core.PackageInfo class method) (nipype.interfaces.diffusion_toolkit.base.Info static method) (nipype.interfaces.minc.base.Info static method) (nipype.interfaces.spm.base.Info class method)

version_cmd (nipype.interfaces.afni.base.Info attribute) (nipype.interfaces.ants.base.Info attribute) (nipype.interfaces.base.core.PackageInfo attribute) (nipype.interfaces.dcm2nii.Info attribute) (nipype.interfaces.mrtrix3.base.Info attribute) (nipype.interfaces.niftyreg.base.Info attribute) (nipype.interfaces.workbench.base.Info attribute) version_file (nipype.interfaces.base.core.PackageInfo attribute) version_from_command() (nipype.interfaces.base.core.CommandLine method) Vest2Text (class in nipype.interfaces.fsl.utils) Vnifti2Image (class in nipype.interfaces.vista.vista) Volcentre (class in nipype.interfaces.minc.minc) Voliso (class in nipype.interfaces.minc.minc) Volpad (class in nipype.interfaces.minc.minc) Volreg (class in nipype.interfaces.afni.preprocess) VolSymm (class in nipype.interfaces.minc.minc) VolumeMask (class in nipype.interfaces.freesurfer.utils) VotingBinaryHoleFillingImageFilter (class in nipype.interfaces.slicer.filtering.votingbinaryholefillingimagefilter) voxels() (nipype.utils.ram_estimator.RamEstimator static method) vtk_old() (in module nipype.interfaces.vtkbase) vtk_output() (in module nipype.interfaces.vtkbase) vtk_version() (in module nipype.interfaces.vtkbase) VtkStreamlines (class in nipype.interfaces.camino.convert) VtoMat (class in nipype.interfaces.vista.vista)

W

walk() (in module nipype.pipeline.engine.utils) walk_files() (in module nipype.pipeline.engine.utils) walk_outputs() (in module nipype.pipeline.engine.utils) Warp (class in nipype.interfaces.afni.preprocess) WarpImageMultiTransform (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.resampling) WarpPoints (class in nipype.algorithms.mesh) (class in nipype.interfaces.fsl.utils) WarpPointsFromStd (class in nipype.interfaces.fsl.utils) WarpPointsToStd (class in nipype.interfaces.fsl.utils) WarpTimeSeriesImageMultiTransform (class in nipype.interfaces.ants) (class in nipype.interfaces.ants.resampling) WarpUtils (class in nipype.interfaces.fsl.utils) WatershedBEM (class in nipype.interfaces.mne.base) WatershedSkullStrip (class in nipype.interfaces.freesurfer.preprocess) WBCommand (class in nipype.interfaces.workbench.base)

which() (in module nipype.utils.filemanip) Workflow (class in nipype.pipeline.engine.workflows) WorkflowDirective (class in nipype.sphinxext.plot_workflow) write_cmdline (nipype.interfaces.base.core.CommandLine property) write_config() (nipype.interfaces.fsl.preprocess.FNIRT method) write_graph() (nipype.pipeline.engine.workflows.Workflow method) write_hierarchical_dotfile() (nipype.pipeline.engine.workflows.Workflow method) write_node_report() (in module nipype.pipeline.engine.utils) write_provenance() (in module nipype.utils.provenance) (nipype.utils.provenance.ProvStore method) write_report() (in module nipype.pipeline.engine.utils) write_rst_dict() (in module nipype.utils.filemanip) write_rst_header() (in module nipype.utils.filemanip) write_rst_list() (in module nipype.utils.filemanip) write_workflow_prov() (in module nipype.pipeline.engine.utils) write_workflow_resources() (in module nipype.pipeline.engine.utils)

X

XFibres (in module nipype.interfaces.fsl.dti) XFibres5 (class in nipype.interfaces.fsl.dti) XfmAvg (class in nipype.interfaces.minc.minc)

XfmConcat (class in nipype.interfaces.minc.minc) XfmInvert (class in nipype.interfaces.minc.minc) XNATSink (class in nipype.interfaces.io) XNATSource (class in nipype.interfaces.io)

Z

Zcat (class in nipype.interfaces.afni.utils)

ZCutUp (class in nipype.interfaces.afni.utils) Zeropad (class in nipype.interfaces.afni.utils)