Index

_

__init__() (nipype.caching.memory.Memory method) (nipype.caching.memory.PipeFunc method) (nipype.interfaces.matlab.MatlabCommand method) (nipype.interfaces.matlab.MatlabInputSpec method) (nipype.pipeline.engine.base.EngineBase method) (nipype.pipeline.engine.nodes.JoinNode method) (nipype.pipeline.engine.nodes.MapNode method) (nipype.pipeline.engine.nodes.Node method) (nipype.pipeline.engine.workflows.Workflow method) (nipype.sphinxext.plot_workflow.GraphError method) (nipype.sphinxext.plot_workflow.ImageFile method)

A

ABoverlap ACompCor ACPCTransform ActivationCount add_class_trait() (nipype.interfaces.matlab.MatlabInputSpec class method) add_nodes() (nipype.pipeline.engine.workflows.Workflow method) add_np() (in module nipype.conftest) add_trait() (nipype.interfaces.matlab.MatlabInputSpec method) add_trait_category() (nipype.interfaces.matlab.MatlabInputSpec class method) add_trait_listener() (nipype.interfaces.matlab.MatlabInputSpec method) AddCSVColumn AddCSVRow AddNoise AddScalarVolumes AddXFormToHeader Affine AffineInitializer AffineRegistration AffineTask AffScalarVol affScalarVolTask AffSymTensor3DVol affSymTensor3DVolTask AFNIPythonCommand AFNItoNIFTI aggregate_outputs() (nipype.interfaces.matlab.MatlabCommand method) AlignEpiAnatPy all_trait_names() (nipype.interfaces.matlab.MatlabInputSpec method) Allineate always_run (nipype.interfaces.matlab.MatlabCommand attribute) Analyze2nii

AnalyzeHeader AnalyzeWarp antsIntroduction AntsJointFusion Aparc2Aseg Apas2Aseg APMQball ApplyDeformations ApplyInverseDeformation ApplyMask, [1] ApplyTOPUP ApplyTransform ApplyTransforms ApplyTransformsToPoints ApplyVolTransform ApplyWarp, [1] ApplyXFM AR1Image args (nipype.sphinxext.plot_workflow.GraphError attribute) ArtifactDetect AssertEqual Atropos Autobox Automask AutoTcorrelate AutoTLRC Average AverageAffineTransform AverageImages AverageNetworks AvScale Axialize

B

B0Calc Bandpass base_trait() (nipype.interfaces.matlab.MatlabInputSpec method) BaseInterface BBox BBRegister BDP Beast BEDPOSTX5 BestLinReg BET Bfc BIDSDataGrabber BigAverage Binarize BinaryMaskEditorBasedOnLandmarks BinaryMaths, [1] BinaryMathsInteger BinaryStats BinThresh BinThreshTask Blob Blur BlurInMask BlurToFWHM BrainExtraction BrainMask BRAINSABC BRAINSAlignMSP BRAINSClipInferior

BRAINSConstellationDetector BRAINSConstellationModeler BRAINSCreateLabelMapFromProbabilityMaps BRAINSCut BRAINSDemonWarp, [1] BRAINSEyeDetector BRAINSFit, [1] BRAINSInitializedControlPoints BRAINSLandmarkInitializer BRAINSLinearModelerEPCA BRAINSLmkTransform BRAINSMultiSTAPLE BRAINSMush BRAINSPosteriorToContinuousClass BRAINSResample, [1] BRAINSResize BRAINSROIAuto, [1] BRAINSSnapShotWriter BRAINSTalairach BRAINSTalairachMask BRAINSTransformConvert BRAINSTransformFromFiducials BRAINSTrimForegroundInDirection BrickStat Bru2 Bse BSplineDeformableRegistration BSplineToDeformationField Bucket BuildConnectome buildtemplateparallel

C

C3d C3dAffineTool cache() (nipype.caching.memory.Memory method) CALabel Calc, [1] CalcCoregAffine CalcTopNCC CalculateMedian CalculateNormalizedMoments Camino2Trackvis can_resume (nipype.interfaces.matlab.MatlabCommand attribute) CannyEdge CannySegmentationLevelSetImageFilter CANormalize CARegister CastScalarVolume Cat CatMatvec CenterMass Cerebro CFFBaseInterface CFFConverter ChangeDataType CheckerBoardFilter CheckTalairachAlignment class_default_traits_view() (nipype.interfaces.matlab.MatlabInputSpec class method) class_editable_traits() (nipype.interfaces.matlab.MatlabInputSpec class method) class_trait_names() (nipype.interfaces.matlab.MatlabInputSpec class method) class_trait_view() (nipype.interfaces.matlab.MatlabInputSpec class method) class_trait_view_elements() (nipype.interfaces.matlab.MatlabInputSpec class method) class_traits() (nipype.interfaces.matlab.MatlabInputSpec class method) class_visible_traits() (nipype.interfaces.matlab.MatlabInputSpec class method) Classifier clean_working_directory() (in module nipype.pipeline.engine.utils) Cleaner CleanUpOverlapLabels clear_previous_runs() (nipype.caching.memory.Memory method) clear_runs_since() (nipype.caching.memory.Memory method) ClipLevel clone() (nipype.pipeline.engine.base.EngineBase method) (nipype.pipeline.engine.nodes.JoinNode method) (nipype.pipeline.engine.nodes.MapNode method) (nipype.pipeline.engine.nodes.Node method) (nipype.pipeline.engine.workflows.Workflow method) clone_traits() (nipype.interfaces.matlab.MatlabInputSpec method) Cluster cmd (nipype.interfaces.matlab.MatlabCommand attribute) cmdline (nipype.interfaces.matlab.MatlabCommand attribute) CoherenceAnalyzer

CommandLine CommandLineDtitk compareTractInclusion CompCor Complex ComposeMultiTransform ComposeXfm ComposeXfmTask ComputeDVARS ComputeEigensystem ComputeFractionalAnisotropy ComputeMask ComputeMeanDiffusivity ComputeMeshWarp ComputeTDI ComputeTensorTrace Concatenate ConcatenateLTA configure_traits() (nipype.interfaces.matlab.MatlabInputSpec method) Conmat connect() (nipype.pipeline.engine.workflows.Workflow method) ConstrainedSphericalDeconvolution contains_doctest() (in module nipype.sphinxext.plot_workflow) Contrast ContrastMgr Convert ConvertDset ConvertScalarImageToRGB ConvertWarp ConvertXFM Copy, [1] copy_traits() (nipype.interfaces.matlab.MatlabInputSpec method) copyable_trait_names() (nipype.interfaces.matlab.MatlabInputSpec method) CopyGeom CopyMeta Coregister Cortex CorticalThickness count_iterables() (in module nipype.pipeline.engine.utils) CreateJacobianDeterminantImage CreateMatrix CreateNifti CreateNodes CreateTiledMosaic CreateWarped CSD CSVReader Curvature CurvatureAnisotropicDiffusion CurvatureStats

D

DARTEL DARTELNorm2MNI DataFinder DataGrabber DataSink Dcm2nii Dcm2niix DcmStack Deconvolve default_traits_view() (nipype.interfaces.matlab.MatlabInputSpec method) DegreeCentrality Denoise DenoiseImage Despike Detrend Dewisp Dfs DICOMConvert DicomImport DicomToNrrdConverter Diffeo DiffeoScalarVol diffeoScalarVolTask DiffeoSymTensor3DVol diffeoSymTensor3DVolTask DiffeoTask DiffusionTensorScalarMeasurements DiffusionTensorStreamlineTrack DiffusionWeightedVolumeMasking DilateImage, [1] DilateMask DipyBaseInterface DipyDiffusionInterface

Directions2Amplitude disconnect() (nipype.pipeline.engine.workflows.Workflow method) Distance, [1] DistanceMap DistanceMaps Dot DT2NIfTI DTI dtiaverage dtiestim DTIexport DTIFit, [1] DTIimport dtiprocess DTIRecon DTITracker DTLUTGen DTMetric DualRegression Dump DumpBinaryTrainingVectors DWI2SphericalHarmonicsImage DWI2Tensor DWICompare DWIConvert DWIDenoise DWIExtract DWIJointRicianLMMSEFilter DWIRicianLMMSEFilter DWISimpleCompare DWIToDTIEstimation DwiTool DWIUnbiasedNonLocalMeansFilter

E

ECM Eddy EddyCorrect Edge3 edit_traits() (nipype.interfaces.matlab.MatlabInputSpec method) editable_traits() (nipype.interfaces.matlab.MatlabInputSpec method) EditTransform EditWMwithAseg EM EMRegister EMSegmentCommandLine EMSegmentTransformToNewFormat EngineBase (class in nipype.pipeline.engine.base) EPIDeWarp EpiReg Erode ErodeImage, [1] ErrorMap

ESLR EstimateContrast, [1] EstimateFOD EstimateModel EstimateResponseForSH EstimateResponseSH EulerNumber Eval evaluate_connect_function() (in module nipype.pipeline.engine.utils) expand_iterables() (in module nipype.pipeline.engine.utils) ExpertAutomatedRegistration export() (nipype.pipeline.engine.workflows.Workflow method) export_graph() (in module nipype.pipeline.engine.utils) Extract ExtractMainComponent extractNrrdVectorIndex ExtractROI ExtractSkeleton

F

FactorialDesign FAST fcsv_to_hdf5 FEAT FEATModel FEATRegister FeatureExtractor fiberprocess fiberstats fibertrack FiducialRegistration FieldMap filename() (nipype.sphinxext.plot_workflow.ImageFile method) filenames() (nipype.sphinxext.plot_workflow.ImageFile method) FillLesions FILMGLS FilterRegressor FilterTracks Fim FindCenterOfBrain FindShPeaks FindTheBiggest FIRST FitAsl

FitDwi FitGLM FitMSParams FitQt1 FitTensor FixTopology FLAMEO FlippedDifference FLIRT FNIRT format_dot() (in module nipype.pipeline.engine.utils) format_node() (in module nipype.pipeline.engine.utils) Fourier FramewiseDisplacement FreeSurferSource FUGUE fullname (nipype.pipeline.engine.base.EngineBase attribute) (nipype.pipeline.engine.nodes.JoinNode attribute) (nipype.pipeline.engine.nodes.MapNode attribute) (nipype.pipeline.engine.nodes.Node attribute) (nipype.pipeline.engine.workflows.Workflow attribute) Function FuseSegmentations FuzzyOverlap, [1] FWHMx

G

GaussianBlurImageFilter GCOR Generate5tt generate_expanded_graph() (in module nipype.pipeline.engine.utils) GenerateBrainClippedImage GenerateCsfClippedFromClassifiedImage GenerateDirections GenerateEdgeMapImage GenerateLabelMapFromProbabilityMap GeneratePurePlugMask GenerateSummedGradientImage GenerateTestImage GenerateWhiteMatterMask Gennlxfm GenWarpFields get() (nipype.interfaces.matlab.MatlabInputSpec method) get_all_files() (in module nipype.pipeline.engine.utils) get_hashval() (nipype.interfaces.matlab.MatlabInputSpec method) get_levels() (in module nipype.pipeline.engine.utils) get_matlab_command() (in module nipype.interfaces.matlab) get_node() (nipype.pipeline.engine.workflows.Workflow method) get_output() (nipype.pipeline.engine.nodes.JoinNode method) (nipype.pipeline.engine.nodes.MapNode method) (nipype.pipeline.engine.nodes.Node method) get_print_name() (in module nipype.pipeline.engine.utils) get_subnodes() (nipype.pipeline.engine.nodes.MapNode method) get_traitsfree() (nipype.interfaces.matlab.MatlabInputSpec method) get_wf_formats() (in module nipype.sphinxext.plot_workflow) GLM GLMFit

GradientAnisotropicDiffusion GradientAnisotropicDiffusionImageFilter GraphError (class in nipype.sphinxext.plot_workflow) GrayscaleFillHoleImageFilter GrayscaleGrindPeakImageFilter GrayscaleModelMaker GroupAndStack gtractAnisotropyMap gtractAverageBvalues gtractClipAnisotropy gtractConcatDwi gtractCopyImageOrientation gtractCoRegAnatomy gtractCoregBvalues gtractCostFastMarching gtractCreateGuideFiber gtractFastMarchingTracking gtractFiberTracking gtractImageConformity gtractInvertBSplineTransform gtractInvertDisplacementField gtractInvertRigidTransform gtractResampleAnisotropy gtractResampleB0 gtractResampleCodeImage gtractResampleDWIInPlace gtractResampleFibers gtractTensor gtractTransformToDisplacementField Gunzip

H

HammerAttributeCreator HARDIMat has_metadata() (nipype.interfaces.matlab.MatlabInputSpec method) has_traits_interface() (nipype.interfaces.matlab.MatlabInputSpec method) hash_exists() (nipype.pipeline.engine.nodes.JoinNode method) (nipype.pipeline.engine.nodes.MapNode method) (nipype.pipeline.engine.nodes.Node method)

help() (nipype.interfaces.matlab.MatlabCommand class method) (nipype.pipeline.engine.nodes.JoinNode method) (nipype.pipeline.engine.nodes.MapNode method) (nipype.pipeline.engine.nodes.Node method) Hemisplit Hist HistogramMatching HistogramMatchingFilter

I

ICA_AROMA ICC IdentityInterface Image2Voxel ImageFile (class in nipype.sphinxext.plot_workflow) ImageLabelCombine ImageMaths ImageMeants ImageRegionPlotter ImageStats, [1] in_testing() (in module nipype.conftest) input_spec (nipype.interfaces.matlab.MatlabCommand attribute) inputs (nipype.pipeline.engine.base.EngineBase attribute) (nipype.pipeline.engine.nodes.JoinNode attribute) (nipype.pipeline.engine.nodes.MapNode attribute) (nipype.pipeline.engine.nodes.Node attribute) (nipype.pipeline.engine.workflows.Workflow attribute)

insertMidACPCpoint IntensityDifferenceMetric interface (nipype.pipeline.engine.nodes.JoinNode attribute) (nipype.pipeline.engine.nodes.MapNode attribute) (nipype.pipeline.engine.nodes.Node attribute) InvWarp IOBase is_cached() (nipype.pipeline.engine.nodes.JoinNode method) (nipype.pipeline.engine.nodes.MapNode method) (nipype.pipeline.engine.nodes.Node method) IsotropicSmooth items() (nipype.interfaces.matlab.MatlabInputSpec method) itername (nipype.pipeline.engine.base.EngineBase attribute) (nipype.pipeline.engine.nodes.JoinNode attribute) (nipype.pipeline.engine.nodes.MapNode attribute) (nipype.pipeline.engine.nodes.Node attribute) (nipype.pipeline.engine.workflows.Workflow attribute)

J

Jacobian JistBrainMgdmSegmentation JistBrainMp2rageDuraEstimation JistBrainMp2rageSkullStripping JistBrainPartialVolumeFilter JistCortexSurfaceMeshInflation JistIntensityMp2rageMasking JistLaminarProfileCalculator JistLaminarProfileGeometry

JistLaminarProfileSampling JistLaminarROIAveraging JistLaminarVolumetricLayering joinfield (nipype.pipeline.engine.nodes.JoinNode attribute) JoinNode (class in nipype.pipeline.engine.nodes) joinsource (nipype.pipeline.engine.nodes.JoinNode attribute) JointFusion JointHistogram JSONFileGrabber JSONFileSink

K

KellyKapowski

L

L2Model Label2Annot Label2Label Label2Vol LabelConfig LabelConvert LabelFusion LabelGeometry LabelMapSmoothing landmarksConstellationAligner landmarksConstellationWeights LaplacianThickness Level1Design, [1] LFCD

LibraryBaseInterface LinearRegistration LinRecon list_node_names() (nipype.pipeline.engine.workflows.Workflow method) load() (nipype.pipeline.engine.base.EngineBase method) (nipype.pipeline.engine.nodes.JoinNode method) (nipype.pipeline.engine.nodes.MapNode method) (nipype.pipeline.engine.nodes.Node method) (nipype.pipeline.engine.workflows.Workflow method) load_inputs_from_json() (nipype.interfaces.matlab.MatlabCommand method) load_resultfile() (in module nipype.pipeline.engine.utils) LocalBistat LookupMeta LTAConvert

M

MakeAverageSubject MakeDyadicVectors MakeSurfaces MapNode (class in nipype.pipeline.engine.nodes) mark_wf_labels() (in module nipype.sphinxext.plot_workflow) Maskave MaskScalarVolume MaskTool Math MathsCommand, [1] Matlab2CSV MatlabCommand (class in nipype.interfaces.matlab) MatlabInputSpec (class in nipype.interfaces.matlab) maxcurvature MaxImage MaxnImage MCFLIRT MeanImage Means MeasureImageSimilarity MedianFilter3D MedianImage MedianImageFilter MedicAlgorithmImageCalculator MedicAlgorithmLesionToads MedicAlgorithmMipavReorient MedicAlgorithmN3 MedicAlgorithmSPECTRE2010 MedicAlgorithmThresholdToBinaryMask MELODIC mem_gb (nipype.pipeline.engine.nodes.JoinNode attribute) (nipype.pipeline.engine.nodes.MapNode attribute) (nipype.pipeline.engine.nodes.Node attribute) Memory (class in nipype.caching.memory) Merge, [1], [2], [3] merge_bundles() (in module nipype.pipeline.engine.utils) merge_dict() (in module nipype.pipeline.engine.utils) MergeCNetworks MergeCSVFiles MergeModels MergeNifti MergeROIs MESD

Mesh2PVE MeshFix MeshWarpMaths MetricResample MinImage MNIBiasCorrection ModelFit ModelMaker ModelToLabelMap modify_paths() (in module nipype.pipeline.engine.utils) ModifyAffine MotionOutliers MpiCommandLine MPRtoMNI305 MRConvert, [1] MRIConvert MRICoreg MRIFill MRIMarchingCubes MRIPretess MRIsCALabel MRIsCalc MRIsCombine MRIsConvert MRIsExpand MRIsInflate MRISPreproc MRISPreprocReconAll MRITessellate MRMath MRMultiply MRTransform MRTrix2TrackVis MRTrix3Base MRTrixViewer MS_LDA MultiImageMaths MultipleRegressDesign MultipleRegressionDesign MultiplyImages MultiplyScalarVolumes MultiResolutionAffineRegistration MySQLSink

N

N4BiasFieldCorrection N4ITKBiasFieldCorrection n_procs (nipype.pipeline.engine.nodes.JoinNode attribute) (nipype.pipeline.engine.nodes.MapNode attribute) (nipype.pipeline.engine.nodes.Node attribute) name (nipype.pipeline.engine.base.EngineBase attribute) (nipype.pipeline.engine.nodes.JoinNode attribute) (nipype.pipeline.engine.nodes.MapNode attribute) (nipype.pipeline.engine.nodes.Node attribute) (nipype.pipeline.engine.workflows.Workflow attribute) needed_outputs (nipype.pipeline.engine.nodes.JoinNode attribute) (nipype.pipeline.engine.nodes.MapNode attribute) (nipype.pipeline.engine.nodes.Node attribute) NeighborhoodMean NeighborhoodMedian NetworkBasedStatistic NetworkXMetrics NewSegment NIfTIDT2Camino NiftiGeneratorBase NiftyFitCommand NiftyRegCommand NiftySegCommand NilearnBaseInterface NipyBaseInterface nipype.algorithms.confounds (module) nipype.algorithms.icc (module) nipype.algorithms.misc (module) nipype.algorithms.modelgen (module) nipype.caching.memory (module) nipype.conftest (module), [1] nipype.interfaces.base.core (module) nipype.interfaces.base.support (module) nipype.interfaces.base.traits_extension (module) nipype.interfaces.brainsuite.brainsuite (module) nipype.interfaces.cmtk.cmtk (module) nipype.interfaces.cmtk.nbs (module) nipype.interfaces.cmtk.nx (module) nipype.interfaces.cmtk.parcellation (module) nipype.interfaces.dcmstack (module) nipype.interfaces.dipy.preprocess (module) nipype.interfaces.freesurfer.utils (module) nipype.interfaces.fsl.model (module) nipype.interfaces.io (module) nipype.interfaces.matlab (module) nipype.interfaces.minc.base (module) nipype.interfaces.minc.testdata (module) nipype.interfaces.mrtrix.convert (module) nipype.interfaces.mrtrix.tensors (module) nipype.interfaces.niftyreg.base (module)

nipype.interfaces.vtkbase (module) nipype.pipeline.engine.base (module) nipype.pipeline.engine.nodes (module) nipype.pipeline.engine.utils (module) nipype.pipeline.engine.workflows (module) nipype.pkg_info (module) nipype.sphinxext.plot_workflow (module), [1] nipype.workflows.data (module) nipype.workflows.dmri.camino.connectivity_mapping (module) nipype.workflows.dmri.camino.diffusion (module) nipype.workflows.dmri.camino.group_connectivity (module) nipype.workflows.dmri.connectivity.group_connectivity (module) nipype.workflows.dmri.connectivity.nx (module) nipype.workflows.dmri.dipy.denoise (module) nipype.workflows.dmri.dtitk.tensor_registration (module) nipype.workflows.dmri.fsl.artifacts (module) nipype.workflows.dmri.fsl.dti (module) nipype.workflows.dmri.fsl.epi (module) nipype.workflows.dmri.fsl.tbss (module) nipype.workflows.dmri.fsl.utils (module) nipype.workflows.dmri.mrtrix.connectivity_mapping (module) nipype.workflows.dmri.mrtrix.diffusion (module) nipype.workflows.dmri.mrtrix.group_connectivity (module) nipype.workflows.fmri.fsl.estimate (module) nipype.workflows.fmri.fsl.preprocess (module) nipype.workflows.fmri.spm.preprocess (module) nipype.workflows.misc.utils (module) nipype.workflows.rsfmri.fsl.resting (module) nipype.workflows.smri.ants.ANTSBuildTemplate (module) nipype.workflows.smri.ants.antsRegistrationBuildTemplate (module) nipype.workflows.smri.freesurfer.autorecon1 (module) nipype.workflows.smri.freesurfer.autorecon2 (module) nipype.workflows.smri.freesurfer.bem (module) nipype.workflows.smri.freesurfer.recon (module) nipype.workflows.smri.freesurfer.utils (module) nipype.workflows.smri.niftyreg.groupwise (module) NitimeBaseInterface NlpFit Node (class in nipype.pipeline.engine.nodes) nodelist_runner() (in module nipype.pipeline.engine.utils) NonSteadyStateDetector Norm Normalize, [1] Normalize12 NormalizeProbabilityMapSet Notes num_subnodes() (nipype.pipeline.engine.nodes.MapNode method) NwarpAdjust NwarpApply NwarpCat

O

ODFRecon ODFTracker on_trait_change() (nipype.interfaces.matlab.MatlabInputSpec method) on_trait_event() (nipype.interfaces.matlab.MatlabInputSpec method) OneDToolPy OneSampleTTest OneSampleTTestDesign OrientScalarVolume OtsuThresholdImageFilter OtsuThresholdSegmentation out_of_date() (in module nipype.sphinxext.plot_workflow)

OutlierCount output_dir() (nipype.pipeline.engine.nodes.JoinNode method) (nipype.pipeline.engine.nodes.MapNode method) (nipype.pipeline.engine.nodes.Node method) output_spec (nipype.interfaces.matlab.MatlabCommand attribute) outputs (nipype.pipeline.engine.base.EngineBase attribute) (nipype.pipeline.engine.nodes.JoinNode attribute) (nipype.pipeline.engine.nodes.MapNode attribute) (nipype.pipeline.engine.nodes.Node attribute) (nipype.pipeline.engine.workflows.Workflow attribute) Overlap, [1] Overlay

P

P2PDistance package_version (nipype.interfaces.matlab.MatlabInputSpec attribute) Paint PairedTTestDesign Parcellate ParcellationStats ParseDICOMDir PatchMatch PercentileImage PETPVC PETStandardUptakeValueComputation Pialmesh PickAtlas PicoPDFs Pik

PipeFunc (class in nipype.caching.memory) PlotMotionParams PlotTimeSeries PointsWarp PowerSpectrum PRELUDE PrepareFieldmap print_traits() (nipype.interfaces.matlab.MatlabInputSpec method) ProbabilisticSphericallyDeconvolutedStreamlineTrack ProbeVolumeWithModel ProbTrackX ProbTrackX2 ProcStreamlines ProjThresh Pvc

Q

QBallMX QualityIndex

Quickshear Qwarp QwarpPlusMinus

R

raise_exception() (nipype.interfaces.matlab.MatlabCommand method) Randomise RandomVol read_log() (in module nipype.caching.memory) Realign RealignUnwarp ReconAll references_ (nipype.interfaces.matlab.MatlabCommand attribute) Refit RegAladin RegAverage RegF3D Register RegisterAVItoTalairach Registration, [1] RegistrationSynQuick RegJacobian RegMeasure RegResample RegTools RegTransform RelabelHypointensities Remlfit remove_coding() (in module nipype.sphinxext.plot_workflow) remove_nodes() (nipype.pipeline.engine.workflows.Workflow method) remove_trait() (nipype.interfaces.matlab.MatlabInputSpec method) remove_trait_listener() (nipype.interfaces.matlab.MatlabInputSpec method) RemoveIntersection RemoveNeck Rename render_figures() (in module nipype.sphinxext.plot_workflow) Reorient Reorient2Std

ReportCapableInterface Resample, [1], [2], [3] ResampleDTIVolume ResampleScalarVectorDWIVolume ResampleScalarVolume Rescale reset_traits() (nipype.interfaces.matlab.MatlabInputSpec method) Reshape Reslice ResliceToReference resource_monitor (nipype.interfaces.matlab.MatlabCommand attribute) ResponseSD RESTORE result (nipype.pipeline.engine.nodes.JoinNode attribute) (nipype.pipeline.engine.nodes.MapNode attribute) (nipype.pipeline.engine.nodes.Node attribute) Retroicor Rigid RigidRegistration RigidTask rm_all_but() (in module nipype.caching.memory) RobustFOV RobustRegister RobustStatisticsSegmenter RobustTemplate ROIGen ROIStats run() (in module nipype.sphinxext.plot_workflow) (nipype.interfaces.matlab.MatlabCommand method) (nipype.pipeline.engine.nodes.JoinNode method) (nipype.pipeline.engine.nodes.MapNode method) (nipype.pipeline.engine.nodes.Node method) (nipype.pipeline.engine.workflows.Workflow method) run_code() (in module nipype.sphinxext.plot_workflow)

S

S3DataGrabber SampleToSurface save() (nipype.pipeline.engine.base.EngineBase method) (nipype.pipeline.engine.nodes.JoinNode method) (nipype.pipeline.engine.nodes.MapNode method) (nipype.pipeline.engine.nodes.Node method) (nipype.pipeline.engine.workflows.Workflow method) save_hashfile() (in module nipype.pipeline.engine.utils) save_inputs_to_json() (nipype.interfaces.matlab.MatlabCommand method) save_resultfile() (in module nipype.pipeline.engine.utils) scalartransform Scrubmask Seg Segment SegmentCC SegmentWM SegStats SegStatsReconAll Select SelectFiles SEMLikeCommandLine set() (nipype.interfaces.matlab.MatlabInputSpec method) set_default_matlab_cmd() (nipype.interfaces.matlab.MatlabCommand class method) set_default_mfile() (nipype.interfaces.matlab.MatlabCommand class method) set_default_paths() (nipype.interfaces.matlab.MatlabCommand class method) set_default_terminal_output() (nipype.interfaces.matlab.MatlabCommand class method) set_input() (nipype.pipeline.engine.nodes.JoinNode method) (nipype.pipeline.engine.nodes.MapNode method) (nipype.pipeline.engine.nodes.Node method) set_trait_dispatch_handler() (nipype.interfaces.matlab.MatlabInputSpec class method) setup() (in module nipype.sphinxext.plot_workflow) SFLUTGen SFPeaks SFPICOCalibData Shredder ShuffleVectorsModule SigLoss, [1] SignalExtraction Similarity, [1] SimilarityIndex SimpleInterface SimpleRegionGrowingSegmentation SimpleThreshold SimulateMultiTensor Skullfinder SkullStrip Slice

Slicer SlicerCommandLine, [1] SliceTimer SliceTiming SMM Smooth, [1], [2] SmoothEstimate SmoothTessellation SpaceTimeRealigner SpatialFilter SpecifyModel SpecifySparseModel SpecifySPMModel Sphere SphericalAverage SphericallyDeconvolutedStreamlineTrack SplineFilter Split, [1] SplitNifti SplitROIs SQLiteSink SSHDataGrabber STAPLEAnalysis StatsCommand StdImage StdOutCommandLine StimulusCorrelation StreamlineTrack StreamlineTractography strip_temp() (in module nipype.pipeline.engine.utils) SubtractScalarVolumes Surface2VolTransform SurfaceSmooth SurfaceSnapshots SurfaceTransform SUSAN SVAdjustVoxSp SVAdjustVoxSpTask SVMTest SVMTrain SVReg SVResample SVResampleTask SwapDimensions sync_trait() (nipype.interfaces.matlab.MatlabInputSpec method) synchronize_iterables() (in module nipype.pipeline.engine.utils) Synthesize SynthesizeFLASH

T

TalairachAVI TalairachQC Tca TCat TCatSubBrick TCK2VTK TCompCor TCorr1D TCorrelate TCorrMap TemporalFilter Tensor2ApparentDiffusion Tensor2FractionalAnisotropy Tensor2Vector TensorMetrics TensorMode terminal_output (nipype.interfaces.matlab.MatlabCommand attribute) TextureFromNoiseImageFilter TextureMeasureFilter ThicknessPVC Threshold, [1], [2] ThresholdScalarVolume ThresholdStatistics Tkregister2 TNorm To3D ToEcat topological_sort() (in module nipype.pipeline.engine.utils) TOPUP ToRaw TProject Track TrackBallStick TrackBayesDirac TrackBedpostxDeter TrackBedpostxProba TrackBootstrap TrackDensityMap TrackDT

TrackMerge TrackPICo Tracks2Prob Trackvis2Camino Tractography TractographyLabelMapSeeding TractShredder TractSkeleton Training TrainingSetCreator trait() (nipype.interfaces.matlab.MatlabInputSpec method) trait_context() (nipype.interfaces.matlab.MatlabInputSpec method) trait_get() (nipype.interfaces.matlab.MatlabInputSpec method) trait_items_event() (nipype.interfaces.matlab.MatlabInputSpec method) trait_monitor() (nipype.interfaces.matlab.MatlabInputSpec class method) trait_names() (nipype.interfaces.matlab.MatlabInputSpec method) trait_property_changed() (nipype.interfaces.matlab.MatlabInputSpec method) trait_set() (nipype.interfaces.matlab.MatlabInputSpec method) trait_setq() (nipype.interfaces.matlab.MatlabInputSpec method) trait_subclasses() (nipype.interfaces.matlab.MatlabInputSpec class method) trait_view() (nipype.interfaces.matlab.MatlabInputSpec method) trait_view_elements() (nipype.interfaces.matlab.MatlabInputSpec method) trait_views() (nipype.interfaces.matlab.MatlabInputSpec method) traits() (nipype.interfaces.matlab.MatlabInputSpec method) traits_init() (nipype.interfaces.matlab.MatlabInputSpec method) traits_inited() (nipype.interfaces.matlab.MatlabInputSpec method) Trim TShift TSNR, [1] TStat TupleMaths TVAdjustOriginTask TVAdjustVoxSp TVAdjustVoxSpTask TVResample TVResampleTask TVTKBaseInterface TVtool TVtoolTask TwoSampleTTestDesign

U

UKFTractography UnaryMaths, [1] UnaryStats UnbiasedNonLocalMeans Undump

unescape_doctest() (in module nipype.sphinxext.plot_workflow) Unifize UnpackSDICOMDir update() (nipype.pipeline.engine.nodes.JoinNode method) (nipype.pipeline.engine.nodes.MapNode method) (nipype.pipeline.engine.nodes.Node method)

V

validate_trait() (nipype.interfaces.matlab.MatlabInputSpec method) VBMSegment VBRAINSDemonWarp, [1] VecReg version (nipype.interfaces.matlab.MatlabCommand attribute) version_from_command() (nipype.interfaces.matlab.MatlabCommand method) visible_traits() (nipype.interfaces.matlab.MatlabInputSpec method) Vnifti2Image

Volcentre Voliso Volpad Volreg VolSymm VolumeMask VotingBinaryHoleFillingImageFilter VtkStreamlines VtoMat

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 WarpImageMultiTransform WarpPoints, [1] WarpPointsFromStd WarpPointsToStd WarpTimeSeriesImageMultiTransform WarpUtils WatershedBEM

WatershedSkullStrip WBCommand wf_directive() (in module nipype.sphinxext.plot_workflow) with_traceback() (nipype.sphinxext.plot_workflow.GraphError method) Workflow (class in nipype.pipeline.engine.workflows) wrappers (nipype.interfaces.matlab.MatlabInputSpec attribute) write_graph() (nipype.pipeline.engine.workflows.Workflow method) write_hierarchical_dotfile() (nipype.pipeline.engine.workflows.Workflow method) write_report() (in module nipype.pipeline.engine.utils) write_workflow_prov() (in module nipype.pipeline.engine.utils) write_workflow_resources() (in module nipype.pipeline.engine.utils)

X

XFibres5 XfmAvg XfmConcat

XfmInvert XNATSink XNATSource

Z

Zcat	ZCutUp Zeropad