Interfaces and Algorithms

Release:1.1.1 Date:August 03, 2018, 17:00 PDT

• algorithms.confounds
  • ACompCor
  • CompCor
  • ComputeDVARS
  • FramewiseDisplacement
  • NonSteadyStateDetector
  • TCompCor
  • TSNR
  • combine_mask_files()
  • compute_dvars()
  • compute_noise_components()
  • cosine_filter()
  • is_outlier()
  • plot_confound()
  • regress_poly()
• algorithms.icc
  • ICC
  • ICC_rep_anova()
• algorithms.mesh
  • ComputeMeshWarp
  • MeshWarpMaths
  • P2PDistance
  • TVTKBaseInterface
  • WarpPoints
• algorithms.metrics
  • Distance
  • ErrorMap
  • FuzzyOverlap
  • Overlap
  • Similarity
• algorithms.misc
  • AddCSVColumn
  • AddCSVRow
  • AddNoise
  • CalculateMedian
  • CalculateNormalizedMoments
  • CreateNifti
  • Distance
  • FuzzyOverlap
  • Gunzip
  • Matlab2CSV
  • MergeCSVFiles
  • MergeROIs
  • ModifyAffine
  • NormalizeProbabilityMapSet
  • Overlap
  • PickAtlas
  • SimpleThreshold
  • SplitROIs
  • TSNR
  • calc_moments()
  • makefmtlist()
  • maketypelist()
  • matlab2csv()
  • merge_csvs()
  • merge_rois()
  • normalize_tpms()
  • remove_identical_paths()
  • replaceext()
  • split_rois()
• algorithms.modelgen
  • SpecifyModel
  • SpecifySPMModel
  • SpecifySparseModel
  • gcd()
  • gen_info()
  • orth()
  • scale_timings()
  • spm_hrf()
• algorithms.rapidart
  • ArtifactDetect
  • StimulusCorrelation
• algorithms.stats
  • ActivationCount
• conftest
  • add_np()
  • in_testing()
• interfaces.afni.base
  • AFNIPythonCommand
• interfaces.afni.model
  • Deconvolve
  • Remlfit
  • Synthesize
• interfaces.afni.preprocess
  • AlignEpiAnatPy
  • Allineate
  • AutoTLRC
  • AutoTcorrelate
  • Automask
  • Bandpass
  • BlurInMask
  • BlurToFWHM
  • ClipLevel
  • DegreeCentrality
  • Despike
  • Detrend
  • ECM
  • Fim
  • Fourier
  • Hist
  • LFCD
  • Maskave
  • Means
  • OutlierCount
  • QualityIndex
  • Qwarp
  • QwarpPlusMinus
  • ROIStats
  • Retroicor
  • Seg
  • SkullStrip
  • TCorr1D
  • TCorrMap
  • TCorrelate
  • TNorm
  • TProject
  • TShift
  • Volreg
  • Warp
• interfaces.afni.svm
  • SVMTest
  • SVMTrain
• interfaces.afni.utils
  • ABoverlap
  • AFNItoNIFTI
  • Autobox
  • Axialize
  • BrickStat
  • Bucket
  • Calc
  • Cat
  • CatMatvec
  • CenterMass
  • ConvertDset
  • Copy
  • Dot
  • Edge3
  • Eval
  • FWHMx
  • GCOR
  • LocalBistat
  • MaskTool
  • Merge
  • Notes
  • NwarpAdjust
  • NwarpApply
  • NwarpCat
  • OneDToolPy
  • Refit
  • Resample
  • TCat
  • TCatSubBrick
  • TStat
  • To3D
  • Undump
  • Unifize
  • ZCutUp
  • Zcat
  • Zeropad
• interfaces.ants.legacy
  • GenWarpFields
  • antsIntroduction
  • buildtemplateparallel
• interfaces.ants.registration
  • MeasureImageSimilarity
  • Registration
  • RegistrationSynQuick
• interfaces.ants.resampling
  • ApplyTransforms
  • ApplyTransformsToPoints
  • WarpImageMultiTransform
  • WarpTimeSeriesImageMultiTransform
• interfaces.ants.segmentation
  • AntsJointFusion
  • Atropos
  • BrainExtraction
  • CorticalThickness
  • DenoiseImage
  • JointFusion
  • KellyKapowski
  • LaplacianThickness
  • N4BiasFieldCorrection
• interfaces.ants.utils
  • AffineInitializer
  • AverageAffineTransform
  • AverageImages
  • ComposeMultiTransform
  • CreateJacobianDeterminantImage
  • LabelGeometry
  • MultiplyImages
• interfaces.ants.visualization
  • ConvertScalarImageToRGB
  • CreateTiledMosaic
• interfaces.base.core
  • BaseInterface
  • CommandLine
  • LibraryBaseInterface
  • MpiCommandLine
  • SEMLikeCommandLine
  • SimpleInterface
  • StdOutCommandLine
  • run_command()
• interfaces.base.support
  • load_template()
• interfaces.base.traits_extension
  • has_metadata()
  • isdefined()
  • length()
• interfaces.brainsuite.brainsuite
  • BDP
  • Bfc
  • Bse
  • Cerebro
  • Cortex
  • Dewisp
  • Dfs
  • Hemisplit
  • Pialmesh
  • Pvc
  • SVReg
  • Scrubmask
  • Skullfinder
  • Tca
  • ThicknessPVC
  • getFileName()
  • l_outputs()
• interfaces.bru2nii
  • Bru2
• interfaces.c3
  • C3d
  • C3dAffineTool
• interfaces.camino.calib
  • SFLUTGen
  • SFPICOCalibData
• interfaces.camino.connectivity
  • Conmat
• interfaces.camino.convert
  • AnalyzeHeader
  • DT2NIfTI
  • Image2Voxel
  • NIfTIDT2Camino
  • ProcStreamlines
  • Shredder
  • TractShredder
  • VtkStreamlines
• interfaces.camino.dti
  • ComputeEigensystem
  • ComputeFractionalAnisotropy
  • ComputeMeanDiffusivity
  • ComputeTensorTrace
  • DTIFit
  • DTLUTGen
  • DTMetric
  • ModelFit
  • PicoPDFs
  • Track
  • TrackBallStick
  • TrackBayesDirac
  • TrackBedpostxDeter
  • TrackBedpostxProba
  • TrackBootstrap
  • TrackDT
  • TrackPICo
• interfaces.camino.odf
  • LinRecon
  • MESD
  • QBallMX
  • SFPeaks
• interfaces.camino.utils
  • ImageStats
• interfaces.camino2trackvis.convert
  • Camino2Trackvis
  • Trackvis2Camino
• interfaces.cmtk.base
  • CFFBaseInterface
• interfaces.cmtk.cmtk
  • CreateMatrix
  • CreateNodes
  • ROIGen
  • cmat()
  • create_allpoints_cmat()
  • create_endpoints_array()
  • create_nodes()
  • get_connectivity_matrix()
  • get_rois_crossed()
  • length()
  • save_fibers()
• interfaces.cmtk.convert
  • CFFConverter
  • MergeCNetworks
• interfaces.cmtk.nbs
  • NetworkBasedStatistic
  • ntwks_to_matrices()
• interfaces.cmtk.nx
  • AverageNetworks
  • NetworkXMetrics
  • add_dicts_by_key()
  • add_edge_data()
  • add_node_data()
  • average_networks()
  • compute_dict_measures()
  • compute_edge_measures()
  • compute_network_measures()
  • compute_node_measures()
  • compute_singlevalued_measures()
  • fix_keys_for_gexf()
  • read_unknown_ntwk()
  • remove_all_edges()
• interfaces.cmtk.parcellation
  • Parcellate
  • create_annot_label()
  • create_roi()
  • create_wm_mask()
  • crop_and_move_datasets()
  • extract()
• interfaces.dcm2nii
  • Dcm2nii
  • Dcm2niix
• interfaces.dcmstack
  • CopyMeta
  • DcmStack
  • GroupAndStack
  • LookupMeta
  • MergeNifti
  • NiftiGeneratorBase
  • SplitNifti
  • make_key_func()
  • sanitize_path_comp()
• interfaces.diffusion_toolkit.dti
  • DTIRecon
  • DTITracker
• interfaces.diffusion_toolkit.odf
  • HARDIMat
  • ODFRecon
  • ODFTracker
• interfaces.diffusion_toolkit.postproc
  • SplineFilter
  • TrackMerge
• interfaces.dipy.anisotropic_power
  • APMQball
• interfaces.dipy.base
  • DipyBaseInterface
  • DipyDiffusionInterface
• interfaces.dipy.preprocess
  • Denoise
  • Resample
  • nlmeans_proxy()
  • resample_proxy()
• interfaces.dipy.reconstruction
  • CSD
  • EstimateResponseSH
  • RESTORE
• interfaces.dipy.simulate
  • SimulateMultiTensor
• interfaces.dipy.tensors
  • DTI
  • TensorMode
• interfaces.dipy.tracks
  • StreamlineTractography
  • TrackDensityMap
• interfaces.dtitk.base
  • CommandLineDtitk
• interfaces.dtitk.registration
  • AffScalarVol
  • AffSymTensor3DVol
  • Affine
  • AffineTask
  • ComposeXfm
  • ComposeXfmTask
  • Diffeo
  • DiffeoScalarVol
  • DiffeoSymTensor3DVol
  • DiffeoTask
  • Rigid
  • RigidTask
  • affScalarVolTask
  • affSymTensor3DVolTask
  • diffeoScalarVolTask
  • diffeoSymTensor3DVolTask
• interfaces.dtitk.utils
  • BinThresh
  • BinThreshTask
  • SVAdjustVoxSp
  • SVAdjustVoxSpTask
  • SVResample
  • SVResampleTask
  • TVAdjustOriginTask
  • TVAdjustVoxSp
  • TVAdjustVoxSpTask
  • TVResample
  • TVResampleTask
  • TVtool
  • TVtoolTask
• interfaces.dynamic_slicer
  • SlicerCommandLine
• interfaces.elastix.registration
  • AnalyzeWarp
  • ApplyWarp
  • PointsWarp
  • Registration
• interfaces.elastix.utils
  • EditTransform
• interfaces.freesurfer.longitudinal
  • FuseSegmentations
  • RobustTemplate
• interfaces.freesurfer.model
  • Binarize
  • Concatenate
  • GLMFit
  • Label2Annot
  • Label2Label
  • Label2Vol
  • MRISPreproc
  • MRISPreprocReconAll
  • MS_LDA
  • OneSampleTTest
  • SegStats
  • SegStatsReconAll
  • SphericalAverage
• interfaces.freesurfer.preprocess
  • ApplyVolTransform
  • BBRegister
  • CALabel
  • CANormalize
  • CARegister
  • ConcatenateLTA
  • DICOMConvert
  • EditWMwithAseg
  • FitMSParams
  • MNIBiasCorrection
  • MRIConvert
  • MRIsCALabel
  • Normalize
  • ParseDICOMDir
  • ReconAll
  • Resample
  • RobustRegister
  • SegmentCC
  • SegmentWM
  • Smooth
  • SynthesizeFLASH
  • UnpackSDICOMDir
  • WatershedSkullStrip
• interfaces.freesurfer.registration
  • EMRegister
  • MPRtoMNI305
  • MRICoreg
  • Paint
  • Register
  • RegisterAVItoTalairach
• interfaces.freesurfer.utils
  • AddXFormToHeader
  • Aparc2Aseg
  • Apas2Aseg
  • ApplyMask
  • CheckTalairachAlignment
  • Contrast
  • Curvature
  • CurvatureStats
  • EulerNumber
  • ExtractMainComponent
  • FixTopology
  • Jacobian
  • LTAConvert
  • MRIFill
  • MRIMarchingCubes
  • MRIPretess
  • MRITessellate
  • MRIsCalc
  • MRIsCombine
  • MRIsConvert
  • MRIsExpand
  • MRIsInflate
  • MakeAverageSubject
  • MakeSurfaces
  • ParcellationStats
  • RelabelHypointensities
  • RemoveIntersection
  • RemoveNeck
  • SampleToSurface
  • SmoothTessellation
  • Sphere
  • Surface2VolTransform
  • SurfaceSmooth
  • SurfaceSnapshots
  • SurfaceTransform
  • TalairachAVI
  • TalairachQC
  • Tkregister2
  • VolumeMask
  • copy2subjdir()
  • createoutputdirs()
• interfaces.fsl.aroma
  • ICA_AROMA
• interfaces.fsl.dti
  • BEDPOSTX5
  • DTIFit
  • DistanceMap
  • FindTheBiggest
  • MakeDyadicVectors
  • ProbTrackX
  • ProbTrackX2
  • ProjThresh
  • TractSkeleton
  • VecReg
  • XFibres5
• interfaces.fsl.epi
  • ApplyTOPUP
  • EPIDeWarp
  • Eddy
  • EddyCorrect
  • EpiReg
  • PrepareFieldmap
  • SigLoss
  • TOPUP
• interfaces.fsl.fix
  • Classifier
  • Cleaner
  • FeatureExtractor
  • Training
  • TrainingSetCreator
• interfaces.fsl.maths
  • AR1Image
  • ApplyMask
  • BinaryMaths
  • ChangeDataType
  • DilateImage
  • ErodeImage
  • IsotropicSmooth
  • MathsCommand
  • MaxImage
  • MaxnImage
  • MeanImage
  • MedianImage
  • MinImage
  • MultiImageMaths
  • PercentileImage
  • SpatialFilter
  • StdImage
  • TemporalFilter
  • Threshold
  • UnaryMaths
• interfaces.fsl.model
  • Cluster
  • ContrastMgr
  • DualRegression
  • FEAT
  • FEATModel
  • FEATRegister
  • FILMGLS
  • FLAMEO
  • GLM
  • L2Model
  • Level1Design
  • MELODIC
  • MultipleRegressDesign
  • Randomise
  • SMM
  • SmoothEstimate
  • load_template()
• interfaces.fsl.possum
  • B0Calc
• interfaces.fsl.preprocess
  • ApplyWarp
  • ApplyXFM
  • BET
  • FAST
  • FIRST
  • FLIRT
  • FNIRT
  • FUGUE
  • MCFLIRT
  • PRELUDE
  • SUSAN
  • SliceTimer
• interfaces.fsl.utils
  • AvScale
  • Complex
  • ConvertWarp
  • ConvertXFM
  • CopyGeom
  • ExtractROI
  • FilterRegressor
  • ImageMaths
  • ImageMeants
  • ImageStats
  • InvWarp
  • Merge
  • MotionOutliers
  • Overlay
  • PlotMotionParams
  • PlotTimeSeries
  • PowerSpectrum
  • Reorient2Std
  • RobustFOV
  • SigLoss
  • Slice
  • Slicer
  • Smooth
  • Split
  • SwapDimensions
  • WarpPoints
  • WarpPointsFromStd
  • WarpPointsToStd
  • WarpUtils
• interfaces.image
  • Reorient
  • Rescale
• interfaces.io
  • BIDSDataGrabber
  • DataFinder
  • DataGrabber
  • DataSink
  • FreeSurferSource
  • IOBase
  • JSONFileGrabber
  • JSONFileSink
  • MySQLSink
  • S3DataGrabber
  • SQLiteSink
  • SSHDataGrabber
  • SelectFiles
  • XNATSink
  • XNATSource
  • add_traits()
  • copytree()
  • push_file()
  • quote_id()
  • unquote_id()
• interfaces.meshfix
  • MeshFix
• interfaces.minc.base
  • aggregate_filename()
• interfaces.minc.minc
  • Average
  • BBox
  • Beast
  • BestLinReg
  • BigAverage
  • Blob
  • Blur
  • Calc
  • Convert
  • Copy
  • Dump
  • Extract
  • Gennlxfm
  • Math
  • NlpFit
  • Norm
  • Pik
  • Resample
  • Reshape
  • ToEcat
  • ToRaw
  • VolSymm
  • Volcentre
  • Voliso
  • Volpad
  • XfmAvg
  • XfmConcat
  • XfmInvert
• interfaces.minc.testdata
  • nonempty_minc_data()
• interfaces.mipav.developer
  • JistBrainMgdmSegmentation
  • JistBrainMp2rageDuraEstimation
  • JistBrainMp2rageSkullStripping
  • JistBrainPartialVolumeFilter
  • JistCortexSurfaceMeshInflation
  • JistIntensityMp2rageMasking
  • JistLaminarProfileCalculator
  • JistLaminarProfileGeometry
  • JistLaminarProfileSampling
  • JistLaminarROIAveraging
  • JistLaminarVolumetricLayering
  • MedicAlgorithmImageCalculator
  • MedicAlgorithmLesionToads
  • MedicAlgorithmMipavReorient
  • MedicAlgorithmN3
  • MedicAlgorithmSPECTRE2010
  • MedicAlgorithmThresholdToBinaryMask
  • RandomVol
• interfaces.mixins.reporting
  • ReportCapableInterface
• interfaces.mne.base
  • WatershedBEM
• interfaces.mrtrix.convert
  • MRTrix2TrackVis
  • read_mrtrix_header()
  • read_mrtrix_streamlines()
  • read_mrtrix_tracks()
  • transform_to_affine()
• interfaces.mrtrix.preprocess
  • DWI2Tensor
  • Erode
  • GenerateWhiteMatterMask
  • MRConvert
  • MRMultiply
  • MRTransform
  • MRTrixViewer
  • MedianFilter3D
  • Tensor2ApparentDiffusion
  • Tensor2FractionalAnisotropy
  • Tensor2Vector
  • Threshold
• interfaces.mrtrix.tensors
  • ConstrainedSphericalDeconvolution
  • DWI2SphericalHarmonicsImage
  • Directions2Amplitude
  • EstimateResponseForSH
  • FindShPeaks
  • GenerateDirections
  • concat_files()
• interfaces.mrtrix.tracking
  • DiffusionTensorStreamlineTrack
  • FilterTracks
  • ProbabilisticSphericallyDeconvolutedStreamlineTrack
  • SphericallyDeconvolutedStreamlineTrack
  • StreamlineTrack
  • Tracks2Prob
• interfaces.mrtrix3.base
  • MRTrix3Base
• interfaces.mrtrix3.connectivity
  • BuildConnectome
  • LabelConfig
  • LabelConvert
• interfaces.mrtrix3.preprocess
  • DWIDenoise
  • ResponseSD
• interfaces.mrtrix3.reconst
  • EstimateFOD
  • FitTensor
• interfaces.mrtrix3.tracking
  • Tractography
• interfaces.mrtrix3.utils
  • BrainMask
  • ComputeTDI
  • DWIExtract
  • Generate5tt
  • MRConvert
  • MRMath
  • Mesh2PVE
  • TCK2VTK
  • TensorMetrics
• interfaces.niftyfit.asl
  • FitAsl
• interfaces.niftyfit.base
  • NiftyFitCommand
• interfaces.niftyfit.dwi
  • DwiTool
  • FitDwi
• interfaces.niftyfit.qt1
  • FitQt1
• interfaces.niftyreg.base
  • NiftyRegCommand
  • get_custom_path()
• interfaces.niftyreg.reg
  • RegAladin
  • RegF3D
• interfaces.niftyreg.regutils
  • RegAverage
  • RegJacobian
  • RegMeasure
  • RegResample
  • RegTools
  • RegTransform
• interfaces.niftyseg.base
  • NiftySegCommand
• interfaces.niftyseg.em
  • EM
• interfaces.niftyseg.label_fusion
  • CalcTopNCC
  • LabelFusion
• interfaces.niftyseg.lesions
  • FillLesions
• interfaces.niftyseg.maths
  • BinaryMaths
  • BinaryMathsInteger
  • MathsCommand
  • Merge
  • TupleMaths
  • UnaryMaths
• interfaces.niftyseg.patchmatch
  • PatchMatch
• interfaces.niftyseg.stats
  • BinaryStats
  • StatsCommand
  • UnaryStats
• interfaces.nilearn
  • NilearnBaseInterface
  • SignalExtraction
• interfaces.nipy.base
  • NipyBaseInterface
• interfaces.nipy.model
  • EstimateContrast
  • FitGLM
• interfaces.nipy.preprocess
  • ComputeMask
  • SpaceTimeRealigner
  • Trim
• interfaces.nipy.utils
  • Similarity
• interfaces.nitime.analysis
  • CoherenceAnalyzer
• interfaces.nitime.base
  • NitimeBaseInterface
• interfaces.petpvc
  • PETPVC
• interfaces.quickshear
  • Quickshear
• interfaces.semtools.brains.classify
  • BRAINSPosteriorToContinuousClass
• interfaces.semtools.brains.segmentation
  • BRAINSTalairach
  • BRAINSTalairachMask
  • SimilarityIndex
• interfaces.semtools.brains.utilities
  • GenerateEdgeMapImage
  • GeneratePurePlugMask
  • HistogramMatchingFilter
• interfaces.semtools.converters
  • DWICompare
  • DWISimpleCompare
• interfaces.semtools.diffusion.diffusion
  • DWIConvert
  • dtiaverage
  • dtiestim
  • dtiprocess
• interfaces.semtools.diffusion.gtract
  • compareTractInclusion
  • extractNrrdVectorIndex
  • gtractAnisotropyMap
  • gtractAverageBvalues
  • gtractClipAnisotropy
  • gtractCoRegAnatomy
  • gtractConcatDwi
  • gtractCopyImageOrientation
  • gtractCoregBvalues
  • gtractCostFastMarching
  • gtractCreateGuideFiber
  • gtractFastMarchingTracking
  • gtractFiberTracking
  • gtractImageConformity
  • gtractInvertBSplineTransform
  • gtractInvertDisplacementField
  • gtractInvertRigidTransform
  • gtractResampleAnisotropy
  • gtractResampleB0
  • gtractResampleCodeImage
  • gtractResampleDWIInPlace
  • gtractResampleFibers
  • gtractTensor
  • gtractTransformToDisplacementField
• interfaces.semtools.diffusion.maxcurvature
  • maxcurvature
• interfaces.semtools.diffusion.tractography.commandlineonly
  • fiberstats
• interfaces.semtools.diffusion.tractography.fiberprocess
  • fiberprocess
• interfaces.semtools.diffusion.tractography.fibertrack
  • fibertrack
• interfaces.semtools.diffusion.tractography.ukftractography
  • UKFTractography
• interfaces.semtools.featurecreator
  • GenerateCsfClippedFromClassifiedImage
• interfaces.semtools.filtering.denoising
  • UnbiasedNonLocalMeans
• interfaces.semtools.filtering.featuredetection
  • CannyEdge
  • CannySegmentationLevelSetImageFilter
  • DilateImage
  • DilateMask
  • DistanceMaps
  • DumpBinaryTrainingVectors
  • ErodeImage
  • FlippedDifference
  • GenerateBrainClippedImage
  • GenerateSummedGradientImage
  • GenerateTestImage
  • GradientAnisotropicDiffusionImageFilter
  • HammerAttributeCreator
  • NeighborhoodMean
  • NeighborhoodMedian
  • STAPLEAnalysis
  • TextureFromNoiseImageFilter
  • TextureMeasureFilter
• interfaces.semtools.legacy.registration
  • scalartransform
• interfaces.semtools.registration.brainsfit
  • BRAINSFit
• interfaces.semtools.registration.brainsresample
  • BRAINSResample
• interfaces.semtools.registration.brainsresize
  • BRAINSResize
• interfaces.semtools.registration.specialized
  • BRAINSDemonWarp
  • BRAINSTransformFromFiducials
  • VBRAINSDemonWarp
• interfaces.semtools.segmentation.specialized
  • BRAINSABC
  • BRAINSConstellationDetector
  • BRAINSCreateLabelMapFromProbabilityMaps
  • BRAINSCut
  • BRAINSMultiSTAPLE
  • BRAINSROIAuto
  • BinaryMaskEditorBasedOnLandmarks
  • ESLR
• interfaces.semtools.utilities.brains
  • BRAINSAlignMSP
  • BRAINSClipInferior
  • BRAINSConstellationModeler
  • BRAINSEyeDetector
  • BRAINSInitializedControlPoints
  • BRAINSLandmarkInitializer
  • BRAINSLinearModelerEPCA
  • BRAINSLmkTransform
  • BRAINSMush
  • BRAINSSnapShotWriter
  • BRAINSTransformConvert
  • BRAINSTrimForegroundInDirection
  • CleanUpOverlapLabels
  • FindCenterOfBrain
  • GenerateLabelMapFromProbabilityMap
  • ImageRegionPlotter
  • JointHistogram
  • ShuffleVectorsModule
  • fcsv_to_hdf5
  • insertMidACPCpoint
  • landmarksConstellationAligner
  • landmarksConstellationWeights
• interfaces.slicer.base
  • SlicerCommandLine
• interfaces.slicer.converters
  • DicomToNrrdConverter
  • OrientScalarVolume
• interfaces.slicer.diffusion.diffusion
  • DTIexport
  • DTIimport
  • DWIJointRicianLMMSEFilter
  • DWIRicianLMMSEFilter
  • DWIToDTIEstimation
  • DiffusionTensorScalarMeasurements
  • DiffusionWeightedVolumeMasking
  • ResampleDTIVolume
  • TractographyLabelMapSeeding
• interfaces.slicer.filtering.arithmetic
  • AddScalarVolumes
  • CastScalarVolume
  • MaskScalarVolume
  • MultiplyScalarVolumes
  • SubtractScalarVolumes
• interfaces.slicer.filtering.checkerboardfilter
  • CheckerBoardFilter
• interfaces.slicer.filtering.denoising
  • CurvatureAnisotropicDiffusion
  • GaussianBlurImageFilter
  • GradientAnisotropicDiffusion
  • MedianImageFilter
• interfaces.slicer.filtering.extractskeleton
  • ExtractSkeleton
• interfaces.slicer.filtering.histogrammatching
  • HistogramMatching
• interfaces.slicer.filtering.imagelabelcombine
  • ImageLabelCombine
• interfaces.slicer.filtering.morphology
  • GrayscaleFillHoleImageFilter
  • GrayscaleGrindPeakImageFilter
• interfaces.slicer.filtering.n4itkbiasfieldcorrection
  • N4ITKBiasFieldCorrection
• interfaces.slicer.filtering.resamplescalarvectordwivolume
  • ResampleScalarVectorDWIVolume
• interfaces.slicer.filtering.thresholdscalarvolume
  • ThresholdScalarVolume
• interfaces.slicer.filtering.votingbinaryholefillingimagefilter
  • VotingBinaryHoleFillingImageFilter
• interfaces.slicer.legacy.converters
  • BSplineToDeformationField
• interfaces.slicer.legacy.diffusion.denoising
  • DWIUnbiasedNonLocalMeansFilter
• interfaces.slicer.legacy.filtering
  • OtsuThresholdImageFilter
  • ResampleScalarVolume
• interfaces.slicer.legacy.registration
  • AffineRegistration
  • BSplineDeformableRegistration
  • ExpertAutomatedRegistration
  • LinearRegistration
  • MultiResolutionAffineRegistration
  • RigidRegistration
• interfaces.slicer.legacy.segmentation
  • OtsuThresholdSegmentation
• interfaces.slicer.quantification.changequantification
  • IntensityDifferenceMetric
• interfaces.slicer.quantification.petstandarduptakevaluecomputation
  • PETStandardUptakeValueComputation
• interfaces.slicer.registration.brainsfit
  • BRAINSFit
• interfaces.slicer.registration.brainsresample
  • BRAINSResample
• interfaces.slicer.registration.specialized
  • ACPCTransform
  • BRAINSDemonWarp
  • FiducialRegistration
  • VBRAINSDemonWarp
• interfaces.slicer.segmentation.simpleregiongrowingsegmentation
  • SimpleRegionGrowingSegmentation
• interfaces.slicer.segmentation.specialized
  • BRAINSROIAuto
  • EMSegmentCommandLine
  • RobustStatisticsSegmenter
• interfaces.slicer.surface
  • GrayscaleModelMaker
  • LabelMapSmoothing
  • MergeModels
  • ModelMaker
  • ModelToLabelMap
  • ProbeVolumeWithModel
• interfaces.slicer.utilities
  • EMSegmentTransformToNewFormat
• interfaces.spm.model
  • EstimateContrast
  • EstimateModel
  • FactorialDesign
  • Level1Design
  • MultipleRegressionDesign
  • OneSampleTTestDesign
  • PairedTTestDesign
  • Threshold
  • ThresholdStatistics
  • TwoSampleTTestDesign
• interfaces.spm.preprocess
  • ApplyDeformations
  • Coregister
  • CreateWarped
  • DARTEL
  • DARTELNorm2MNI
  • FieldMap
  • NewSegment
  • Normalize
  • Normalize12
  • Realign
  • Segment
  • SliceTiming
  • Smooth
  • VBMSegment
• interfaces.spm.utils
  • Analyze2nii
  • ApplyInverseDeformation
  • ApplyTransform
  • CalcCoregAffine
  • DicomImport
  • Reslice
  • ResliceToReference
• interfaces.utility.base
  • AssertEqual
  • IdentityInterface
  • Merge
  • Rename
  • Select
  • Split
• interfaces.utility.csv
  • CSVReader
• interfaces.utility.wrappers
  • Function
• interfaces.vista.vista
  • Vnifti2Image
  • VtoMat
• interfaces.vtkbase
  • configure_input_data()
  • vtk_old()
  • vtk_output()
• interfaces.workbench.base
  • WBCommand
• interfaces.workbench.metric
  • MetricResample
• pkg_info
  • get_pkg_info()
  • pkg_commit_hash()
• sphinxext.plot_workflow
  • contains_doctest()
  • get_wf_formats()
  • mark_wf_labels()
  • out_of_date()
  • remove_coding()
  • render_figures()
  • run()
  • run_code()
  • setup()
  • unescape_doctest()
  • wf_directive()
• workflows.data
  • get_flirt_schedule()
• workflows.dmri.camino.connectivity_mapping
  • create_connectivity_pipeline()
• workflows.dmri.camino.diffusion
  • create_camino_dti_pipeline()
• workflows.dmri.camino.group_connectivity
  • create_group_connectivity_pipeline()
• workflows.dmri.connectivity.group_connectivity
  • concatcsv()
  • create_average_networks_by_group_workflow()
  • create_merge_group_network_results_workflow()
  • create_merge_group_networks_workflow()
  • create_merge_network_results_by_group_workflow()
  • create_merge_networks_by_group_workflow()
  • pullnodeIDs()
• workflows.dmri.connectivity.nx
  • create_cmats_to_csv_pipeline()
  • create_networkx_pipeline()
  • add_global_to_filename()
  • add_nodal_to_filename()
• workflows.dmri.dipy.denoise
  • nlmeans_pipeline()
  • bg_mask()
  • csf_mask()
• workflows.dmri.dtitk.tensor_registration
  • affine_tensor_pipeline()
  • diffeomorphic_tensor_pipeline()
• workflows.dmri.fsl.artifacts
  • all_fmb_pipeline()
  • all_fsl_pipeline()
  • all_peb_pipeline()
  • ecc_pipeline()
  • hmc_pipeline()
  • remove_bias()
  • sdc_fmb()
  • sdc_peb()
• workflows.dmri.fsl.dti
  • bedpostx_parallel()
  • create_bedpostx_pipeline()
  • merge_and_mean()
  • merge_and_mean_parallel()
  • transpose()
• workflows.dmri.fsl.epi
  • create_dmri_preprocessing()
  • create_eddy_correct_pipeline()
  • create_epidewarp_pipeline()
  • create_motion_correct_pipeline()
  • fieldmap_correction()
  • topup_correction()
• workflows.dmri.fsl.tbss
  • create_tbss_1_preproc()
  • create_tbss_2_reg()
  • create_tbss_3_postreg()
  • create_tbss_4_prestats()
  • create_tbss_all()
  • create_tbss_non_FA()
  • tbss1_op_string()
  • tbss4_op_string()
• workflows.dmri.fsl.utils
  • apply_all_corrections()
  • cleanup_edge_pipeline()
  • dwi_flirt()
  • vsm2warp()
  • add_empty_vol()
  • b0_average()
  • b0_indices()
  • compute_readout()
  • copy_hdr()
  • demean_image()
  • eddy_rotate_bvecs()
  • enhance()
  • extract_bval()
  • hmc_split()
  • insert_mat()
  • rads2radsec()
  • recompose_dwi()
  • recompose_xfm()
  • remove_comp()
  • reorient_bvecs()
  • rotate_bvecs()
  • siemens2rads()
  • time_avg()
• workflows.dmri.mrtrix.connectivity_mapping
  • create_connectivity_pipeline()
• workflows.dmri.mrtrix.diffusion
  • create_mrtrix_dti_pipeline()
• workflows.dmri.mrtrix.group_connectivity
  • create_group_connectivity_pipeline()
• workflows.fmri.fsl.estimate
  • create_fixed_effects_flow()
  • create_modelfit_workflow()
  • create_overlay_workflow()
• workflows.fmri.fsl.preprocess
  • create_featreg_preproc()
  • create_fsl_fs_preproc()
  • create_parallelfeat_preproc()
  • create_susan_smooth()
  • chooseindex()
  • create_reg_workflow()
  • getbtthresh()
  • getmeanscale()
  • getthreshop()
  • getusans()
  • pickfirst()
  • pickmiddle()
  • pickrun()
  • pickvol()
• workflows.fmri.spm.preprocess
  • create_DARTEL_template()
  • create_spm_preproc()
  • create_vbm_preproc()
• workflows.misc.utils
  • get_affine()
  • get_data_dims()
  • get_vox_dims()
  • id_list_from_lookup_table()
  • region_list_from_volume()
  • select_aparc()
  • select_aparc_annot()
• workflows.rsfmri.fsl.resting
  • create_realign_flow()
  • create_resting_preproc()
  • select_volume()
• workflows.smri.ants.ANTSBuildTemplate
  • ANTSTemplateBuildSingleIterationWF()
  • FlattenTransformAndImagesList()
  • GetFirstListElement()
  • MakeListsOfTransformLists()
  • MakeTransformListWithGradientWarps()
  • RenestDeformedPassiveImages()
• workflows.smri.ants.antsRegistrationBuildTemplate
  • antsRegistrationTemplateBuildSingleIterationWF()
  • FlattenTransformAndImagesList()
  • GetFirstListElement()
  • GetMovingImages()
  • GetPassiveImages()
  • MakeTransformListWithGradientWarps()
  • RenestDeformedPassiveImages()
  • SplitAffineAndWarpComponents()
  • makeListOfOneElement()
• workflows.smri.freesurfer.autorecon1
  • checkT1s()
  • create_AutoRecon1()
• workflows.smri.freesurfer.autorecon2
  • copy_ltas()
• workflows.smri.freesurfer.bem
  • create_bem_flow()
• workflows.smri.freesurfer.recon
  • create_reconall_workflow()
  • create_skullstripped_recon_flow()
• workflows.smri.freesurfer.utils
  • create_get_stats_flow()
  • create_getmask_flow()
  • create_tessellation_flow()
  • copy_file()
  • copy_files()
  • get_aparc_aseg()
  • getdefaultconfig()
  • mkdir_p()
• workflows.smri.niftyreg.groupwise
  • create_groupwise_average()
  • create_linear_gw_step()
  • create_nonlinear_gw_step()