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Interfaces and Algorithms
¶
Release:
0.11.0
Date:
September 18, 2015, 23:40 PDT
algorithms.icc
ICC
ICC_rep_anova()
algorithms.mesh
ComputeMeshWarp
MeshWarpMaths
P2PDistance
WarpPoints
algorithms.metrics
Distance
ErrorMap
FuzzyOverlap
Overlap
Similarity
algorithms.misc
AddCSVColumn
AddCSVRow
AddNoise
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
interfaces.afni.preprocess
Allineate
AutoTcorrelate
Autobox
Automask
Bandpass
BlurInMask
BrickStat
Calc
Copy
Despike
Detrend
Eval
Fim
Fourier
Maskave
Means
Merge
ROIStats
Refit
Resample
Retroicor
SkullStrip
TCat
TCorr1D
TCorrMap
TCorrelate
TShift
TStat
To3D
Volreg
Warp
ZCutUp
interfaces.afni.svm
SVMTest
SVMTrain
interfaces.ants.legacy
GenWarpFields
antsIntroduction
buildtemplateparallel
interfaces.ants.registration
Registration
interfaces.ants.resampling
ApplyTransforms
ApplyTransformsToPoints
WarpImageMultiTransform
WarpTimeSeriesImageMultiTransform
interfaces.ants.segmentation
Atropos
JointFusion
LaplacianThickness
N4BiasFieldCorrection
antsCorticalThickness
interfaces.ants.utils
AverageAffineTransform
AverageImages
JacobianDeterminant
MultiplyImages
interfaces.ants.visualization
ConvertScalarImageToRGB
CreateTiledMosaic
interfaces.c3
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.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
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.preprocess
Denoise
Resample
nlmeans_proxy()
resample_proxy()
interfaces.dipy.simulate
SimulateMultiTensor
interfaces.dipy.tensors
DTI
TensorMode
tensor_fitting()
interfaces.dipy.tracks
TrackDensityMap
interfaces.dynamic_slicer
SlicerCommandLine
interfaces.elastix.registration
AnalyzeWarp
ApplyWarp
PointsWarp
Registration
interfaces.elastix.utils
EditTransform
interfaces.freesurfer.model
Binarize
Concatenate
GLMFit
Label2Vol
MRISPreproc
MS_LDA
OneSampleTTest
SegStats
interfaces.freesurfer.preprocess
ApplyVolTransform
BBRegister
DICOMConvert
FitMSParams
MRIConvert
ParseDICOMDir
ReconAll
Resample
RobustRegister
Smooth
SynthesizeFLASH
UnpackSDICOMDir
interfaces.freesurfer.utils
ApplyMask
ExtractMainComponent
MRIMarchingCubes
MRIPretess
MRITessellate
MRIsConvert
MakeAverageSubject
SampleToSurface
SmoothTessellation
Surface2VolTransform
SurfaceSmooth
SurfaceSnapshots
SurfaceTransform
Tkregister2
interfaces.fsl.dti
BEDPOSTX
BEDPOSTX4
BEDPOSTX5
DTIFit
DistanceMap
FindTheBiggest
MakeDyadicVectors
ProbTrackX
ProbTrackX2
ProjThresh
TractSkeleton
VecReg
XFibres
XFibres4
XFibres5
interfaces.fsl.epi
ApplyTOPUP
EPIDeWarp
Eddy
EddyCorrect
EpiReg
PrepareFieldmap
SigLoss
TOPUP
interfaces.fsl.maths
ApplyMask
BinaryMaths
ChangeDataType
DilateImage
ErodeImage
IsotropicSmooth
MathsCommand
MaxImage
MeanImage
MultiImageMaths
SpatialFilter
TemporalFilter
Threshold
UnaryMaths
interfaces.fsl.model
Cluster
ContrastMgr
FEAT
FEATModel
FEATRegister
FILMGLS
FLAMEO
GLM
L2Model
Level1Design
MELODIC
MultipleRegressDesign
Randomise
SMM
SmoothEstimate
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
Slicer
Smooth
Split
SwapDimensions
WarpPoints
WarpPointsToStd
WarpUtils
interfaces.io
DataFinder
DataGrabber
DataSink
FreeSurferSource
IOBase
JSONFileGrabber
JSONFileSink
MySQLSink
SQLiteSink
SSHDataGrabber
SelectFiles
XNATSink
XNATSource
add_traits()
copytree()
push_file()
quote_id()
unquote_id()
interfaces.meshfix
MeshFix
interfaces.mipav.developer
JistBrainMgdmSegmentation
JistBrainMp2rageDuraEstimation
JistBrainMp2rageSkullStripping
JistBrainPartialVolumeFilter
JistCortexSurfaceMeshInflation
JistIntensityMp2rageMasking
JistLaminarProfileCalculator
JistLaminarProfileGeometry
JistLaminarProfileSampling
JistLaminarROIAveraging
JistLaminarVolumetricLayering
MedicAlgorithmImageCalculator
MedicAlgorithmLesionToads
MedicAlgorithmMipavReorient
MedicAlgorithmN3
MedicAlgorithmSPECTRE2010
MedicAlgorithmThresholdToBinaryMask
RandomVol
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
interfaces.mrtrix3.preprocess
ResponseSD
interfaces.mrtrix3.reconst
EstimateFOD
FitTensor
interfaces.mrtrix3.tracking
Tractography
interfaces.mrtrix3.utils
BrainMask
ComputeTDI
Generate5tt
Mesh2PVE
TCK2VTK
TensorMetrics
interfaces.nipy.model
EstimateContrast
FitGLM
interfaces.nipy.preprocess
ComputeMask
FmriRealign4d
SpaceTimeRealigner
Trim
interfaces.nipy.utils
Similarity
interfaces.nitime.analysis
CoherenceAnalyzer
interfaces.semtools.brains.classify
BRAINSPosteriorToContinuousClass
interfaces.semtools.brains.segmentation
BRAINSTalairach
BRAINSTalairachMask
SimilarityIndex
interfaces.semtools.brains.utilities
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
NewSegment
Normalize
Normalize12
Realign
Segment
SliceTiming
Smooth
VBMSegment
interfaces.spm.utils
Analyze2nii
ApplyInverseDeformation
ApplyTransform
CalcCoregAffine
DicomImport
Reslice
ResliceToReference
interfaces.utility
AssertEqual
CSVReader
Function
IdentityInterface
Merge
Rename
Select
Split
interfaces.vista.vista
Vnifti2Image
VtoMat
pkg_info
get_pkg_info()
pkg_commit_hash()
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.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()
merge_and_mean()
merge_and_mean_parallel()
create_bedpostx_pipeline()
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()
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()
extract_noise_components()
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.bem
create_bem_flow()
workflows.smri.freesurfer.recon
create_skullstripped_recon_flow()
workflows.smri.freesurfer.utils
create_get_stats_flow()
create_getmask_flow()
create_tessellation_flow()
get_aparc_aseg()