Home
·
Quickstart
·
User Guide and Examples
·
Interfaces Index
·
Developers
·
About
·
Nipy
Versions
Release
Devel
1.5.0-dev
1.5.0.dev0
Download
Github
Links
Docs:
Stable
·
Dev
Code:
Github
·
Bugs-Requests
Forum:
User
·
Developer
Chat:
Gitter
·
Slack
Funding
·
·
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
Z
A
ABoverlap
ACompCor
ACPCTransform
ActivationCount
ACTPrepareFSL
add_class_to_package() (in module nipype.interfaces.slicer.generate_classes)
add_dicts_by_key() (in module nipype.interfaces.cmtk.nx)
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
AddCSVRow
AddNoise
AddScalarVolumes
AddXFormToHeader
Affine
AffineInitializer
AffineRegistration
AffineTask
AffScalarVol
affScalarVolTask
AffSymTensor3DVol
affSymTensor3DVolTask
AFNICommand
AFNICommandBase
AFNIPythonCommand
AFNItoNIFTI
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.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)
AlignEpiAnatPy
Allineate
always_run() (nipype.interfaces.base.core.Interface property)
Analyze2nii
AnalyzeHeader
AnalyzeWarp
ANTS
ANTSCommand
AntsJointFusion
Aparc2Aseg
Apas2Aseg
APMQball
ApplyDeformations
ApplyInverseDeformation
ApplyMask
,
[1]
ApplyTOPUP
ApplyTransform
ApplyTransforms
ApplyTransformsToPoints
ApplyVolTransform
ApplyWarp
,
[1]
ApplyXFM
AR1Image
ArtifactDetect
AssertEqual
Atropos
Autobox
Automask
AutoTcorrelate
AutoTLRC
Average
average_networks() (in module nipype.interfaces.cmtk.nx)
AverageAffineTransform
AverageImages
AverageNetworks
AvScale
Axialize
B
B0Calc
Bandpass
base_dir (nipype.pipeline.engine.base.EngineBase attribute)
BaseInterface
BasePath (class in nipype.interfaces.base.traits_extension)
BaseTraitedSpec (class in nipype.interfaces.base.specs)
BBox
BBRegister
BDP
Beast
BEDPOSTX
BEDPOSTX5
BestLinReg
BET
Bfc
bids_gen_info() (in module nipype.algorithms.modelgen)
BIDSDataGrabber
BIDSDataGrabberInputSpec (class in nipype.interfaces.io)
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
build_doc() (in module nipype.utils.docparse)
BuildConnectome
Bunch (class in nipype.interfaces.base.support)
C
C3d
C3dAffineTool
cache() (nipype.caching.memory.Memory method)
,
[1]
CALabel
Calc
,
[1]
calc_moments() (in module nipype.algorithms.misc)
CalcCoregAffine
CalcTopNCC
calculate_resource_timeseries() (in module nipype.utils.draw_gantt_chart)
CalculateMedian
CalculateNormalizedMoments
Camino2Trackvis
can_resume() (nipype.interfaces.base.core.Interface property)
CannyEdge
CannySegmentationLevelSetImageFilter
canonicalize_env() (in module nipype.utils.filemanip)
CANormalize
capture_provenance() (in module nipype.interfaces.io)
CARegister
CastScalarVolume
Cat
CatMatvec
CenterMass
Cerebro
CFFBaseInterface
CFFConverter
ChangeDataType
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
CheckTalairachAlignment
CiftiSmooth
Classifier
clean_working_directory() (in module nipype.pipeline.engine.utils)
Cleaner
cleanup() (nipype.utils.tmpdirs.TemporaryDirectory method)
CleanUpOverlapLabels
clear_previous_runs() (nipype.caching.memory.Memory method)
,
[1]
,
[2]
clear_runs_since() (nipype.caching.memory.Memory method)
ClipLevel
clone() (nipype.pipeline.engine.base.EngineBase method)
(nipype.pipeline.engine.workflows.Workflow method)
Cluster
cmat() (in module nipype.interfaces.cmtk.cmtk)
cmd (nipype.interfaces.fsl.fix.Classifier attribute)
(nipype.interfaces.fsl.fix.Cleaner attribute)
(nipype.interfaces.fsl.fix.FeatureExtractor attribute)
(nipype.interfaces.fsl.fix.Training attribute)
cmd() (nipype.interfaces.afni.base.AFNIPythonCommand property)
(nipype.interfaces.base.core.CommandLine property)
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
combine_mask_files() (in module nipype.algorithms.confounds)
CommandLine
CommandLineDtitk
compareTractInclusion
CompCor
Complex
ComposeMultiTransform
ComposeXfm
ComposeXfmTask
CompositeTransformUtil
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
ComputeEigensystem
ComputeFractionalAnisotropy
ComputeMask
ComputeMeanDiffusivity
ComputeMeshWarp
ComputeTDI
ComputeTensorTrace
concat_files() (in module nipype.interfaces.mrtrix.tensors)
Concatenate
ConcatenateLTA
CondorDAGManPlugin (class in nipype.pipeline.plugins.dagman)
CondorPlugin (class in nipype.pipeline.plugins.condor)
configuration() (in module nipype.interfaces.dipy.setup)
configure_input_data() (in module nipype.interfaces.vtkbase)
Conmat
connect() (nipype.pipeline.engine.workflows.Workflow method)
ConstrainedSphericalDeconvolution
container_to_string() (in module nipype.utils.misc)
Contrast
ContrastMgr
Convert
convert_to_traits_type() (in module nipype.interfaces.dipy.base)
ConvertDset
ConvertScalarImageToRGB
ConvertWarp
ConvertXFM
Copy
,
[1]
copy2subjdir() (in module nipype.interfaces.freesurfer.utils)
copyfile() (in module nipype.utils.filemanip)
copyfiles() (in module nipype.utils.filemanip)
CopyGeom
CopyMeta
copytree() (in module nipype.interfaces.io)
Coregister
Cortex
CorticalThickness
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
CreateMatrix
CreateNifti
CreateNodes
createoutputdirs() (in module nipype.interfaces.freesurfer.utils)
CreateTiledMosaic
CreateWarped
crop_and_move_datasets() (in module nipype.interfaces.cmtk.parcellation)
CSD
CSVReader
Curvature
CurvatureAnisotropicDiffusion
CurvatureStats
cwd() (nipype.utils.config.NipypeConfig property)
D
daemon() (nipype.pipeline.plugins.legacymultiproc.NonDaemonMixin property)
DARTEL
DARTELNorm2MNI
DataFinder
DataGrabber
DataSink
datefmt (nipype.utils.logger.Logging attribute)
Dcm2nii
Dcm2niix
DcmStack
DebugPlugin (class in nipype.pipeline.plugins.debug)
Deconvolve
DEF_SAMPLING_STRATEGY (nipype.interfaces.ants.registration.Registration attribute)
default_submit_template (nipype.pipeline.plugins.dagman.CondorDAGManPlugin attribute)
DegreeCentrality
Denoise
DenoiseImage
Despike
Detrend
Dewisp
Dfs
DICOMConvert
DicomImport
DicomToNrrdConverter
dict_diff() (in module nipype.utils.misc)
dictcopy() (nipype.interfaces.base.support.Bunch method)
Diffeo
DiffeoScalarVol
diffeoScalarVolTask
DiffeoSymTensor3DVol
diffeoSymTensor3DVolTask
DiffeoTask
DiffusionTensorScalarMeasurements
DiffusionTensorStreamlineTrack
DiffusionWeightedVolumeMasking
DilateImage
,
[1]
DilateMask
dipy_to_nipype_interface() (in module nipype.interfaces.dipy.base)
dipy_version() (in module nipype.interfaces.dipy.base)
DipyBaseInterface
DipyDiffusionInterface
Directions2Amplitude
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
,
[1]
DistanceMap
DistanceMaps
DistributedPluginBase (class in nipype.pipeline.plugins.base)
Dot
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
DTI
dtiaverage
dtiestim
DTIexport
DTIFit
,
[1]
DTIimport
dtiprocess
DTIRecon
DTITKRenameMixin (class in nipype.interfaces.dtitk.base)
DTITracker
DTLUTGen
DTMetric
DualRegression
Dump
DumpBinaryTrainingVectors
DWI2SphericalHarmonicsImage
DWI2Tensor
DWIBiasCorrect
DWICompare
DWIConvert
DWIDenoise
DWIExtract
DWIJointRicianLMMSEFilter
DWIRicianLMMSEFilter
DWISimpleCompare
DWIToDTIEstimation
DwiTool
DWIUnbiasedNonLocalMeansFilter
DynamicTraitedSpec (class in nipype.interfaces.base.specs)
E
ECM
Eddy
EddyCorrect
EddyQuad
Edge3
EditTransform
EditWMwithAseg
EM
emptydirs() (in module nipype.utils.filemanip)
EMRegister
EMSegmentCommandLine
EMSegmentTransformToNewFormat
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
EpiReg
Erode
ErodeImage
,
[1]
ErrorMap
ESLR
EstimateContrast
,
[1]
EstimateFOD
EstimateModel
EstimateResponseForSH
EstimateResponseSH
EulerNumber
Eval
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
export() (nipype.pipeline.engine.workflows.Workflow method)
export_graph() (in module nipype.pipeline.engine.utils)
ExportFile
Extract
extract() (in module nipype.interfaces.cmtk.parcellation)
ExtractMainComponent
extractNrrdVectorIndex
ExtractROI
ExtractSkeleton
F
FactorialDesign
fallback_svd() (in module nipype.algorithms.confounds)
FAST
fcsv_to_hdf5
FEAT
FEATModel
FEATRegister
FeatureExtractor
fiberprocess
fiberstats
fibertrack
FiducialRegistration
FieldMap
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_to_list() (in module nipype.utils.filemanip)
fileno() (nipype.utils.subprocess.Stream method)
fill_in_missing_output_path() (in module nipype.utils.nipype2boutiques)
FillLesions
FILMGLS
FilterRegressor
FilterTracks
Fim
find_indices() (in module nipype.utils.misc)
FindCenterOfBrain
FindShPeaks
FindTheBiggest
FIRST
FitAsl
FitDwi
FitGLM
FitMSParams
FitQt1
FitTensor
fix_keys_for_gexf() (in module nipype.interfaces.cmtk.nx)
FixTopology
FLAMEO
flatten() (in module nipype.utils.misc)
FlippedDifference
FLIRT
fltcols() (in module nipype.utils.matlabtools)
fmt (nipype.utils.logger.Logging attribute)
fname() (nipype.utils.profiler.ResourceMonitor property)
fname_presuffix() (in module nipype.utils.filemanip)
fnames_presuffix() (in module nipype.utils.filemanip)
FNIRT
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)
Fourier
FramewiseDisplacement
free_display() (in module nipype.utils.config)
FreeSurferSource
FSCommand
FSCommandOpenMP
FSL2MRTrix
FSL2Scheme
FSLCommand
FSLXCommand
FSScriptCommand
FSSurfaceCommand
ftypes (nipype.interfaces.afni.base.Info attribute)
(nipype.interfaces.fsl.base.Info attribute)
FUGUE
fullname() (nipype.pipeline.engine.base.EngineBase property)
func_is_3d() (in module nipype.interfaces.spm.base)
Function
FuseSegmentations
FuzzyOverlap
,
[1]
FWHMx
G
GaussianBlurImageFilter
gcd() (in module nipype.algorithms.modelgen)
GCOR
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
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
GenerateBrainClippedImage
GenerateCsfClippedFromClassifiedImage
GenerateDirections
GenerateEdgeMapImage
GenerateLabelMapFromProbabilityMap
GeneratePurePlugMask
GenerateSummedGradientImage
GenerateTestImage
GenerateWhiteMatterMask
Gennlxfm
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_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_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_version() (nipype.interfaces.niftyseg.base.NiftySegCommand method)
get_vox_dims() (in module nipype.interfaces.mrtrix.convert)
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
GLMFit
grab_doc() (in module nipype.utils.docparse)
(in module nipype.utils.spm_docs)
grab_xml() (in module nipype.interfaces.slicer.generate_classes)
GradientAnisotropicDiffusion
GradientAnisotropicDiffusionImageFilter
GraphPluginBase (class in nipype.pipeline.plugins.base)
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() (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
Hist
HistogramMatching
HistogramMatchingFilter
human_order_sorted() (in module nipype.utils.misc)
I
ICA_AROMA
ICC
ICC_rep_anova() (in module nipype.algorithms.icc)
IdentityInterface
Image2Voxel
ImageFile (class in nipype.interfaces.base.traits_extension)
ImageFileSPM (class in nipype.interfaces.spm.base)
ImageInfo
ImageLabelCombine
ImageMaths
ImageMeants
ImageRegionPlotter
ImageStats
,
[1]
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.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
InTemporaryDirectory (class in nipype.utils.tmpdirs)
IntensityDifferenceMetric
intensitymap_file_basename() (nipype.interfaces.fsl.preprocess.FNIRT class method)
Interface (class in nipype.interfaces.base.core)
interface() (nipype.pipeline.engine.nodes.Node property)
InterfaceResult (class in nipype.interfaces.base.support)
InvWarp
IOBase
IPythonPlugin (class in nipype.pipeline.plugins.ipython)
is_cached() (nipype.pipeline.engine.nodes.Node method)
is_container() (in module nipype.utils.misc)
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
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
JistBrainMgdmSegmentation
JistBrainMp2rageDuraEstimation
JistBrainMp2rageSkullStripping
JistBrainPartialVolumeFilter
JistCortexSurfaceMeshInflation
JistIntensityMp2rageMasking
JistLaminarProfileCalculator
JistLaminarProfileGeometry
JistLaminarProfileSampling
JistLaminarROIAveraging
JistLaminarVolumetricLayering
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
JointHistogram
JSONFileGrabber
JSONFileSink
K
KellyKapowski
keywords (nipype.interfaces.nipy.preprocess.SpaceTimeRealigner attribute)
L
L2Model
l_outputs() (in module nipype.interfaces.brainsuite.brainsuite)
Label2Annot
Label2Label
Label2Vol
LabelConfig
LabelConvert
LabelFusion
LabelGeometry
LabelMapSmoothing
LandmarksCompare
landmarksConstellationAligner
landmarksConstellationWeights
LaplacianThickness
LegacyMultiProcPlugin (class in nipype.pipeline.plugins.legacymultiproc)
length() (in module nipype.interfaces.cmtk.cmtk)
Level1Design
,
[1]
LFCD
LibraryBaseInterface
LinearPlugin (class in nipype.pipeline.plugins.linear)
LinearRegistration
LinRecon
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_template() (in module nipype.interfaces.fsl.model)
loadcrash() (in module nipype.utils.filemanip)
loadpkl() (in module nipype.utils.filemanip)
LocalBistat
Localstat
log_nodes_cb() (in module nipype.utils.profiler)
log_to_dict() (in module nipype.utils.draw_gantt_chart)
logdebug_dict_differences() (nipype.utils.logger.Logging method)
Logging (class in nipype.utils.logger)
LookupMeta
looseversion() (nipype.interfaces.freesurfer.base.Info class method)
(nipype.interfaces.mrtrix3.base.Info class method)
LSFPlugin (class in nipype.pipeline.plugins.lsf)
LTAConvert
M
main() (in module nipype.utils.nipype_cmd)
make_key_func() (in module nipype.interfaces.dcmstack)
MakeAverageSubject
MakeDyadicVectors
makefmtlist() (in module nipype.algorithms.misc)
MakeSurfaces
maketypelist() (in module nipype.algorithms.misc)
MapNode (class in nipype.pipeline.engine.nodes)
Maskave
MaskScalarVolume
MaskTool
Math
MathsCommand
,
[1]
Matlab2CSV
MatlabCommand
maxcurvature
MaxImage
MaxnImage
MCFLIRT
MeanImage
Means
MeasureImageSimilarity
MedianFilter3D
MedianImage
MedianImageFilter
MedicAlgorithmImageCalculator
MedicAlgorithmLesionToads
MedicAlgorithmMipavReorient
MedicAlgorithmN3
MedicAlgorithmSPECTRE2010
MedicAlgorithmThresholdToBinaryMask
MELODIC
mem_gb() (nipype.pipeline.engine.nodes.Node property)
Memory (class in nipype.caching.memory)
Merge
,
[1]
,
[2]
,
[3]
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
MergeCSVFiles
MergeModels
MergeNifti
MergeROIs
MESD
Mesh2PVE
MeshFix
MeshWarpMaths
MetricResample
MinImage
mkdir_p() (in module nipype.utils.config)
mlab_tempfile() (in module nipype.utils.matlabtools)
MNIBiasCorrection
ModelFit
ModelMaker
ModelToLabelMap
modify_paths() (in module nipype.pipeline.engine.utils)
ModifyAffine
MotionOutliers
MpiCommandLine
MPRtoMNI305
MRConvert
,
[1]
MRDeGibbs
MRIConvert
MRICoreg
MRIFill
MRIMarchingCubes
MRIPretess
MRIsCALabel
MRIsCalc
MRIsCombine
MRIsConvert
MRIsExpand
MRIsInflate
MRISPreproc
MRISPreprocReconAll
MRITessellate
MRMath
MRMultiply
MRResize
MRTransform
MRTrix2TrackVis
MRTrix3Base
MRTrixInfo
MRTrixViewer
MS_LDA
MultiImageMaths
MultiObject (class in nipype.interfaces.base.traits_extension)
MultipleRegressDesign
MultipleRegressionDesign
MultiplyImages
MultiplyScalarVolumes
MultiProcPlugin (class in nipype.pipeline.plugins.multiproc)
MultiResolutionAffineRegistration
MySQLSink
N
N4BiasFieldCorrection
N4ITKBiasFieldCorrection
n_procs() (nipype.pipeline.engine.nodes.Node property)
name() (nipype.interfaces.spm.base.Info class method)
(nipype.pipeline.engine.base.EngineBase property)
needed_outputs() (nipype.pipeline.engine.nodes.Node property)
NeighborhoodMean
NeighborhoodMedian
NetworkBasedStatistic
NetworkXMetrics
NewSegment
NIfTIDT2Camino
NiftiGeneratorBase
NiftyFitCommand
NiftyRegCommand
NiftySegCommand
NilearnBaseInterface
NipyBaseInterface
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.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.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.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.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.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.utils (module)
nipype.utils.config (module)
nipype.utils.docparse (module)
nipype.utils.draw_gantt_chart (module)
nipype.utils.filemanip (module)
nipype.utils.functions (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.spm_docs (module)
nipype.utils.subprocess (module)
nipype.utils.tmpdirs (module)
NipypeConfig (class in nipype.utils.config)
NipypeInterfaceError (class in nipype.interfaces.base.support)
NipypeTester (class in nipype)
NitimeBaseInterface
nlmeans_proxy() (in module nipype.interfaces.dipy.preprocess)
NlpFit
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)
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
Norm
Normalize
,
[1]
Normalize12
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
Notes
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
NwarpApply
NwarpCat
O
OARPlugin (class in nipype.pipeline.plugins.oar)
ODFRecon
ODFTracker
on_cifs() (in module nipype.utils.filemanip)
OneDToolPy
OneSampleTTest
OneSampleTTestDesign
OneTimeProperty (class in nipype.utils.onetime)
OrientScalarVolume
orth() (in module nipype.algorithms.modelgen)
OtsuThresholdImageFilter
OtsuThresholdSegmentation
OutlierCount
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
,
[1]
Overlay
P
P2PDistance
package_check() (in module nipype.utils.misc)
package_version (nipype.interfaces.base.specs.BaseTraitedSpec attribute)
PackageInfo (class in nipype.interfaces.base.core)
Paint
PairedTTestDesign
Parcellate
ParcellationStats
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.workbench.base.Info static method)
ParseDICOMDir
PatchMatch
path() (nipype.interfaces.spm.base.Info class method)
path_resolve() (in module nipype.utils.filemanip)
PBSGraphPlugin (class in nipype.pipeline.plugins.pbsgraph)
PBSPlugin (class in nipype.pipeline.plugins.pbs)
PercentileImage
PETPVC
PETStandardUptakeValueComputation
Pialmesh
PickAtlas
PicoPDFs
Pik
PipeFunc (class in nipype.caching.memory)
plot_confound() (in module nipype.algorithms.confounds)
PlotMotionParams
PlotTimeSeries
PluginBase (class in nipype.pipeline.plugins.base)
PointsWarp
PowerSpectrum
PRELUDE
PrepareFieldmap
print_dictionary() (nipype.pipeline.plugins.sge.QstatSubstitute method)
ProbabilisticSphericallyDeconvolutedStreamlineTrack
ProbeVolumeWithModel
ProbTrackX
ProbTrackX2
Process (nipype.pipeline.plugins.legacymultiproc.NonDaemonForkContext attribute)
(nipype.pipeline.plugins.legacymultiproc.NonDaemonForkServerContext attribute)
(nipype.pipeline.plugins.legacymultiproc.NonDaemonSpawnContext attribute)
ProcStreamlines
ProgressPercentage (class in nipype.interfaces.io)
ProjThresh
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
Q
QBallMX
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
Quickshear
quote_id() (in module nipype.interfaces.io)
Qwarp
QwarpPlusMinus
R
raise_exception() (nipype.interfaces.base.core.CommandLine method)
Randomise
RandomVol
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
RealignUnwarp
rebase_path_traits() (in module nipype.interfaces.base.traits_extension)
ReconAll
references_ (nipype.algorithms.confounds.CompCor attribute)
(nipype.algorithms.confounds.ComputeDVARS attribute)
(nipype.algorithms.confounds.FramewiseDisplacement attribute)
(nipype.interfaces.afni.base.AFNICommand attribute)
(nipype.interfaces.afni.utils.Edge3 attribute)
(nipype.interfaces.afni.utils.FWHMx attribute)
(nipype.interfaces.ants.segmentation.KellyKapowski attribute)
(nipype.interfaces.base.core.BaseInterface attribute)
(nipype.interfaces.fsl.base.FSLCommand attribute)
(nipype.interfaces.fsl.model.FLAMEO attribute)
(nipype.interfaces.petpvc.PETPVC attribute)
(nipype.interfaces.quickshear.Quickshear attribute)
(nipype.interfaces.spm.base.SPMCommand attribute)
Refit
RegAladin
RegAverage
RegF3D
Register
RegisterAVItoTalairach
Registration
,
[1]
RegistrationSynQuick
RegJacobian
RegMeasure
RegResample
regress_poly() (in module nipype.algorithms.confounds)
RegTools
RegTransform
ReHo
RelabelHypointensities
relpath() (in module nipype.utils.filemanip)
Remlfit
remove_all_edges() (in module nipype.interfaces.cmtk.nx)
remove_identical_paths() (in module nipype.algorithms.misc)
remove_nodes() (nipype.pipeline.engine.workflows.Workflow method)
RemoveIntersection
RemoveNeck
Rename
RenameInputSpec (class in nipype.interfaces.utility.base)
reorder_cmd_line_args() (in module nipype.utils.nipype2boutiques)
Reorient
Reorient2Std
replace_opts() (in module nipype.utils.docparse)
replaceext() (in module nipype.algorithms.misc)
ReplaceFSwithFIRST
report_crash() (in module nipype.pipeline.plugins.tools)
report_nodes_not_run() (in module nipype.pipeline.plugins.tools)
ReportCapableInterface
Resample
,
[1]
,
[2]
,
[3]
resample_proxy() (in module nipype.interfaces.dipy.preprocess)
ResampleDTIVolume
ResampleScalarVectorDWIVolume
ResampleScalarVolume
Rescale
Reshape
Reslice
ResliceToReference
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)
resource_monitor() (nipype.utils.config.NipypeConfig property)
ResourceMonitor (class in nipype.utils.profiler)
ResponseSD
RESTORE
result() (nipype.pipeline.engine.nodes.Node property)
Retroicor
reverse_opt_map() (in module nipype.utils.docparse)
rgetcwd() (in module nipype.utils.misc)
Rigid
RigidRegistration
RigidTask
rm_all_but() (in module nipype.caching.memory)
RobustFOV
RobustRegister
RobustStatisticsSegmenter
RobustTemplate
ROIGen
ROIStats
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.utils.profiler.ResourceMonitor method)
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)
S
S3DataGrabber
s3tolocal() (nipype.interfaces.io.S3DataGrabber method)
safe_encode() (in module nipype.utils.provenance)
SampleToSurface
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
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
search_files() (in module nipype.interfaces.dcm2nii)
Seg
Segment
SegmentCC
SegmentWM
SegStats
SegStatsReconAll
Select
SelectFiles
SEMLikeCommandLine
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_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)
SFLUTGen
SFPeaks
SFPICOCalibData
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)
Shredder
ShuffleVectorsModule
SigLoss
,
[1]
SignalExtraction
silentrm() (in module nipype.utils.filemanip)
Similarity
,
[1]
SimilarityIndex
SimpleInterface
SimpleRegionGrowingSegmentation
SimpleThreshold
simplify_list() (in module nipype.utils.filemanip)
SimulateMultiTensor
Skullfinder
SkullStrip
Slice
Slicer
SlicerCommandLine
,
[1]
SliceTimer
SliceTiming
SLURMGraphPlugin (class in nipype.pipeline.plugins.slurmgraph)
SLURMPlugin (class in nipype.pipeline.plugins.slurm)
SMM
Smooth
,
[1]
,
[2]
SmoothEstimate
SmoothTessellation
SomaFlowPlugin (class in nipype.pipeline.plugins.somaflow)
SpaceTimeRealigner
SpatialFilter
SpecifyModel
SpecifySparseModel
SpecifySPMModel
Sphere
SphericalAverage
SphericalCoordinateGeneration
SphericallyDeconvolutedStreamlineTrack
SplineFilter
Split
,
[1]
split_filename() (in module nipype.utils.filemanip)
split_rois() (in module nipype.algorithms.misc)
SplitNifti
SplitROIs
spm_hrf() (in module nipype.algorithms.modelgen)
SPMCommand
SQLiteSink
SSHDataGrabber
standard_image() (nipype.interfaces.afni.base.Info static method)
(nipype.interfaces.fsl.base.Info static method)
STAPLEAnalysis
StatsCommand
StdImage
StdOutCommandLine
StimulusCorrelation
stop() (nipype.utils.profiler.ResourceMonitor 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
StreamlineTractography
strip_temp() (in module nipype.pipeline.engine.utils)
subjectsdir() (nipype.interfaces.freesurfer.base.Info class method)
SubtractScalarVolumes
Surface2VolTransform
SurfaceSmooth
SurfaceSnapshots
SurfaceTransform
SUSAN
SVAdjustVoxSp
SVAdjustVoxSpTask
SVMTest
SVMTrain
SVReg
SVResample
SVResampleTask
SwapDimensions
synchronize_iterables() (in module nipype.pipeline.engine.utils)
Synthesize
SynthesizeFLASH
T
TalairachAVI
TalairachQC
Tca
TCat
TCatSubBrick
TCK2VTK
TCompCor
TCorr1D
TCorrelate
TCorrMap
TemporalFilter
TemporaryDirectory (class in nipype.utils.tmpdirs)
Tensor2ApparentDiffusion
Tensor2FractionalAnisotropy
Tensor2Vector
TensorMetrics
TensorMode
terminal_output() (nipype.interfaces.base.core.CommandLine property)
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_get() (nipype.interfaces.base.specs.BaseTraitedSpec method)
transform_to_affine() (in module nipype.interfaces.mrtrix.convert)
Trim
trim() (in module nipype.utils.misc)
TShift
TSmooth
TSNR
,
[1]
TStat
TupleMaths
TVAdjustOriginTask
TVAdjustVoxSp
TVAdjustVoxSpTask
TVResample
TVResampleTask
TVTKBaseInterface
TVtool
TVtoolTask
TwoSampleTTestDesign
U
UKFTractography
UnaryMaths
,
[1]
UnaryStats
UnbiasedNonLocalMeans
Undump
unflatten() (in module nipype.utils.misc)
Unifize
UnpackSDICOMDir
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)
V
validate() (nipype.interfaces.base.traits_extension.BasePath method)
(nipype.interfaces.base.traits_extension.File method)
(nipype.interfaces.base.traits_extension.MultiObject method)
VBMSegment
VBRAINSDemonWarp
,
[1]
VecReg
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.core.PackageInfo class method)
(nipype.interfaces.base.support.InterfaceResult property)
(nipype.interfaces.dcm2nii.Dcm2niix property)
(nipype.interfaces.diffusion_toolkit.base.Info static method)
(nipype.interfaces.freesurfer.base.FSCommand property)
(nipype.interfaces.freesurfer.preprocess.ReconAll property)
(nipype.interfaces.fsl.base.FSLCommand property)
(nipype.interfaces.minc.base.Info static method)
(nipype.interfaces.mrtrix3.base.MRTrix3Base property)
(nipype.interfaces.niftyreg.base.NiftyRegCommand property)
(nipype.interfaces.spm.base.Info class method)
(nipype.interfaces.spm.base.SPMCommand property)
(nipype.interfaces.workbench.base.WBCommand property)
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.workbench.base.Info attribute)
version_file (nipype.interfaces.base.core.PackageInfo attribute)
version_from_command() (nipype.interfaces.base.core.CommandLine method)
Vnifti2Image
Volcentre
Voliso
Volpad
Volreg
VolSymm
VolumeMask
VotingBinaryHoleFillingImageFilter
vtk_old() (in module nipype.interfaces.vtkbase)
vtk_output() (in module nipype.interfaces.vtkbase)
vtk_version() (in module nipype.interfaces.vtkbase)
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
which() (in module nipype.utils.filemanip)
Workflow (class in nipype.pipeline.engine.workflows)
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
XFibres5
XfmAvg
XfmConcat
XfmInvert
XNATSink
XNATSource
Z
Zcat
ZCutUp
Zeropad