Library API (application program interface)

Information on specific functions, classes, and methods.

• niworkflows.anat package
  • Submodules
    • niworkflows.anat.ants module
      • init_atropos_wf()
      • init_brain_extraction_wf()
      • init_n4_only_wf()
    • niworkflows.anat.coregistration module
      • compare_xforms()
      • init_bbreg_wf()
    • niworkflows.anat.freesurfer module
      • init_gifti_surface_wf()
    • niworkflows.anat.skullstrip module
      • afni_wf()
• niworkflows.cli package
  • Submodules
    • niworkflows.cli.boldref module
      • get_parser()
      • main()
• niworkflows.data package
  • load()
  • load.readable()
  • load.as_path()
  • load.cached()
• niworkflows.dwi package
• niworkflows.engine package
  • Submodules
    • niworkflows.engine.plugin module
      • DistributedPluginBase
        • DistributedPluginBase.run()
      • MultiProcPlugin
      • PluginBase
        • PluginBase.run()
      • run_node()
    • niworkflows.engine.workflows module
      • LiterateWorkflow
        • LiterateWorkflow.visit_desc()
• niworkflows.func package
  • Submodules
    • niworkflows.func.util module
      • init_bold_reference_wf()
      • init_enhance_and_skullstrip_bold_wf()
      • init_skullstrip_bold_wf()
• niworkflows.interfaces package
  • Subpackages
    • niworkflows.interfaces.reportlets package
      • Submodules
        • niworkflows.interfaces.reportlets.base module
          • RegistrationRC
          • ReportingInterface
          • SegmentationRC
          • SurfaceSegmentationRC
        • niworkflows.interfaces.reportlets.masks module
          • ACompCorRPT
          • BETRPT
          • BrainExtractionRPT
          • ROIsPlot
          • SimpleShowMaskRPT
          • TCompCorRPT
        • niworkflows.interfaces.reportlets.registration module
          • ANTSApplyTransformsRPT
          • ANTSRegistrationRPT
          • ApplyTOPUPRPT
          • ApplyXFMRPT
          • BBRegisterRPT
          • FLIRTRPT
          • FUGUERPT
          • MRICoregRPT
          • ResampleBeforeAfterRPT
          • SimpleBeforeAfterRPT
          • SpatialNormalizationRPT
        • niworkflows.interfaces.reportlets.segmentation module
          • FASTRPT
          • ICA_AROMARPT
          • MELODICRPT
          • ReconAllRPT
  • Submodules
    • niworkflows.interfaces.bids module
      • BIDSDataGrabber
      • BIDSFreeSurferDir
      • BIDSInfo
        • BIDSInfo.output_spec
      • DerivativesDataSink
        • DerivativesDataSink.out_path_base
      • PrepareDerivative
      • ReadSidecarJSON
        • ReadSidecarJSON.layout
        • ReadSidecarJSON.output_spec
      • SaveDerivative
    • niworkflows.interfaces.bold module
      • NonsteadyStatesDetector
    • niworkflows.interfaces.cifti module
      • CiftiNameSource
      • GenerateCifti
    • niworkflows.interfaces.confounds module
      • ExpandModel
      • NormalizeMotionParams
      • SpikeRegressors
      • exponential_terms()
      • parse_expression()
      • parse_formula()
      • spike_regressors()
      • temporal_derivatives()
    • niworkflows.interfaces.conftest module
      • data_dir()
    • niworkflows.interfaces.fixes module
      • FixHeaderApplyTransforms
      • FixHeaderRegistration
      • FixN4BiasFieldCorrection
    • niworkflows.interfaces.freesurfer module
      • FSDetectInputs
      • FSInjectBrainExtracted
      • MakeMidthickness
        • MakeMidthickness.cmdline
      • MedialNaNs
      • PatchedBBRegisterRPT
      • PatchedConcatenateLTA
        • PatchedConcatenateLTA.lta_outputs
      • PatchedLTAConvert
        • PatchedLTAConvert.lta_outputs
      • PatchedMRICoregRPT
      • PatchedRobustRegister
        • PatchedRobustRegister.lta_outputs
      • RefineBrainMask
      • StructuralReference
        • StructuralReference.cmdline
      • TruncateLTA
        • TruncateLTA.lta_outputs
      • detect_inputs()
      • fix_lta_length()
      • grow_mask()
      • inject_skullstripped()
      • medial_wall_to_nan()
      • mri_info()
      • refine_aseg()
    • niworkflows.interfaces.header module
      • CopyHeader
      • CopyXForm
        • CopyXForm.output_spec
      • MatchHeader
      • SanitizeImage
      • ValidateImage
    • niworkflows.interfaces.images module
      • Conform
      • IntraModalMerge
      • RegridToZooms
      • RobustAverage
      • SignalExtraction
      • TemplateDimensions
      • normalize_xform()
      • reorient()
    • niworkflows.interfaces.itk module
      • MCFLIRT2ITK
      • MultiApplyTransforms
    • niworkflows.interfaces.morphology module
      • BinaryDilation
      • BinarySubtraction
      • image_binary_dilation()
    • niworkflows.interfaces.nibabel module
      • ApplyMask
      • Binarize
      • BinaryDilation
      • DemeanImage
      • FilledImageLike
      • GenerateSamplingReference
      • IntensityClip
      • MapLabels
      • MergeROIs
      • MergeSeries
      • RegridToZooms
      • ReorientImage
      • SplitSeries
      • reorient_file()
      • reorient_image()
    • niworkflows.interfaces.nilearn module
      • ComputeEPIMask
      • MaskEPI
      • Merge
    • niworkflows.interfaces.nitransforms module
      • ConcatenateXFMs
      • concatenate_xfms()
    • niworkflows.interfaces.norm module
      • SpatialNormalization
      • create_cfm()
      • mask()
    • niworkflows.interfaces.patches module
      • FreeSurferSource
      • RobustACompCor
      • RobustTCompCor
    • niworkflows.interfaces.plotting module
      • CompCorVariancePlot
      • ConfoundsCorrelationPlot
      • FMRISummary
    • niworkflows.interfaces.probmaps module
      • AddTPMs
      • TPM2ROI
    • niworkflows.interfaces.space module
      • SpaceDataSource
    • niworkflows.interfaces.surf module
      • CSVToGifti
      • CreateSurfaceROI
      • GiftiNameSource
      • GiftiSetAnatomicalStructure
      • GiftiToCSV
      • NormalizeSurf
      • PLYtoGifti
      • Path2BIDS
        • Path2BIDS.output_spec
      • PoissonRecon
      • SurfacesToPointCloud
      • UnzipJoinedSurfaces
      • get_gii_meta()
      • load_transform()
      • normalize_surfs()
      • ply2gii()
      • pointcloud2ply()
      • vertex_normals()
    • niworkflows.interfaces.utility module
      • AddTSVHeader
      • DictMerge
      • JoinTSVColumns
      • KeySelect
        • KeySelect.input_spec
        • KeySelect.output_spec
      • TSV2JSON
    • niworkflows.interfaces.workbench module
      • MetricDilate
      • MetricFillHoles
      • MetricMask
      • MetricRemoveIslands
      • MetricResample
      • OpenMPCommandMixin
        • OpenMPCommandMixin.run()
      • VolumeToSurfaceMapping
• niworkflows.reports package
  • generate_reports()
  • Submodules
    • niworkflows.reports.core module
      • Element
      • Report
        • Report.generate_report()
        • Report.index()
        • Report.init_layout()
      • Reportlet
        • Reportlet.is_empty()
      • Smallest
      • SubReport
      • generate_reports()
      • run_reports()
• niworkflows.utils package
  • Submodules
    • niworkflows.utils.bids module
      • BIDSError
      • BIDSWarning
      • check_pipeline_version()
      • collect_data()
      • collect_participants()
      • get_metadata_for_nifti()
      • group_multiecho()
      • relative_to_root()
    • niworkflows.utils.connections module
      • listify()
      • pop_file()
    • niworkflows.utils.debug module
      • is_interactive()
      • setup_exceptionhook()
    • niworkflows.utils.images module
      • demean()
      • dseg_label()
      • nii_ones_like()
      • overwrite_header()
      • resample_by_spacing()
      • rotate_affine()
      • rotation2canonical()
      • set_consumables()
      • unsafe_write_nifti_header_and_data()
      • update_header_fields()
    • niworkflows.utils.misc module
      • add_suffix()
      • clean_directory()
      • fix_multi_T1w_source_name()
      • get_template_specs()
      • read_crashfile()
      • splitext()
    • niworkflows.utils.spaces module
      • FSAVERAGE_DENSITY
      • FSAVERAGE_LEGACY
      • NONSTANDARD_2D_REFERENCES
      • NONSTANDARD_REFERENCES
      • OutputReferencesAction
      • Reference
        • Reference.dim
        • Reference.from_string()
        • Reference.fullname
        • Reference.legacyname
        • Reference.space
        • Reference.spec
        • Reference.standard
      • SpatialReferences
        • SpatialReferences.add()
        • SpatialReferences.append()
        • SpatialReferences.cached
        • SpatialReferences.check_space()
        • SpatialReferences.checkpoint()
        • SpatialReferences.get_fs_spaces()
        • SpatialReferences.get_nonstandard()
        • SpatialReferences.get_spaces()
        • SpatialReferences.get_standard()
        • SpatialReferences.insert()
        • SpatialReferences.is_cached()
        • SpatialReferences.references
        • SpatialReferences.standard_spaces
      • format_reference()
      • hasspec()
      • reference2dict()
    • niworkflows.utils.testing module
      • combine_entities()
      • generate_bids_skeleton()
      • to_json()
    • niworkflows.utils.timeseries module
• niworkflows.viz package
  • plot_carpet()
  • Submodules
    • niworkflows.viz.notebook module
      • display()
    • niworkflows.viz.plots module
      • cifti_surfaces_plot()
      • compcor_variance_plot()
      • confoundplot()
      • confounds_correlation_plot()
      • fMRIPlot
        • fMRIPlot.confounds
        • fMRIPlot.nskip
        • fMRIPlot.paired_carpet
        • fMRIPlot.plot()
        • fMRIPlot.segments
        • fMRIPlot.sort_carpet
        • fMRIPlot.spikes
        • fMRIPlot.timeseries
        • fMRIPlot.tr
      • plot_carpet()
      • spikesplot()
      • spikesplot_cb()
    • niworkflows.viz.utils module
      • compose_view()
      • cuts_from_bbox()
      • extract_svg()
      • plot_melodic_components()
      • plot_registration()
      • plot_segs()
      • robust_set_limits()
      • svg2str()
      • svg_compress()
      • transform_to_2d()
• niworkflows.workflows package
  • Subpackages
    • niworkflows.workflows.epi package
      • Submodules
        • niworkflows.workflows.epi.refmap module
          • init_epi_reference_wf()