Index

A

ACompCorRPT (class in niworkflows.interfaces.reportlets.masks) add() (niworkflows.utils.spaces.SpatialReferences method) add_suffix() (in module niworkflows.utils.misc) AddTPMs (class in niworkflows.interfaces.probmaps) AddTSVHeader (class in niworkflows.interfaces.utility) afni_wf() (in module niworkflows.anat.skullstrip)

ANTSApplyTransformsRPT (class in niworkflows.interfaces.reportlets.registration) ANTSRegistrationRPT (class in niworkflows.interfaces.reportlets.registration) append() (niworkflows.utils.spaces.SpatialReferences method) ApplyMask (class in niworkflows.interfaces.nibabel) ApplyTOPUPRPT (class in niworkflows.interfaces.reportlets.registration) ApplyXFMRPT (class in niworkflows.interfaces.reportlets.registration) as_path() (niworkflows.data.load method)

B

BBRegisterRPT (class in niworkflows.interfaces.reportlets.registration) BETRPT (class in niworkflows.interfaces.reportlets.masks) BIDSDataGrabber (class in niworkflows.interfaces.bids) BIDSError BIDSFreeSurferDir (class in niworkflows.interfaces.bids) BIDSInfo (class in niworkflows.interfaces.bids)

BIDSWarning Binarize (class in niworkflows.interfaces.nibabel) BinaryDilation (class in niworkflows.interfaces.morphology) (class in niworkflows.interfaces.nibabel) BinarySubtraction (class in niworkflows.interfaces.morphology) BrainExtractionRPT (class in niworkflows.interfaces.reportlets.masks)

C

cached (niworkflows.utils.spaces.SpatialReferences property) cached() (niworkflows.data.load method) check_pipeline_version() (in module niworkflows.utils.bids) check_space() (niworkflows.utils.spaces.SpatialReferences static method) checkpoint() (niworkflows.utils.spaces.SpatialReferences method) cifti_surfaces_plot() (in module niworkflows.viz.plots) CiftiNameSource (class in niworkflows.interfaces.cifti) clean_directory() (in module niworkflows.utils.misc) cmdline (niworkflows.interfaces.freesurfer.MakeMidthickness property) (niworkflows.interfaces.freesurfer.StructuralReference property) collect_data() (in module niworkflows.utils.bids) collect_participants() (in module niworkflows.utils.bids) combine_entities() (in module niworkflows.utils.testing) compare_xforms() (in module niworkflows.anat.coregistration) compcor_variance_plot() (in module niworkflows.viz.plots)

CompCorVariancePlot (class in niworkflows.interfaces.plotting) compose_view() (in module niworkflows.viz.utils) ComputeEPIMask (class in niworkflows.interfaces.nilearn) concatenate_xfms() (in module niworkflows.interfaces.nitransforms) ConcatenateXFMs (class in niworkflows.interfaces.nitransforms) Conform (class in niworkflows.interfaces.images) confoundplot() (in module niworkflows.viz.plots) confounds (niworkflows.viz.plots.fMRIPlot attribute) confounds_correlation_plot() (in module niworkflows.viz.plots) ConfoundsCorrelationPlot (class in niworkflows.interfaces.plotting) CopyHeader (class in niworkflows.interfaces.header) CopyXForm (class in niworkflows.interfaces.header) create_cfm() (in module niworkflows.interfaces.norm) CreateSurfaceROI (class in niworkflows.interfaces.surf) CSVToGifti (class in niworkflows.interfaces.surf) cuts_from_bbox() (in module niworkflows.viz.utils)

D

data_dir() (in module niworkflows.interfaces.conftest) demean() (in module niworkflows.utils.images) DemeanImage (class in niworkflows.interfaces.nibabel) DerivativesDataSink (class in niworkflows.interfaces.bids) detect_inputs() (in module niworkflows.interfaces.freesurfer)

DictMerge (class in niworkflows.interfaces.utility) dim (niworkflows.utils.spaces.Reference attribute) display() (in module niworkflows.viz.notebook) DistributedPluginBase (class in niworkflows.engine.plugin) dseg_label() (in module niworkflows.utils.images)

E

Element (class in niworkflows.reports.core) ExpandModel (class in niworkflows.interfaces.confounds)

exponential_terms() (in module niworkflows.interfaces.confounds) extract_svg() (in module niworkflows.viz.utils)

F

FASTRPT (class in niworkflows.interfaces.reportlets.segmentation) FilledImageLike (class in niworkflows.interfaces.nibabel) fix_lta_length() (in module niworkflows.interfaces.freesurfer) fix_multi_T1w_source_name() (in module niworkflows.utils.misc) FixHeaderApplyTransforms (class in niworkflows.interfaces.fixes) FixHeaderRegistration (class in niworkflows.interfaces.fixes) FixN4BiasFieldCorrection (class in niworkflows.interfaces.fixes) FLIRTRPT (class in niworkflows.interfaces.reportlets.registration) fMRIPlot (class in niworkflows.viz.plots)

FMRISummary (class in niworkflows.interfaces.plotting) format_reference() (in module niworkflows.utils.spaces) FreeSurferSource (class in niworkflows.interfaces.patches) from_string() (niworkflows.utils.spaces.Reference class method) FSAVERAGE_DENSITY (in module niworkflows.utils.spaces) FSAVERAGE_LEGACY (in module niworkflows.utils.spaces) FSDetectInputs (class in niworkflows.interfaces.freesurfer) FSInjectBrainExtracted (class in niworkflows.interfaces.freesurfer) FUGUERPT (class in niworkflows.interfaces.reportlets.registration) fullname (niworkflows.utils.spaces.Reference property)

G

generate_bids_skeleton() (in module niworkflows.utils.testing) generate_report() (niworkflows.reports.core.Report method) generate_reports() (in module niworkflows.reports) (in module niworkflows.reports.core) GenerateCifti (class in niworkflows.interfaces.cifti) GenerateSamplingReference (class in niworkflows.interfaces.nibabel) get_fs_spaces() (niworkflows.utils.spaces.SpatialReferences method) get_gii_meta() (in module niworkflows.interfaces.surf) get_metadata_for_nifti() (in module niworkflows.utils.bids)

get_nonstandard() (niworkflows.utils.spaces.SpatialReferences method) get_parser() (in module niworkflows.cli.boldref) get_spaces() (niworkflows.utils.spaces.SpatialReferences method) get_standard() (niworkflows.utils.spaces.SpatialReferences method) get_template_specs() (in module niworkflows.utils.misc) GiftiNameSource (class in niworkflows.interfaces.surf) GiftiSetAnatomicalStructure (class in niworkflows.interfaces.surf) GiftiToCSV (class in niworkflows.interfaces.surf) group_multiecho() (in module niworkflows.utils.bids) grow_mask() (in module niworkflows.interfaces.freesurfer)

H

hasspec() (in module niworkflows.utils.spaces)

I

ICA_AROMARPT (class in niworkflows.interfaces.reportlets.segmentation) image_binary_dilation() (in module niworkflows.interfaces.morphology) index() (niworkflows.reports.core.Report method) init_atropos_wf() (in module niworkflows.anat.ants) init_bbreg_wf() (in module niworkflows.anat.coregistration) init_bold_reference_wf() (in module niworkflows.func.util) init_brain_extraction_wf() (in module niworkflows.anat.ants) init_enhance_and_skullstrip_bold_wf() (in module niworkflows.func.util) init_epi_reference_wf() (in module niworkflows.workflows.epi.refmap) init_gifti_surface_wf() (in module niworkflows.anat.freesurfer)

init_layout() (niworkflows.reports.core.Report method) init_n4_only_wf() (in module niworkflows.anat.ants) init_skullstrip_bold_wf() (in module niworkflows.func.util) inject_skullstripped() (in module niworkflows.interfaces.freesurfer) input_spec (niworkflows.interfaces.utility.KeySelect attribute) insert() (niworkflows.utils.spaces.SpatialReferences method) IntensityClip (class in niworkflows.interfaces.nibabel) IntraModalMerge (class in niworkflows.interfaces.images) is_cached() (niworkflows.utils.spaces.SpatialReferences method) is_empty() (niworkflows.reports.core.Reportlet method) is_interactive() (in module niworkflows.utils.debug)

J

JoinTSVColumns (class in niworkflows.interfaces.utility)

K

KeySelect (class in niworkflows.interfaces.utility)

L

layout (niworkflows.interfaces.bids.ReadSidecarJSON attribute) legacyname (niworkflows.utils.spaces.Reference property) listify() (in module niworkflows.utils.connections) LiterateWorkflow (class in niworkflows.engine.workflows) load() (in module niworkflows.data)

load_transform() (in module niworkflows.interfaces.surf) lta_outputs (niworkflows.interfaces.freesurfer.PatchedConcatenateLTA attribute) (niworkflows.interfaces.freesurfer.PatchedLTAConvert attribute) (niworkflows.interfaces.freesurfer.PatchedRobustRegister attribute) (niworkflows.interfaces.freesurfer.TruncateLTA attribute)

M

main() (in module niworkflows.cli.boldref) MakeMidthickness (class in niworkflows.interfaces.freesurfer) MapLabels (class in niworkflows.interfaces.nibabel) mask() (in module niworkflows.interfaces.norm) MaskEPI (class in niworkflows.interfaces.nilearn) MatchHeader (class in niworkflows.interfaces.header) MCFLIRT2ITK (class in niworkflows.interfaces.itk) medial_wall_to_nan() (in module niworkflows.interfaces.freesurfer) MedialNaNs (class in niworkflows.interfaces.freesurfer) MELODICRPT (class in niworkflows.interfaces.reportlets.segmentation) Merge (class in niworkflows.interfaces.nilearn) MergeROIs (class in niworkflows.interfaces.nibabel) MergeSeries (class in niworkflows.interfaces.nibabel) MetricDilate (class in niworkflows.interfaces.workbench) MetricFillHoles (class in niworkflows.interfaces.workbench) MetricMask (class in niworkflows.interfaces.workbench) MetricRemoveIslands (class in niworkflows.interfaces.workbench) MetricResample (class in niworkflows.interfaces.workbench) module niworkflows.anat niworkflows.anat.ants niworkflows.anat.coregistration niworkflows.anat.freesurfer niworkflows.anat.skullstrip niworkflows.cli niworkflows.cli.boldref niworkflows.data niworkflows.dwi niworkflows.engine niworkflows.engine.plugin niworkflows.engine.workflows niworkflows.func niworkflows.func.util niworkflows.interfaces niworkflows.interfaces.bids niworkflows.interfaces.bold niworkflows.interfaces.cifti niworkflows.interfaces.confounds niworkflows.interfaces.conftest niworkflows.interfaces.fixes niworkflows.interfaces.freesurfer niworkflows.interfaces.header niworkflows.interfaces.images niworkflows.interfaces.itk niworkflows.interfaces.morphology niworkflows.interfaces.nibabel niworkflows.interfaces.nilearn niworkflows.interfaces.nitransforms niworkflows.interfaces.norm niworkflows.interfaces.patches niworkflows.interfaces.plotting niworkflows.interfaces.probmaps niworkflows.interfaces.reportlets niworkflows.interfaces.reportlets.base niworkflows.interfaces.reportlets.masks niworkflows.interfaces.reportlets.registration niworkflows.interfaces.reportlets.segmentation niworkflows.interfaces.space niworkflows.interfaces.surf niworkflows.interfaces.utility niworkflows.interfaces.workbench niworkflows.reports niworkflows.reports.core niworkflows.utils niworkflows.utils.bids niworkflows.utils.connections niworkflows.utils.debug niworkflows.utils.images niworkflows.utils.misc niworkflows.utils.spaces niworkflows.utils.testing niworkflows.utils.timeseries niworkflows.viz niworkflows.viz.notebook niworkflows.viz.plots niworkflows.viz.utils niworkflows.workflows niworkflows.workflows.epi niworkflows.workflows.epi.refmap

mri_info() (in module niworkflows.interfaces.freesurfer) MRICoregRPT (class in niworkflows.interfaces.reportlets.registration) MultiApplyTransforms (class in niworkflows.interfaces.itk) MultiProcPlugin (class in niworkflows.engine.plugin)

N

nii_ones_like() (in module niworkflows.utils.images) niworkflows.anat module niworkflows.anat.ants module niworkflows.anat.coregistration module niworkflows.anat.freesurfer module niworkflows.anat.skullstrip module niworkflows.cli module niworkflows.cli.boldref module niworkflows.data module niworkflows.dwi module niworkflows.engine module niworkflows.engine.plugin module niworkflows.engine.workflows module niworkflows.func module niworkflows.func.util module niworkflows.interfaces module niworkflows.interfaces.bids module niworkflows.interfaces.bold module niworkflows.interfaces.cifti module niworkflows.interfaces.confounds module niworkflows.interfaces.conftest module niworkflows.interfaces.fixes module niworkflows.interfaces.freesurfer module niworkflows.interfaces.header module niworkflows.interfaces.images module niworkflows.interfaces.itk module niworkflows.interfaces.morphology module niworkflows.interfaces.nibabel module niworkflows.interfaces.nilearn module niworkflows.interfaces.nitransforms module niworkflows.interfaces.norm module niworkflows.interfaces.patches module niworkflows.interfaces.plotting module

niworkflows.interfaces.probmaps module niworkflows.interfaces.reportlets module niworkflows.interfaces.reportlets.base module niworkflows.interfaces.reportlets.masks module niworkflows.interfaces.reportlets.registration module niworkflows.interfaces.reportlets.segmentation module niworkflows.interfaces.space module niworkflows.interfaces.surf module niworkflows.interfaces.utility module niworkflows.interfaces.workbench module niworkflows.reports module niworkflows.reports.core module niworkflows.utils module niworkflows.utils.bids module niworkflows.utils.connections module niworkflows.utils.debug module niworkflows.utils.images module niworkflows.utils.misc module niworkflows.utils.spaces module niworkflows.utils.testing module niworkflows.utils.timeseries module niworkflows.viz module niworkflows.viz.notebook module niworkflows.viz.plots module niworkflows.viz.utils module niworkflows.workflows module niworkflows.workflows.epi module niworkflows.workflows.epi.refmap module NONSTANDARD_2D_REFERENCES (in module niworkflows.utils.spaces) NONSTANDARD_REFERENCES (in module niworkflows.utils.spaces) NonsteadyStatesDetector (class in niworkflows.interfaces.bold) normalize_surfs() (in module niworkflows.interfaces.surf) normalize_xform() (in module niworkflows.interfaces.images) NormalizeMotionParams (class in niworkflows.interfaces.confounds) NormalizeSurf (class in niworkflows.interfaces.surf) nskip (niworkflows.viz.plots.fMRIPlot attribute)

O

OpenMPCommandMixin (class in niworkflows.interfaces.workbench) out_path_base (niworkflows.interfaces.bids.DerivativesDataSink attribute) output_spec (niworkflows.interfaces.bids.BIDSInfo attribute) (niworkflows.interfaces.bids.ReadSidecarJSON attribute) (niworkflows.interfaces.header.CopyXForm attribute) (niworkflows.interfaces.surf.Path2BIDS attribute) (niworkflows.interfaces.utility.KeySelect attribute)

OutputReferencesAction (class in niworkflows.utils.spaces) overwrite_header() (in module niworkflows.utils.images)

P

paired_carpet (niworkflows.viz.plots.fMRIPlot attribute) parse_expression() (in module niworkflows.interfaces.confounds) parse_formula() (in module niworkflows.interfaces.confounds) PatchedBBRegisterRPT (class in niworkflows.interfaces.freesurfer) PatchedConcatenateLTA (class in niworkflows.interfaces.freesurfer) PatchedLTAConvert (class in niworkflows.interfaces.freesurfer) PatchedMRICoregRPT (class in niworkflows.interfaces.freesurfer) PatchedRobustRegister (class in niworkflows.interfaces.freesurfer) Path2BIDS (class in niworkflows.interfaces.surf) plot() (niworkflows.viz.plots.fMRIPlot method) plot_carpet() (in module niworkflows.viz) (in module niworkflows.viz.plots)

plot_melodic_components() (in module niworkflows.viz.utils) plot_registration() (in module niworkflows.viz.utils) plot_segs() (in module niworkflows.viz.utils) PluginBase (class in niworkflows.engine.plugin) ply2gii() (in module niworkflows.interfaces.surf) PLYtoGifti (class in niworkflows.interfaces.surf) pointcloud2ply() (in module niworkflows.interfaces.surf) PoissonRecon (class in niworkflows.interfaces.surf) pop_file() (in module niworkflows.utils.connections) PrepareDerivative (class in niworkflows.interfaces.bids)

R

read_crashfile() (in module niworkflows.utils.misc) readable() (niworkflows.data.load method) ReadSidecarJSON (class in niworkflows.interfaces.bids) ReconAllRPT (class in niworkflows.interfaces.reportlets.segmentation) Reference (class in niworkflows.utils.spaces) reference2dict() (in module niworkflows.utils.spaces) references (niworkflows.utils.spaces.SpatialReferences property) refine_aseg() (in module niworkflows.interfaces.freesurfer) RefineBrainMask (class in niworkflows.interfaces.freesurfer) RegistrationRC (class in niworkflows.interfaces.reportlets.base) RegridToZooms (class in niworkflows.interfaces.images) (class in niworkflows.interfaces.nibabel) relative_to_root() (in module niworkflows.utils.bids) reorient() (in module niworkflows.interfaces.images) reorient_file() (in module niworkflows.interfaces.nibabel) reorient_image() (in module niworkflows.interfaces.nibabel) ReorientImage (class in niworkflows.interfaces.nibabel)

Report (class in niworkflows.reports.core) ReportingInterface (class in niworkflows.interfaces.reportlets.base) Reportlet (class in niworkflows.reports.core) resample_by_spacing() (in module niworkflows.utils.images) ResampleBeforeAfterRPT (class in niworkflows.interfaces.reportlets.registration) robust_set_limits() (in module niworkflows.viz.utils) RobustACompCor (class in niworkflows.interfaces.patches) RobustAverage (class in niworkflows.interfaces.images) RobustTCompCor (class in niworkflows.interfaces.patches) ROIsPlot (class in niworkflows.interfaces.reportlets.masks) rotate_affine() (in module niworkflows.utils.images) rotation2canonical() (in module niworkflows.utils.images) run() (niworkflows.engine.plugin.DistributedPluginBase method) (niworkflows.engine.plugin.PluginBase method) (niworkflows.interfaces.workbench.OpenMPCommandMixin method) run_node() (in module niworkflows.engine.plugin) run_reports() (in module niworkflows.reports.core)

S

SanitizeImage (class in niworkflows.interfaces.header) SaveDerivative (class in niworkflows.interfaces.bids) SegmentationRC (class in niworkflows.interfaces.reportlets.base) segments (niworkflows.viz.plots.fMRIPlot attribute) set_consumables() (in module niworkflows.utils.images) setup_exceptionhook() (in module niworkflows.utils.debug) SignalExtraction (class in niworkflows.interfaces.images) SimpleBeforeAfterRPT (class in niworkflows.interfaces.reportlets.registration) SimpleShowMaskRPT (class in niworkflows.interfaces.reportlets.masks) Smallest (class in niworkflows.reports.core) sort_carpet (niworkflows.viz.plots.fMRIPlot attribute) space (niworkflows.utils.spaces.Reference attribute) SpaceDataSource (class in niworkflows.interfaces.space) SpatialNormalization (class in niworkflows.interfaces.norm) SpatialNormalizationRPT (class in niworkflows.interfaces.reportlets.registration) SpatialReferences (class in niworkflows.utils.spaces)

spec (niworkflows.utils.spaces.Reference attribute) spike_regressors() (in module niworkflows.interfaces.confounds) SpikeRegressors (class in niworkflows.interfaces.confounds) spikes (niworkflows.viz.plots.fMRIPlot attribute) spikesplot() (in module niworkflows.viz.plots) spikesplot_cb() (in module niworkflows.viz.plots) splitext() (in module niworkflows.utils.misc) SplitSeries (class in niworkflows.interfaces.nibabel) standard (niworkflows.utils.spaces.Reference attribute) standard_spaces (niworkflows.utils.spaces.SpatialReferences attribute) StructuralReference (class in niworkflows.interfaces.freesurfer) SubReport (class in niworkflows.reports.core) SurfaceSegmentationRC (class in niworkflows.interfaces.reportlets.base) SurfacesToPointCloud (class in niworkflows.interfaces.surf) svg2str() (in module niworkflows.viz.utils) svg_compress() (in module niworkflows.viz.utils)

T

TCompCorRPT (class in niworkflows.interfaces.reportlets.masks) TemplateDimensions (class in niworkflows.interfaces.images) temporal_derivatives() (in module niworkflows.interfaces.confounds) timeseries (niworkflows.viz.plots.fMRIPlot attribute) to_json() (in module niworkflows.utils.testing)

TPM2ROI (class in niworkflows.interfaces.probmaps) tr (niworkflows.viz.plots.fMRIPlot attribute) transform_to_2d() (in module niworkflows.viz.utils) TruncateLTA (class in niworkflows.interfaces.freesurfer) TSV2JSON (class in niworkflows.interfaces.utility)

U

unsafe_write_nifti_header_and_data() (in module niworkflows.utils.images)

UnzipJoinedSurfaces (class in niworkflows.interfaces.surf) update_header_fields() (in module niworkflows.utils.images)

V

ValidateImage (class in niworkflows.interfaces.header) vertex_normals() (in module niworkflows.interfaces.surf)

visit_desc() (niworkflows.engine.workflows.LiterateWorkflow method) VolumeToSurfaceMapping (class in niworkflows.interfaces.workbench)