Index

A

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

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

B

BBRegisterRPT (class in niworkflows.interfaces.registration) BETRPT (class in niworkflows.interfaces.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) BrainExtractionRPT (class in niworkflows.interfaces.masks)

C

cached (niworkflows.utils.spaces.SpatialReferences property) check_pipeline_version() (in module niworkflows.utils.bids) check_space() (niworkflows.utils.spaces.SpatialReferences static method) checkpoint() (niworkflows.utils.spaces.SpatialReferences method) 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) 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.masks) 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.utils) CopyXForm (class in niworkflows.interfaces.utils) create_cfm() (in module niworkflows.interfaces.mni) CSVToGifti (class in niworkflows.interfaces.surf) cuts_from_bbox() (in module niworkflows.viz.utils)

D

demean() (in module niworkflows.interfaces.images) DemeanImage (class in niworkflows.interfaces.images) DerivativesDataSink (class in niworkflows.interfaces.bids) detect_inputs() (in module niworkflows.interfaces.freesurfer)

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

E

Element (class in niworkflows.reports.core) EstimateReferenceImage (class in niworkflows.interfaces.registration)

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.segmentation) FilledImageLike (class in niworkflows.interfaces.images) 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.registration) fMRIPlot (class in niworkflows.viz.plots)

FMRISummary (class in niworkflows.interfaces.plotting) format_reference() (in module niworkflows.utils.spaces) 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.registration) fullname (niworkflows.utils.spaces.Reference property) func_file (niworkflows.viz.plots.fMRIPlot attribute)

G

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.utils) 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.segmentation) index() (niworkflows.reports.core.Report method) init_atropos_wf() (in module niworkflows.anat.ants) 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_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) IntraModalMerge (class in niworkflows.interfaces.images) is_cached() (niworkflows.utils.spaces.SpatialReferences method) is_empty() (niworkflows.reports.core.Reportlet method)

J

JoinTSVColumns (class in niworkflows.interfaces.utils)

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_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) mask() (in module niworkflows.interfaces.mni) mask_data (niworkflows.viz.plots.fMRIPlot attribute) MaskEPI (class in niworkflows.interfaces.nilearn) MatchHeader (class in niworkflows.interfaces.images) 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.segmentation) Merge (class in niworkflows.interfaces.nilearn) MergeSeries (class in niworkflows.interfaces.nibabel) module niworkflows.anat niworkflows.anat.ants niworkflows.anat.freesurfer niworkflows.anat.skullstrip niworkflows.cli niworkflows.cli.boldref niworkflows.dwi niworkflows.engine niworkflows.engine.workflows niworkflows.func niworkflows.func.util niworkflows.interfaces niworkflows.interfaces.bids niworkflows.interfaces.cifti niworkflows.interfaces.confounds niworkflows.interfaces.fixes niworkflows.interfaces.freesurfer niworkflows.interfaces.images niworkflows.interfaces.itk niworkflows.interfaces.masks niworkflows.interfaces.mni niworkflows.interfaces.nibabel niworkflows.interfaces.nilearn niworkflows.interfaces.nitransforms niworkflows.interfaces.patches niworkflows.interfaces.plotting niworkflows.interfaces.registration niworkflows.interfaces.report_base niworkflows.interfaces.segmentation niworkflows.interfaces.space niworkflows.interfaces.surf niworkflows.interfaces.utility niworkflows.interfaces.utils niworkflows.reports niworkflows.reports.core niworkflows.utils niworkflows.utils.bids niworkflows.utils.connections niworkflows.utils.images niworkflows.utils.misc niworkflows.utils.spaces niworkflows.viz niworkflows.viz.notebook niworkflows.viz.plots niworkflows.viz.utils

mri_info() (in module niworkflows.interfaces.freesurfer) MRICoregRPT (class in niworkflows.interfaces.registration) MultiApplyTransforms (class in niworkflows.interfaces.itk)

N

nii_ones_like() (in module niworkflows.interfaces.images) niworkflows.anat module niworkflows.anat.ants module niworkflows.anat.freesurfer module niworkflows.anat.skullstrip module niworkflows.cli module niworkflows.cli.boldref module niworkflows.dwi module niworkflows.engine module niworkflows.engine.workflows module niworkflows.func module niworkflows.func.util module niworkflows.interfaces module niworkflows.interfaces.bids module niworkflows.interfaces.cifti module niworkflows.interfaces.confounds module niworkflows.interfaces.fixes module niworkflows.interfaces.freesurfer module niworkflows.interfaces.images module niworkflows.interfaces.itk module niworkflows.interfaces.masks module niworkflows.interfaces.mni module niworkflows.interfaces.nibabel module niworkflows.interfaces.nilearn module niworkflows.interfaces.nitransforms module

niworkflows.interfaces.patches module niworkflows.interfaces.plotting module niworkflows.interfaces.registration module niworkflows.interfaces.report_base module niworkflows.interfaces.segmentation module niworkflows.interfaces.space module niworkflows.interfaces.surf module niworkflows.interfaces.utility module niworkflows.interfaces.utils module niworkflows.reports module niworkflows.reports.core module niworkflows.utils module niworkflows.utils.bids module niworkflows.utils.connections module niworkflows.utils.images module niworkflows.utils.misc module niworkflows.utils.spaces module niworkflows.viz module niworkflows.viz.notebook module niworkflows.viz.plots module niworkflows.viz.utils module NONSTANDARD_REFERENCES (in module niworkflows.utils.spaces) normalize_surfs() (in module niworkflows.interfaces.surf) normalize_xform() (in module niworkflows.interfaces.images) NormalizeMotionParams (class in niworkflows.interfaces.utils) NormalizeSurf (class in niworkflows.interfaces.surf)

O

out_path_base (niworkflows.interfaces.bids.DerivativesDataSink attribute) output_spec (niworkflows.interfaces.bids.BIDSInfo attribute) (niworkflows.interfaces.bids.ReadSidecarJSON attribute) (niworkflows.interfaces.surf.Path2BIDS attribute) (niworkflows.interfaces.utility.KeySelect attribute) (niworkflows.interfaces.utils.CopyXForm attribute)

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

P

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) 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)

R

read_crashfile() (in module niworkflows.utils.misc) ReadSidecarJSON (class in niworkflows.interfaces.bids) ReconAllRPT (class in niworkflows.interfaces.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.report_base) RegridToZooms (class in niworkflows.interfaces.images) relative_to_root() (in module niworkflows.utils.bids) reorient() (in module niworkflows.interfaces.images) Report (class in niworkflows.reports.core)

ReportingInterface (class in niworkflows.interfaces.report_base) Reportlet (class in niworkflows.reports.core) resample_by_spacing() (in module niworkflows.utils.images) ResampleBeforeAfterRPT (class in niworkflows.interfaces.registration) robust_set_limits() (in module niworkflows.viz.utils) RobustACompCor (class in niworkflows.interfaces.patches) RobustMNINormalization (class in niworkflows.interfaces.mni) RobustMNINormalizationRPT (class in niworkflows.interfaces.registration) RobustTCompCor (class in niworkflows.interfaces.patches) ROIsPlot (class in niworkflows.interfaces.masks) rotate_affine() (in module niworkflows.utils.images) rotation2canonical() (in module niworkflows.utils.images) run_reports() (in module niworkflows.reports.core)

S

SanitizeImage (class in niworkflows.interfaces.utils) seg_data (niworkflows.viz.plots.fMRIPlot attribute) SegmentationRC (class in niworkflows.interfaces.report_base) set_consumables() (in module niworkflows.utils.images) SignalExtraction (class in niworkflows.interfaces.images) SimpleBeforeAfterRPT (class in niworkflows.interfaces.registration) SimpleShowMaskRPT (class in niworkflows.interfaces.masks) space (niworkflows.utils.spaces.Reference attribute) SpaceDataSource (class in niworkflows.interfaces.space) 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.report_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.masks) TemplateDimensions (class in niworkflows.interfaces.images) temporal_derivatives() (in module niworkflows.interfaces.confounds) TPM2ROI (class in niworkflows.interfaces.utils)

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.utils)

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.images)

vertex_normals() (in module niworkflows.interfaces.surf) visit_desc() (niworkflows.engine.workflows.LiterateWorkflow method)