Index

A

add_suffix() (in module niworkflows.utils.misc) AddTSVHeader (class in niworkflows.interfaces.utility)

afni_wf() (in module niworkflows.anat.skullstrip) ApplyMask (class in niworkflows.interfaces.nibabel)

B

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)

C

check_pipeline_version() (in module niworkflows.utils.bids) 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.nilearn) 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) CSVToGifti (class in niworkflows.interfaces.surf) cuts_from_bbox() (in module niworkflows.viz.utils)

D

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) 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

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) fMRIPlot (class in niworkflows.viz.plots) FMRISummary (class in niworkflows.interfaces.plotting) FSDetectInputs (class in niworkflows.interfaces.freesurfer) FSInjectBrainExtracted (class in niworkflows.interfaces.freesurfer) 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.nibabel) get_gii_meta() (in module niworkflows.interfaces.surf)

get_metadata_for_nifti() (in module niworkflows.utils.bids) 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)

I

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.bids.BIDSDataGrabber attribute) (niworkflows.interfaces.bids.BIDSFreeSurferDir attribute) (niworkflows.interfaces.bids.BIDSInfo attribute) (niworkflows.interfaces.bids.DerivativesDataSink attribute) (niworkflows.interfaces.bids.ReadSidecarJSON attribute) (niworkflows.interfaces.cifti.CiftiNameSource attribute) (niworkflows.interfaces.cifti.GenerateCifti attribute) (niworkflows.interfaces.confounds.ExpandModel attribute) (niworkflows.interfaces.confounds.NormalizeMotionParams attribute) (niworkflows.interfaces.confounds.SpikeRegressors attribute) (niworkflows.interfaces.fixes.FixHeaderApplyTransforms attribute) (niworkflows.interfaces.fixes.FixHeaderRegistration attribute) (niworkflows.interfaces.freesurfer.FSDetectInputs attribute) (niworkflows.interfaces.freesurfer.FSInjectBrainExtracted attribute) (niworkflows.interfaces.freesurfer.MakeMidthickness attribute) (niworkflows.interfaces.freesurfer.MedialNaNs attribute) (niworkflows.interfaces.freesurfer.RefineBrainMask attribute) (niworkflows.interfaces.images.Conform attribute) (niworkflows.interfaces.images.IntraModalMerge attribute) (niworkflows.interfaces.images.RegridToZooms attribute) (niworkflows.interfaces.images.RobustAverage attribute) (niworkflows.interfaces.images.SignalExtraction attribute) (niworkflows.interfaces.images.TemplateDimensions attribute) (niworkflows.interfaces.itk.MCFLIRT2ITK attribute) (niworkflows.interfaces.itk.MultiApplyTransforms attribute) (niworkflows.interfaces.nibabel.ApplyMask attribute) (niworkflows.interfaces.nibabel.Binarize attribute) (niworkflows.interfaces.nibabel.DemeanImage attribute) (niworkflows.interfaces.nibabel.FilledImageLike attribute) (niworkflows.interfaces.nibabel.GenerateSamplingReference attribute) (niworkflows.interfaces.nibabel.IntensityClip attribute) (niworkflows.interfaces.nibabel.MergeSeries attribute) (niworkflows.interfaces.nibabel.RegridToZooms attribute) (niworkflows.interfaces.nibabel.SplitSeries attribute) (niworkflows.interfaces.nilearn.ComputeEPIMask attribute) (niworkflows.interfaces.nilearn.MaskEPI attribute) (niworkflows.interfaces.nilearn.Merge attribute) (niworkflows.interfaces.plotting.CompCorVariancePlot attribute) (niworkflows.interfaces.plotting.ConfoundsCorrelationPlot attribute) (niworkflows.interfaces.plotting.FMRISummary attribute) (niworkflows.interfaces.surf.CSVToGifti attribute) (niworkflows.interfaces.surf.GiftiNameSource attribute) (niworkflows.interfaces.surf.GiftiSetAnatomicalStructure attribute) (niworkflows.interfaces.surf.GiftiToCSV attribute) (niworkflows.interfaces.surf.NormalizeSurf attribute) (niworkflows.interfaces.surf.Path2BIDS attribute) (niworkflows.interfaces.surf.PLYtoGifti attribute) (niworkflows.interfaces.surf.PoissonRecon attribute) (niworkflows.interfaces.surf.SurfacesToPointCloud attribute) (niworkflows.interfaces.surf.UnzipJoinedSurfaces attribute) (niworkflows.interfaces.utility.AddTSVHeader attribute) (niworkflows.interfaces.utility.DictMerge attribute) (niworkflows.interfaces.utility.JoinTSVColumns attribute) (niworkflows.interfaces.utility.KeySelect attribute) (niworkflows.interfaces.utility.TSV2JSON attribute)

IntensityClip (class in niworkflows.interfaces.nibabel) IntraModalMerge (class in niworkflows.interfaces.images) is_empty() (niworkflows.reports.core.Reportlet method)

J

JoinTSVColumns (class in niworkflows.interfaces.utility)

K

KeySelect (class in niworkflows.interfaces.utility)

L

layout (niworkflows.interfaces.bids.ReadSidecarJSON attribute) 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

MakeMidthickness (class in niworkflows.interfaces.freesurfer) mask_data (niworkflows.viz.plots.fMRIPlot attribute) MaskEPI (class in niworkflows.interfaces.nilearn) MCFLIRT2ITK (class in niworkflows.interfaces.itk) medial_wall_to_nan() (in module niworkflows.interfaces.freesurfer) MedialNaNs (class in niworkflows.interfaces.freesurfer) 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.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.nibabel niworkflows.interfaces.nilearn niworkflows.interfaces.patches niworkflows.interfaces.plotting niworkflows.interfaces.surf niworkflows.interfaces.utility niworkflows.reports niworkflows.reports.core niworkflows.utils niworkflows.utils.bids niworkflows.utils.images niworkflows.utils.misc niworkflows.viz niworkflows.viz.plots niworkflows.viz.utils

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

N

nii_ones_like() (in module niworkflows.utils.images) niworkflows.anat module niworkflows.anat.ants module niworkflows.anat.freesurfer module niworkflows.anat.skullstrip 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.nibabel module niworkflows.interfaces.nilearn module niworkflows.interfaces.patches module niworkflows.interfaces.plotting module niworkflows.interfaces.surf module niworkflows.interfaces.utility module niworkflows.reports module niworkflows.reports.core module niworkflows.utils module niworkflows.utils.bids module niworkflows.utils.images module niworkflows.utils.misc module niworkflows.viz module niworkflows.viz.plots module niworkflows.viz.utils module 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)

O

out_path_base (niworkflows.interfaces.bids.DerivativesDataSink attribute) output_spec (niworkflows.interfaces.bids.BIDSDataGrabber attribute) (niworkflows.interfaces.bids.BIDSFreeSurferDir attribute) (niworkflows.interfaces.bids.BIDSInfo attribute) (niworkflows.interfaces.bids.DerivativesDataSink attribute) (niworkflows.interfaces.bids.ReadSidecarJSON attribute) (niworkflows.interfaces.cifti.CiftiNameSource attribute) (niworkflows.interfaces.cifti.GenerateCifti attribute) (niworkflows.interfaces.confounds.ExpandModel attribute) (niworkflows.interfaces.confounds.NormalizeMotionParams attribute) (niworkflows.interfaces.confounds.SpikeRegressors attribute) (niworkflows.interfaces.fixes.FixN4BiasFieldCorrection attribute) (niworkflows.interfaces.freesurfer.FSDetectInputs attribute) (niworkflows.interfaces.freesurfer.FSInjectBrainExtracted attribute) (niworkflows.interfaces.freesurfer.MedialNaNs attribute) (niworkflows.interfaces.freesurfer.RefineBrainMask attribute) (niworkflows.interfaces.images.Conform attribute) (niworkflows.interfaces.images.IntraModalMerge attribute) (niworkflows.interfaces.images.RegridToZooms attribute) (niworkflows.interfaces.images.RobustAverage attribute) (niworkflows.interfaces.images.SignalExtraction attribute) (niworkflows.interfaces.images.TemplateDimensions attribute) (niworkflows.interfaces.itk.MCFLIRT2ITK attribute) (niworkflows.interfaces.itk.MultiApplyTransforms attribute) (niworkflows.interfaces.nibabel.ApplyMask attribute) (niworkflows.interfaces.nibabel.Binarize attribute) (niworkflows.interfaces.nibabel.DemeanImage attribute) (niworkflows.interfaces.nibabel.FilledImageLike attribute) (niworkflows.interfaces.nibabel.GenerateSamplingReference attribute) (niworkflows.interfaces.nibabel.IntensityClip attribute) (niworkflows.interfaces.nibabel.MergeSeries attribute) (niworkflows.interfaces.nibabel.RegridToZooms attribute) (niworkflows.interfaces.nibabel.SplitSeries attribute) (niworkflows.interfaces.nilearn.ComputeEPIMask attribute) (niworkflows.interfaces.nilearn.MaskEPI attribute) (niworkflows.interfaces.nilearn.Merge attribute) (niworkflows.interfaces.plotting.CompCorVariancePlot attribute) (niworkflows.interfaces.plotting.ConfoundsCorrelationPlot attribute) (niworkflows.interfaces.plotting.FMRISummary attribute) (niworkflows.interfaces.surf.CSVToGifti attribute) (niworkflows.interfaces.surf.GiftiNameSource attribute) (niworkflows.interfaces.surf.GiftiSetAnatomicalStructure attribute) (niworkflows.interfaces.surf.GiftiToCSV attribute) (niworkflows.interfaces.surf.NormalizeSurf attribute) (niworkflows.interfaces.surf.Path2BIDS attribute) (niworkflows.interfaces.surf.PLYtoGifti attribute) (niworkflows.interfaces.surf.PoissonRecon attribute) (niworkflows.interfaces.surf.SurfacesToPointCloud attribute) (niworkflows.interfaces.surf.UnzipJoinedSurfaces attribute) (niworkflows.interfaces.utility.AddTSVHeader attribute) (niworkflows.interfaces.utility.DictMerge attribute) (niworkflows.interfaces.utility.JoinTSVColumns attribute) (niworkflows.interfaces.utility.KeySelect attribute) (niworkflows.interfaces.utility.TSV2JSON attribute)

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)

R

read_crashfile() (in module niworkflows.utils.misc) ReadSidecarJSON (class in niworkflows.interfaces.bids) refine_aseg() (in module niworkflows.interfaces.freesurfer) RefineBrainMask (class in niworkflows.interfaces.freesurfer) 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) Report (class in niworkflows.reports.core)

Reportlet (class in niworkflows.reports.core) resample_by_spacing() (in module niworkflows.utils.images) 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) rotate_affine() (in module niworkflows.utils.images) rotation2canonical() (in module niworkflows.utils.images) run_reports() (in module niworkflows.reports.core)

S

seg_data (niworkflows.viz.plots.fMRIPlot attribute) set_consumables() (in module niworkflows.utils.images) SignalExtraction (class in niworkflows.interfaces.images) 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) StructuralReference (class in niworkflows.interfaces.freesurfer) SubReport (class in niworkflows.reports.core) SurfacesToPointCloud (class in niworkflows.interfaces.surf) svg2str() (in module niworkflows.viz.utils) svg_compress() (in module niworkflows.viz.utils)

T

TemplateDimensions (class in niworkflows.interfaces.images) temporal_derivatives() (in module niworkflows.interfaces.confounds) 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

vertex_normals() (in module niworkflows.interfaces.surf)

visit_desc() (niworkflows.engine.workflows.LiterateWorkflow method)