Index

A

abcc_qc (xcp_d.config.workflow attribute), [1] ABCCQC (class in xcp_d.interfaces.utils) AboutSummary (class in xcp_d.interfaces.report)

aggr_ses_reports (xcp_d.config.execution attribute), [1] AnatomicalPlot (class in xcp_d.interfaces.plotting) ApplyTransforms (class in xcp_d.interfaces.ants) atlases (xcp_d.config.execution attribute), [1]

B

band_stop_max (xcp_d.config.workflow attribute), [1] band_stop_min (xcp_d.config.workflow attribute), [1] bandpass_filter (xcp_d.config.workflow attribute), [1] before_send() (in module xcp_d.utils.sentry) bids_database_dir (xcp_d.config.execution attribute), [1] bids_description_hash (xcp_d.config.execution attribute), [1] bids_filters (xcp_d.config.execution attribute), [1]

BIDSError BIDSURI (class in xcp_d.interfaces.bids) BIDSWarning BinaryMath (class in xcp_d.interfaces.nilearn) boilerplate_only (xcp_d.config.execution attribute), [1] bpf_order (xcp_d.config.workflow attribute), [1] build_boilerplate() (in module xcp_d.cli.workflow) build_workflow() (in module xcp_d.cli.workflow)

C

calculate_exact_scans() (in module xcp_d.utils.modified_data) Censor (class in xcp_d.interfaces.censoring) CensoringPlot (class in xcp_d.interfaces.plotting) check_deps() (in module xcp_d.utils.utils) check_latest() (in module xcp_d.cli.version) check_pipeline_version() (in module xcp_d.utils.bids) CiftiConvert (class in xcp_d.interfaces.workbench) CiftiCorrelation (class in xcp_d.interfaces.workbench) CiftiCreateDenseFromTemplate (class in xcp_d.interfaces.workbench) CiftiCreateDenseScalar (class in xcp_d.interfaces.workbench) CiftiMask (class in xcp_d.interfaces.connectivity) CiftiMath (class in xcp_d.interfaces.workbench) CiftiParcellateWorkbench (class in xcp_d.interfaces.workbench) CiftiSeparateMetric (class in xcp_d.interfaces.workbench) CiftiSeparateVolumeAll (class in xcp_d.interfaces.workbench) CiftiSmooth (class in xcp_d.interfaces.workbench) CiftiSurfaceResample (class in xcp_d.interfaces.workbench) CiftiToTSV (class in xcp_d.interfaces.connectivity) CiftiVertexMask (class in xcp_d.interfaces.connectivity) clean_datasinks() (in module xcp_d.workflows.base) CleanNameSource (class in xcp_d.interfaces.concatenation) cli (xcp_d.config.loggers attribute), [1] collect_anatomical_files() (in module xcp_d.ingression.utils) collect_atlases() (in module xcp_d.utils.atlas) collect_confounds() (in module xcp_d.utils.bids) collect_data() (in module xcp_d.utils.bids) collect_hcp_confounds() (in module xcp_d.ingression.utils) collect_inputs() (xcp_d.interfaces.execsummary.ExecutiveSummary method) collect_mesh_data() (in module xcp_d.utils.bids) collect_meshes() (in module xcp_d.ingression.utils) collect_morphometry_data() (in module xcp_d.utils.bids) collect_morphs() (in module xcp_d.ingression.utils)

collect_participants() (in module xcp_d.utils.bids) collect_run_data() (in module xcp_d.utils.bids) collect_ukbiobank_confounds() (in module xcp_d.ingression.utils) CollectRegistrationFiles (class in xcp_d.interfaces.bids) combine_runs (xcp_d.config.workflow attribute), [1] compute_2d_reho() (in module xcp_d.utils.restingstate) compute_alff() (in module xcp_d.utils.restingstate) compute_alff_chunk() (in module xcp_d.utils.restingstate) compute_dvars() (in module xcp_d.utils.qcmetrics) compute_fd() (in module xcp_d.utils.modified_data) compute_registration_qc() (in module xcp_d.utils.qcmetrics) ComputeALFF (class in xcp_d.interfaces.restingstate) concatenate_niimgs() (in module xcp_d.utils.concatenation) concatenate_tsvs() (in module xcp_d.utils.concatenation) ConcatenateInputs (class in xcp_d.interfaces.concatenation) confounds (xcp_d.utils.plotting.FMRIPlot attribute) confounds_config (xcp_d.config.execution attribute), [1] ConfoundsAction (class in xcp_d.cli.parser_utils) ConnectPlot (class in xcp_d.interfaces.connectivity) convert_dcan2bids() (in module xcp_d.ingression.abcdbids) convert_dcan_to_bids_single_subject() (in module xcp_d.ingression.abcdbids) convert_hcp2bids() (in module xcp_d.ingression.hcpya) convert_hcp_to_bids_single_subject() (in module xcp_d.ingression.hcpya) convert_ukb2bids() (in module xcp_d.ingression.ukbiobank) convert_ukb_to_bids_single_subject() (in module xcp_d.ingression.ukbiobank) ConvertTo32 (class in xcp_d.interfaces.utils) copy_file() (in module xcp_d.ingression.utils) copy_files_in_dict() (in module xcp_d.ingression.utils) CopyAtlas (class in xcp_d.interfaces.bids) correlate_timeseries() (in module xcp_d.interfaces.connectivity) correlation_lengths (xcp_d.config.workflow attribute), [1] cpu_count (xcp_d.config.environment attribute), [1] crashfile_format (xcp_d.config.nipype attribute), [1]

D

dataset_links (xcp_d.config.execution attribute), [1] datasets (xcp_d.config.execution attribute), [1] debug (xcp_d.config.execution attribute), [1] default (xcp_d.config.loggers attribute), [1] denoise_with_nilearn() (in module xcp_d.utils.utils) DenoiseCifti (class in xcp_d.interfaces.nilearn) DenoiseNifti (class in xcp_d.interfaces.nilearn) DerivativesDataSink (class in xcp_d.interfaces.bids) describe_atlases() (in module xcp_d.utils.boilerplate)

describe_censoring() (in module xcp_d.utils.boilerplate) describe_motion_parameters() (in module xcp_d.utils.boilerplate) describe_regression() (in module xcp_d.utils.boilerplate) despike (xcp_d.config.workflow attribute), [1] DespikePatch (class in xcp_d.interfaces.restingstate) dice() (in module xcp_d.utils.qcmetrics) downcast_to_32() (in module xcp_d.utils.modified_data) download_example_data() (in module xcp_d.utils.doc) dummy_scans (xcp_d.config.workflow attribute), [1] dumps() (in module xcp_d.config)

E

ensure_list() (in module xcp_d.utils.filemanip) environment (class in xcp_d.config), [1] estimate_brain_radius() (in module xcp_d.utils.utils) exec_docker_version (xcp_d.config.environment attribute), [1]

exec_env (xcp_d.config.environment attribute), [1] execution (class in xcp_d.config), [1] ExecutiveSummary (class in xcp_d.interfaces.execsummary) extract_mean_signal() (in module xcp_d.ingression.utils)

F

fd_thresh (xcp_d.config.workflow attribute), [1] file_format (xcp_d.config.workflow attribute), [1] fill_doc() (in module xcp_d.utils.doc) filter_motion() (in module xcp_d.utils.confounds) FilterOutFailedRuns (class in xcp_d.interfaces.concatenation) FilterUndefined (class in xcp_d.interfaces.utils) FixCiftiIntent (class in xcp_d.interfaces.workbench) flag_bad_run() (in module xcp_d.utils.modified_data) fmri_dir (xcp_d.config.execution attribute), [1]

FMRIPlot (class in xcp_d.utils.plotting) fname_presuffix() (in module xcp_d.utils.filemanip) FormatForBrainSwipes (class in xcp_d.interfaces.execsummary) free_mem (xcp_d.config.environment attribute), [1] from_dict() (in module xcp_d.config) fs_license_file (xcp_d.config.execution attribute), [1] func_file (xcp_d.utils.plotting.FMRIPlot attribute) FunctionalSummary (class in xcp_d.interfaces.report) fwhm2sigma() (in module xcp_d.utils.utils)

G

generate_report() (xcp_d.interfaces.execsummary.ExecutiveSummary method) generate_reports() (in module xcp_d.reports.core) GenerateConfounds (class in xcp_d.interfaces.censoring) get() (in module xcp_d.config) get_bold2std_and_t1w_xfms() (in module xcp_d.utils.utils) get_cifti_intents() (in module xcp_d.utils.write_save) get_entity() (in module xcp_d.utils.bids)

get_linked_libs (xcp_d.config.nipype attribute), [1] get_n_frames() (in module xcp_d.utils.execsummary) get_parser() (in module xcp_d.cli.combineqc) get_plugin() (xcp_d.config.nipype class method), [1] get_png_image_names() (in module xcp_d.utils.execsummary) get_preproc_pipeline_info() (in module xcp_d.utils.bids) get_std2bold_xfms() (in module xcp_d.utils.utils) group_across_runs() (in module xcp_d.utils.bids)

H

head_radius (xcp_d.config.workflow attribute), [1]

high_pass (xcp_d.config.workflow attribute), [1]

I

IndexImage (class in xcp_d.interfaces.nilearn) init() (xcp_d.config.execution class method), [1] (xcp_d.config.loggers class method), [1] (xcp_d.config.nipype class method), [1] (xcp_d.config.seeds class method) (xcp_d.config.workflow class method) init_alff_wf() (in module xcp_d.workflows.bold.metrics) init_brainsprite_figures_wf() (in module xcp_d.workflows.anatomical.plotting) init_concatenate_data_wf() (in module xcp_d.workflows.bold.concatenation) init_copy_inputs_to_outputs_wf() (in module xcp_d.workflows.anatomical.outputs) init_denoise_bold_wf() (in module xcp_d.workflows.bold.postprocessing) init_despike_wf() (in module xcp_d.workflows.bold.postprocessing) init_execsummary_anatomical_plots_wf() (in module xcp_d.workflows.anatomical.plotting) init_execsummary_functional_plots_wf() (in module xcp_d.workflows.bold.plotting) init_fsnative_to_fsLR_wf() (in module xcp_d.workflows.anatomical.surface) init_functional_connectivity_cifti_wf() (in module xcp_d.workflows.bold.connectivity) init_functional_connectivity_nifti_wf() (in module xcp_d.workflows.bold.connectivity) init_generate_hcp_surfaces_wf() (in module xcp_d.workflows.anatomical.surface) init_itk_warp_gifti_surface_wf() (in module xcp_d.workflows.anatomical.plotting) init_load_atlases_wf() (in module xcp_d.workflows.parcellation) init_parcellate_cifti_wf() (in module xcp_d.workflows.parcellation)

init_parcellate_surfaces_wf() (in module xcp_d.workflows.anatomical.parcellation) init_plot_custom_slices_wf() (in module xcp_d.workflows.plotting) init_plot_overlay_wf() (in module xcp_d.workflows.plotting) init_postproc_derivatives_wf() (in module xcp_d.workflows.bold.outputs) init_postprocess_anat_wf() (in module xcp_d.workflows.anatomical.volume) init_postprocess_cifti_wf() (in module xcp_d.workflows.bold.cifti) init_postprocess_nifti_wf() (in module xcp_d.workflows.bold.nifti) init_postprocess_surfaces_wf() (in module xcp_d.workflows.anatomical.surface) init_prepare_confounds_wf() (in module xcp_d.workflows.bold.postprocessing) init_qc_report_wf() (in module xcp_d.workflows.bold.plotting) init_reho_cifti_wf() (in module xcp_d.workflows.bold.metrics) init_reho_nifti_wf() (in module xcp_d.workflows.bold.metrics) init_resd_smoothing_wf() (in module xcp_d.workflows.bold.postprocessing) init_single_subject_wf() (in module xcp_d.workflows.base) init_xcpd_wf() (in module xcp_d.workflows.base) input_spec (xcp_d.interfaces.bids.BIDSURI attribute) input_type (xcp_d.config.workflow attribute), [1] interface (xcp_d.config.loggers attribute), [1] is_flagged() (in module xcp_d.cli.version) is_interactive() (in module xcp_d.utils.debug) is_number() (in module xcp_d.utils.utils)

L

layout (xcp_d.config.execution attribute), [1] linc_qc (xcp_d.config.workflow attribute), [1] LINCQC (class in xcp_d.interfaces.utils) list_to_str() (in module xcp_d.utils.utils) load() (in module xcp_d.config)

load_motion() (in module xcp_d.utils.confounds) log_dir (xcp_d.config.execution attribute), [1] log_level (xcp_d.config.execution attribute), [1] loggers (class in xcp_d.config), [1] low_mem (xcp_d.config.execution attribute), [1] low_pass (xcp_d.config.workflow attribute), [1]

M

main() (in module xcp_d.cli.combineqc) (in module xcp_d.cli.run) make_mosaic() (in module xcp_d.utils.execsummary) mask_data (xcp_d.utils.plotting.FMRIPlot attribute) master (xcp_d.config.seeds attribute) md_only_boilerplate (xcp_d.config.execution attribute), [1] memory_gb (xcp_d.config.nipype attribute), [1] Merge (class in xcp_d.interfaces.nilearn) mesh_adjacency() (in module xcp_d.utils.restingstate) min_coverage (xcp_d.config.workflow attribute), [1] min_time (xcp_d.config.workflow attribute), [1] mode (xcp_d.config.workflow attribute), [1] modify_brainsprite_scene_template() (in module xcp_d.utils.execsummary) modify_pngs_scene_template() (in module xcp_d.utils.execsummary) module xcp_d xcp_d.cli xcp_d.cli.combineqc xcp_d.cli.parser xcp_d.cli.parser_utils xcp_d.cli.run xcp_d.cli.version xcp_d.cli.workflow xcp_d.config xcp_d.ingression xcp_d.ingression.abcdbids xcp_d.ingression.hcpya xcp_d.ingression.ukbiobank xcp_d.ingression.utils xcp_d.interfaces xcp_d.interfaces.ants xcp_d.interfaces.bids xcp_d.interfaces.censoring xcp_d.interfaces.concatenation xcp_d.interfaces.connectivity xcp_d.interfaces.execsummary xcp_d.interfaces.nilearn xcp_d.interfaces.plotting xcp_d.interfaces.report xcp_d.interfaces.restingstate xcp_d.interfaces.utils xcp_d.interfaces.workbench xcp_d.reports xcp_d.reports.core xcp_d.utils xcp_d.utils.atlas xcp_d.utils.bids xcp_d.utils.boilerplate xcp_d.utils.concatenation xcp_d.utils.confounds xcp_d.utils.debug xcp_d.utils.doc xcp_d.utils.execsummary xcp_d.utils.filemanip xcp_d.utils.modified_data xcp_d.utils.plotting xcp_d.utils.qcmetrics xcp_d.utils.restingstate xcp_d.utils.sentry xcp_d.utils.utils xcp_d.utils.write_save xcp_d.workflows xcp_d.workflows.anatomical xcp_d.workflows.anatomical.outputs xcp_d.workflows.anatomical.parcellation xcp_d.workflows.anatomical.plotting xcp_d.workflows.anatomical.surface xcp_d.workflows.anatomical.volume xcp_d.workflows.base xcp_d.workflows.bold xcp_d.workflows.bold.cifti xcp_d.workflows.bold.concatenation xcp_d.workflows.bold.connectivity xcp_d.workflows.bold.metrics xcp_d.workflows.bold.nifti xcp_d.workflows.bold.outputs xcp_d.workflows.bold.plotting xcp_d.workflows.bold.postprocessing xcp_d.workflows.parcellation xcp_d.workflows.plotting

motion_filter_order (xcp_d.config.workflow attribute), [1] motion_filter_type (xcp_d.config.workflow attribute), [1]

N

NiftiParcellate (class in xcp_d.interfaces.connectivity) nipype (class in xcp_d.config), [1] nipype_version (xcp_d.config.environment attribute), [1]

notrack (xcp_d.config.execution attribute), [1] nprocs (xcp_d.config.nipype attribute), [1] num_threads (xcp_d.interfaces.workbench.WBCommand property)

O

omp_nthreads (xcp_d.config.nipype attribute), [1] out_path_base (xcp_d.interfaces.bids.DerivativesDataSink attribute) output_dir (xcp_d.config.execution attribute), [1]

output_interpolated (xcp_d.config.workflow attribute), [1] overcommit_limit (xcp_d.config.environment attribute), [1] overcommit_policy (xcp_d.config.environment attribute), [1] overlap() (in module xcp_d.utils.qcmetrics)

P

parse_args() (in module xcp_d.cli.parser) participant_label (xcp_d.config.execution attribute), [1] pearson() (in module xcp_d.utils.qcmetrics) plot() (xcp_d.utils.plotting.FMRIPlot method) plot_bbreg() (in module xcp_d.ingression.utils) plot_carpet() (in module xcp_d.utils.plotting) plot_confounds() (in module xcp_d.utils.plotting) plot_design_matrix() (in module xcp_d.utils.plotting) plot_dvars_es() (in module xcp_d.utils.plotting) plot_fmri_es() (in module xcp_d.utils.plotting) plot_framewise_displacement_es() (in module xcp_d.utils.plotting)

plot_global_signal_es() (in module xcp_d.utils.plotting) plot_matrix() (xcp_d.interfaces.connectivity.ConnectPlot method) PlotCiftiParcellation (class in xcp_d.interfaces.plotting) PlotDenseCifti (class in xcp_d.interfaces.plotting) PlotNifti (class in xcp_d.interfaces.plotting) plugin (xcp_d.config.nipype attribute), [1] plugin_args (xcp_d.config.nipype attribute), [1] PNGAppend (class in xcp_d.interfaces.plotting) process_crashfile() (in module xcp_d.utils.sentry) process_surfaces (xcp_d.config.workflow attribute), [1] ProcessMotion (class in xcp_d.interfaces.censoring)

Q

QCPlots (class in xcp_d.interfaces.plotting)

QCPlotsES (class in xcp_d.interfaces.plotting)

R

RandomCensor (class in xcp_d.interfaces.censoring) read_gii() (in module xcp_d.utils.write_save) read_ndata() (in module xcp_d.utils.write_save) ReHoNamePatch (class in xcp_d.interfaces.restingstate) RemoveDummyVolumes (class in xcp_d.interfaces.censoring)

reports_only (xcp_d.config.execution attribute), [1] ResampleToImage (class in xcp_d.interfaces.nilearn) resource_monitor (xcp_d.config.nipype attribute), [1] run_reports() (in module xcp_d.reports.core) run_uuid (xcp_d.config.execution attribute), [1]

S

seeds (class in xcp_d.config) seg_data (xcp_d.utils.plotting.FMRIPlot attribute) select_atlases() (in module xcp_d.utils.atlas) sentry_setup() (in module xcp_d.utils.sentry) setup_exceptionhook() (in module xcp_d.utils.debug) ShowScene (class in xcp_d.interfaces.workbench) SlicesDir (class in xcp_d.interfaces.plotting) Smooth (class in xcp_d.interfaces.nilearn) smoothing (xcp_d.config.workflow attribute), [1]

spikes (xcp_d.utils.plotting.FMRIPlot attribute) split_filename() (in module xcp_d.utils.filemanip) stop_on_first_crash (xcp_d.config.nipype attribute), [1] SubjectSummary (class in xcp_d.interfaces.report) SummaryInterface (class in xcp_d.interfaces.report) surf_data_from_cifti() (in module xcp_d.utils.plotting) SurfaceAverage (class in xcp_d.interfaces.workbench) SurfaceGenerateInflated (class in xcp_d.interfaces.workbench) SurfaceReHo (class in xcp_d.interfaces.restingstate) SurfaceSphereProjectUnproject (class in xcp_d.interfaces.workbench)

T

task_id (xcp_d.config.execution attribute), [1] templateflow_home (xcp_d.config.execution attribute), [1] templateflow_version (xcp_d.config.environment attribute), [1]

to_filename() (in module xcp_d.config) ToDict (class in xcp_d.cli.parser_utils) TR (xcp_d.utils.plotting.FMRIPlot attribute) TSVConnect (class in xcp_d.interfaces.connectivity)

U

utils (xcp_d.config.loggers attribute), [1]

V

version (xcp_d.config.environment attribute), [1]

volterra() (in module xcp_d.utils.confounds)

W

WBCommand (class in xcp_d.interfaces.workbench) work_dir (xcp_d.config.execution attribute), [1] workflow (class in xcp_d.config), [1] (xcp_d.config.loggers attribute), [1] write_atlas_dataset_description() (in module xcp_d.utils.bids)

write_derivative_description() (in module xcp_d.utils.bids) write_gii() (in module xcp_d.utils.write_save) write_graph (xcp_d.config.execution attribute), [1] write_html() (xcp_d.interfaces.execsummary.ExecutiveSummary method) write_json() (in module xcp_d.ingression.utils) write_ndata() (in module xcp_d.utils.write_save)

X

xcp_d module xcp_d.cli module xcp_d.cli.combineqc module xcp_d.cli.parser module xcp_d.cli.parser_utils module xcp_d.cli.run module xcp_d.cli.version module xcp_d.cli.workflow module xcp_d.config module xcp_d.ingression module xcp_d.ingression.abcdbids module xcp_d.ingression.hcpya module xcp_d.ingression.ukbiobank module xcp_d.ingression.utils module xcp_d.interfaces module xcp_d.interfaces.ants module xcp_d.interfaces.bids module xcp_d.interfaces.censoring module xcp_d.interfaces.concatenation module xcp_d.interfaces.connectivity module xcp_d.interfaces.execsummary module xcp_d.interfaces.nilearn module xcp_d.interfaces.plotting module xcp_d.interfaces.report module xcp_d.interfaces.restingstate module xcp_d.interfaces.utils module xcp_d.interfaces.workbench module xcp_d.reports module xcp_d.reports.core module xcp_d.utils module xcp_d.utils.atlas module xcp_d.utils.bids module xcp_d.utils.boilerplate module

xcp_d.utils.concatenation module xcp_d.utils.confounds module xcp_d.utils.debug module xcp_d.utils.doc module xcp_d.utils.execsummary module xcp_d.utils.filemanip module xcp_d.utils.modified_data module xcp_d.utils.plotting module xcp_d.utils.qcmetrics module xcp_d.utils.restingstate module xcp_d.utils.sentry module xcp_d.utils.utils module xcp_d.utils.write_save module xcp_d.workflows module xcp_d.workflows.anatomical module xcp_d.workflows.anatomical.outputs module xcp_d.workflows.anatomical.parcellation module xcp_d.workflows.anatomical.plotting module xcp_d.workflows.anatomical.surface module xcp_d.workflows.anatomical.volume module xcp_d.workflows.base module xcp_d.workflows.bold module xcp_d.workflows.bold.cifti module xcp_d.workflows.bold.concatenation module xcp_d.workflows.bold.connectivity module xcp_d.workflows.bold.metrics module xcp_d.workflows.bold.nifti module xcp_d.workflows.bold.outputs module xcp_d.workflows.bold.plotting module xcp_d.workflows.bold.postprocessing module xcp_d.workflows.parcellation module xcp_d.workflows.plotting module

Y

YesNoAction (class in xcp_d.cli.parser_utils)