Developers - API

xcp_d-combineqc

Aggregate qc of all the subjects.

usage: xcp_d-combineqc [-h] xcpd_dir output_prefix

Positional Arguments

xcpd_dir

xcp_d output dir

output_prefix

output prefix for group

Library API

• xcp_d.cli package
  • Submodules
    • xcp_d.cli.combineqc module
      • get_parser()
      • main()
    • xcp_d.cli.parser module
      • xcp_d preprocessing workflow
      • parse_args()
    • xcp_d.cli.parser_utils module
      • check_deps()
      • json_file()
    • xcp_d.cli.run module
      • XCP-D postprocessing workflow
      • main()
    • xcp_d.cli.version module
      • check_latest()
      • is_flagged()
    • xcp_d.cli.workflow module
      • build_boilerplate()
      • build_workflow()
• xcp_d.workflows package
  • Submodules
    • xcp_d.workflows.anatomical module
      • init_ants_xfm_to_fsl_wf()
      • init_generate_hcp_surfaces_wf()
      • init_postprocess_anat_wf()
      • init_postprocess_surfaces_wf()
      • init_warp_one_hemisphere_wf()
      • init_warp_surfaces_to_template_wf()
    • xcp_d.workflows.base module
      • init_single_subject_wf()
      • init_xcpd_wf()
    • xcp_d.workflows.bold module
      • init_postprocess_nifti_wf()
    • xcp_d.workflows.cifti module
      • init_postprocess_cifti_wf()
    • xcp_d.workflows.concatenation module
      • init_concatenate_data_wf()
    • xcp_d.workflows.connectivity module
      • init_functional_connectivity_cifti_wf()
      • init_functional_connectivity_nifti_wf()
      • init_load_atlases_wf()
      • init_parcellate_surfaces_wf()
    • xcp_d.workflows.execsummary module
      • init_brainsprite_figures_wf()
      • init_execsummary_anatomical_plots_wf()
      • init_execsummary_functional_plots_wf()
      • init_plot_custom_slices_wf()
      • init_plot_overlay_wf()
    • xcp_d.workflows.outputs module
      • init_copy_inputs_to_outputs_wf()
      • init_postproc_derivatives_wf()
    • xcp_d.workflows.plotting module
      • init_qc_report_wf()
    • xcp_d.workflows.postprocessing module
      • init_denoise_bold_wf()
      • init_despike_wf()
      • init_prepare_confounds_wf()
      • init_resd_smoothing_wf()
    • xcp_d.workflows.restingstate module
      • init_alff_wf()
      • init_reho_cifti_wf()
      • init_reho_nifti_wf()
• xcp_d.interfaces package
  • Submodules
    • xcp_d.interfaces.ants module
      • ApplyTransforms
      • CompositeInvTransformUtil
      • ConvertTransformFile
    • xcp_d.interfaces.bids module
      • CollectRegistrationFiles
      • CopyAtlas
      • DerivativesDataSink
        • DerivativesDataSink.out_path_base
    • xcp_d.interfaces.c3 module
      • C3d
    • xcp_d.interfaces.censoring module
      • Censor
      • GenerateConfounds
      • RandomCensor
      • RemoveDummyVolumes
    • xcp_d.interfaces.concatenation module
      • CleanNameSource
      • ConcatenateInputs
      • FilterOutFailedRuns
    • xcp_d.interfaces.connectivity module
      • CiftiConnect
      • CiftiParcellate
      • ConnectPlot
        • ConnectPlot.plot_matrix()
      • NiftiParcellate
      • TSVConnect
      • correlate_timeseries()
    • xcp_d.interfaces.execsummary module
      • ExecutiveSummary
        • ExecutiveSummary.collect_inputs()
        • ExecutiveSummary.generate_report()
        • ExecutiveSummary.write_html()
      • FormatForBrainSwipes
    • xcp_d.interfaces.nilearn module
      • BinaryMath
      • DenoiseCifti
      • DenoiseNifti
      • IndexImage
      • Merge
      • ResampleToImage
      • Smooth
    • xcp_d.interfaces.plotting module
      • AnatomicalPlot
      • CensoringPlot
      • PNGAppend
      • QCPlots
      • QCPlotsES
      • SlicesDir
    • xcp_d.interfaces.report module
      • AboutSummary
      • FunctionalSummary
      • SubjectSummary
      • SummaryInterface
    • xcp_d.interfaces.report_core module
      • Report
      • generate_reports()
      • run_reports()
    • xcp_d.interfaces.restingstate module
      • ComputeALFF
      • DespikePatch
      • ReHoNamePatch
      • SurfaceReHo
    • xcp_d.interfaces.utils module
      • ConvertTo32
      • FilterUndefined
    • xcp_d.interfaces.workbench module
      • ApplyAffine
      • ApplyWarpfield
      • ChangeXfmType
      • CiftiChangeMapping
      • CiftiConvert
      • CiftiCreateDenseFromTemplate
      • CiftiCreateDenseScalar
      • CiftiParcellateWorkbench
      • CiftiSeparateMetric
      • CiftiSeparateVolumeAll
      • CiftiSurfaceResample
      • ConvertAffine
      • FixCiftiIntent
      • ShowScene
      • SurfaceAverage
      • SurfaceGenerateInflated
      • SurfaceSphereProjectUnproject
• xcp_d.utils package
  • Submodules
    • xcp_d.utils.atlas module
      • get_atlas_cifti()
      • get_atlas_nifti()
      • select_atlases()
    • xcp_d.utils.bids module
      • BIDSError
      • BIDSWarning
      • check_pipeline_version()
      • collect_data()
      • collect_mesh_data()
      • collect_morphometry_data()
      • collect_participants()
      • collect_run_data()
      • get_entity()
      • get_freesurfer_dir()
      • get_preproc_pipeline_info()
      • group_across_runs()
      • write_atlas_dataset_description()
      • write_dataset_description()
    • xcp_d.utils.boilerplate module
      • describe_atlases()
      • describe_censoring()
      • describe_motion_parameters()
      • describe_regression()
    • xcp_d.utils.concatenation module
      • concatenate_niimgs()
      • concatenate_tsvs()
    • xcp_d.utils.confounds module
      • get_custom_confounds()
      • load_confound_matrix()
      • load_motion()
      • motion_regression_filter()
    • xcp_d.utils.debug module
      • is_interactive()
      • setup_exceptionhook()
    • xcp_d.utils.doc module
      • download_example_data()
      • fill_doc()
    • xcp_d.utils.execsummary module
      • get_n_frames()
      • get_png_image_names()
      • make_mosaic()
      • modify_brainsprite_scene_template()
      • modify_pngs_scene_template()
    • xcp_d.utils.filemanip module
      • ensure_list()
      • fname_presuffix()
      • split_filename()
    • xcp_d.utils.modified_data module
      • compute_fd()
      • downcast_to_32()
      • flag_bad_run()
    • xcp_d.utils.plotting module
      • FMRIPlot
        • FMRIPlot.TR
        • FMRIPlot.confounds
        • FMRIPlot.func_file
        • FMRIPlot.mask_data
        • FMRIPlot.plot()
        • FMRIPlot.seg_data
        • FMRIPlot.spikes
      • plot_alff_reho_surface()
      • plot_alff_reho_volumetric()
      • plot_carpet()
      • plot_confounds()
      • plot_design_matrix()
      • plot_dvars_es()
      • plot_fmri_es()
      • plot_framewise_displacement_es()
      • plot_global_signal_es()
      • surf_data_from_cifti()
    • xcp_d.utils.qcmetrics module
      • compute_dvars()
      • compute_registration_qc()
      • dice()
      • make_dcan_df()
      • make_dcan_qc_file()
      • overlap()
      • pearson()
    • xcp_d.utils.restingstate module
      • compute_2d_reho()
      • compute_alff()
      • mesh_adjacency()
    • xcp_d.utils.sentry module
      • before_send()
      • process_crashfile()
      • sentry_setup()
    • xcp_d.utils.utils module
      • butter_bandpass()
      • check_deps()
      • denoise_with_nilearn()
      • estimate_brain_radius()
      • fwhm2sigma()
      • get_bold2std_and_t1w_xfms()
      • get_std2bold_xfms()
      • list_to_str()
    • xcp_d.utils.write_save module
      • get_cifti_intents()
      • read_gii()
      • read_ndata()
      • write_gii()
      • write_ndata()
• xcp_d.ingression package
  • Submodules
    • xcp_d.ingression.abcdbids module
      • convert_dcan2bids()
      • convert_dcan_to_bids_single_subject()
    • xcp_d.ingression.hcpya module
      • convert_hcp2bids()
      • convert_hcp_to_bids_single_subject()
    • xcp_d.ingression.ukbiobank module
      • convert_ukb2bids()
      • convert_ukb_to_bids_single_subject()
    • xcp_d.ingression.utils module
      • collect_anatomical_files()
      • collect_hcp_confounds()
      • collect_meshes()
      • collect_morphs()
      • collect_ukbiobank_confounds()
      • copy_file()
      • copy_files_in_dict()
      • extract_mean_signal()
      • plot_bbreg()
      • write_json()