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 package
  • Subpackages
    • 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
          • ConfoundsAction
          • ToDict
          • YesNoAction
        • 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.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()
          • get_identity_transform_destinations()
          • plot_bbreg()
          • write_json()
          • write_scans_tsv()
    • xcp_d.interfaces package
      • Submodules
        • xcp_d.interfaces.ants module
          • ApplyTransforms
        • xcp_d.interfaces.bids module
          • AddHashToTSV
          • BIDSURI
            • BIDSURI.input_spec
          • CollectRegistrationFiles
          • CopyAtlas
          • CopyAtlasDescription
          • DerivativesDataSink
            • DerivativesDataSink.out_path_base
        • xcp_d.interfaces.censoring module
          • Censor
          • GenerateConfounds
          • ProcessMotion
          • RandomCensor
          • RemoveDummyVolumes
        • xcp_d.interfaces.concatenation module
          • CleanNameSource
          • ConcatenateInputs
          • FilterOutFailedRuns
          • ZScoreInputs
        • xcp_d.interfaces.connectivity module
          • CiftiMask
          • CiftiToTSV
          • CiftiVertexMask
          • ConnectPlot
            • ConnectPlot.plot_matrix()
          • NiftiParcellate
          • TSVConnect
          • correlate_timeseries()
        • xcp_d.interfaces.execsummary module
          • ExecutiveSummary
            • ExecutiveSummary.collect_inputs()
            • ExecutiveSummary.generate_report()
            • ExecutiveSummary.write_html()
          • FormatForBrainSwipes
          • PlotSlicesForBrainSprite
        • xcp_d.interfaces.nilearn module
          • ApplyMask
          • BinaryMath
          • DenoiseCifti
          • DenoiseNifti
          • IndexImage
          • Merge
          • ResampleToImage
          • Smooth
        • xcp_d.interfaces.plotting module
          • AnatomicalPlot
          • CensoringPlot
          • PNGAppend
          • PlotCiftiParcellation
          • PlotDenseCifti
          • PlotNifti
          • QCPlots
          • QCPlotsES
          • SlicesDir
        • xcp_d.interfaces.report module
          • AboutSummary
          • FunctionalSummary
          • SubjectSummary
          • SummaryInterface
        • xcp_d.interfaces.restingstate module
          • ComputeALFF
          • DespikePatch
          • ReHoNamePatch
          • SurfaceReHo
        • xcp_d.interfaces.utils module
          • ABCCQC
          • ConvertTo32
          • FilterUndefined
          • LINCQC
        • xcp_d.interfaces.workbench module
          • CiftiConvert
          • CiftiCorrelation
          • CiftiCreateDenseFromTemplate
          • CiftiCreateDenseScalar
          • CiftiMath
          • CiftiParcellateWorkbench
          • CiftiSeparateMetric
          • CiftiSeparateVolumeAll
          • CiftiSmooth
          • CiftiSurfaceResample
          • FixCiftiIntent
          • ShowScene
          • SurfaceAverage
          • SurfaceGenerateInflated
          • SurfaceSphereProjectUnproject
          • WBCommand
            • WBCommand.num_threads
    • xcp_d.reports package
      • Submodules
        • xcp_d.reports.core module
          • generate_reports()
          • run_reports()
    • xcp_d.utils package
      • Submodules
        • xcp_d.utils.atlas module
          • collect_atlases()
          • select_atlases()
        • xcp_d.utils.bids module
          • BIDSError
          • BIDSWarning
          • check_pipeline_version()
          • collect_confounds()
          • collect_data()
          • collect_mesh_data()
          • collect_morphometry_data()
          • collect_participants()
          • collect_run_data()
          • get_entity()
          • get_preproc_pipeline_info()
          • group_across_runs()
          • write_atlas_dataset_description()
          • write_derivative_description()
        • xcp_d.utils.boilerplate module
          • describe_atlases()
          • describe_censoring()
          • describe_motion_parameters()
          • describe_regression()
        • xcp_d.utils.concatenation module
          • concatenate_niimgs()
          • concatenate_tsvs()
          • zscore_niimg()
          • zscore_tsv()
        • xcp_d.utils.confounds module
          • filter_motion()
          • load_motion()
          • volterra()
        • 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_mesh()
          • get_png_image_names()
          • make_mosaic()
          • modify_pngs_scene_template()
          • plot_gii()
        • xcp_d.utils.filemanip module
          • ensure_list()
          • fname_presuffix()
          • split_filename()
        • xcp_d.utils.modified_data module
          • calculate_exact_scans()
          • 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_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()
          • overlap()
          • pearson()
        • xcp_d.utils.restingstate module
          • compute_2d_reho()
          • compute_alff()
          • compute_alff_chunk()
          • mesh_adjacency()
        • xcp_d.utils.sentry module
          • before_send()
          • process_crashfile()
          • sentry_setup()
        • xcp_d.utils.utils module
          • check_deps()
          • denoise_with_nilearn()
          • estimate_brain_radius()
          • fwhm2sigma()
          • get_bold2std_and_t1w_xfms()
          • get_col()
          • get_std2bold_xfms()
          • is_number()
          • list_to_str()
        • xcp_d.utils.write_save module
          • get_cifti_intents()
          • read_gii()
          • read_ndata()
          • write_gii()
          • write_ndata()
    • xcp_d.workflows package
      • Subpackages
        • xcp_d.workflows.anatomical package
          • Submodules
            • xcp_d.workflows.anatomical.outputs module
              • init_copy_inputs_to_outputs_wf()
            • xcp_d.workflows.anatomical.parcellation module
              • init_parcellate_surfaces_wf()
            • xcp_d.workflows.anatomical.plotting module
              • init_brainsprite_figures_wf()
              • init_execsummary_anatomical_plots_wf()
              • init_itk_warp_gifti_surface_wf()
            • xcp_d.workflows.anatomical.surface module
              • init_fsnative_to_fsLR_wf()
              • init_generate_hcp_surfaces_wf()
              • init_postprocess_surfaces_wf()
            • xcp_d.workflows.anatomical.volume module
              • init_postprocess_anat_wf()
        • xcp_d.workflows.bold package
          • Submodules
            • xcp_d.workflows.bold.cifti module
              • init_postprocess_cifti_wf()
            • xcp_d.workflows.bold.concatenation module
              • init_concatenate_data_wf()
            • xcp_d.workflows.bold.connectivity module
              • init_functional_connectivity_cifti_wf()
              • init_functional_connectivity_nifti_wf()
            • xcp_d.workflows.bold.metrics module
              • init_alff_wf()
              • init_reho_cifti_wf()
              • init_reho_nifti_wf()
            • xcp_d.workflows.bold.nifti module
              • init_postprocess_nifti_wf()
            • xcp_d.workflows.bold.outputs module
              • init_postproc_derivatives_wf()
            • xcp_d.workflows.bold.plotting module
              • init_execsummary_functional_plots_wf()
              • init_qc_report_wf()
            • xcp_d.workflows.bold.postprocessing module
              • init_denoise_bold_wf()
              • init_despike_wf()
              • init_prepare_confounds_wf()
              • init_resd_smoothing_wf()
      • Submodules
        • xcp_d.workflows.base module
          • clean_datasinks()
          • init_single_subject_wf()
          • init_xcpd_wf()
        • xcp_d.workflows.parcellation module
          • init_load_atlases_wf()
          • init_parcellate_cifti_wf()
        • xcp_d.workflows.plotting module
          • init_plot_custom_slices_wf()
          • init_plot_overlay_wf()
  • Submodules
    • xcp_d.config module
      • Configuration sections
      • Usage
      • Logging
      • Other responsibilities
      • dismiss_hash()
      • dumps()
      • environment
        • environment.cpu_count
        • environment.exec_docker_version
        • environment.exec_env
        • environment.free_mem
        • environment.nipype_version
        • environment.overcommit_limit
        • environment.overcommit_policy
        • environment.templateflow_version
        • environment.version
      • execution
        • execution.aggr_ses_reports
        • execution.atlases
        • execution.bids_database_dir
        • execution.bids_description_hash
        • execution.bids_filters
        • execution.boilerplate_only
        • execution.confounds_config
        • execution.dataset_links
        • execution.datasets
        • execution.debug
        • execution.fmri_dir
        • execution.fs_license_file
        • execution.init()
        • execution.layout
        • execution.log_dir
        • execution.log_level
        • execution.low_mem
        • execution.md_only_boilerplate
        • execution.notrack
        • execution.output_dir
        • execution.output_layout
        • execution.parameters_hash
        • execution.participant_label
        • execution.processing_list
        • execution.report_output_level
        • execution.reports_only
        • execution.run_uuid
        • execution.session_id
        • execution.task_id
        • execution.templateflow_home
        • execution.work_dir
        • execution.write_graph
      • from_dict()
      • get()
      • hash_config()
      • load()
      • loggers
        • loggers.cli
        • loggers.default
        • loggers.init()
        • loggers.interface
        • loggers.utils
        • loggers.workflow
      • nipype
        • nipype.crashfile_format
        • nipype.get_linked_libs
        • nipype.get_plugin()
        • nipype.init()
        • nipype.memory_gb
        • nipype.nprocs
        • nipype.omp_nthreads
        • nipype.plugin
        • nipype.plugin_args
        • nipype.resource_monitor
        • nipype.stop_on_first_crash
      • seeds
        • seeds.init()
        • seeds.master
      • to_filename()
      • workflow
        • workflow.abcc_qc
        • workflow.band_stop_max
        • workflow.band_stop_min
        • workflow.bandpass_filter
        • workflow.bpf_order
        • workflow.combine_runs
        • workflow.correlation_lengths
        • workflow.despike
        • workflow.dummy_scans
        • workflow.fd_thresh
        • workflow.file_format
        • workflow.head_radius
        • workflow.high_pass
        • workflow.init()
        • workflow.input_type
        • workflow.linc_qc
        • workflow.low_pass
        • workflow.min_coverage
        • workflow.min_time
        • workflow.mode
        • workflow.motion_filter_order
        • workflow.motion_filter_type
        • workflow.output_interpolated
        • workflow.output_run_wise_correlations
        • workflow.process_surfaces
        • workflow.skip_outputs
        • workflow.smoothing