Developers - API

• xcp_d package
  • Subpackages
    • xcp_d.cli package
      • Submodules
        • xcp_d.cli.combineqc module
          • get_parser()
          • main()
        • xcp_d.cli.run module
          • xcp_d preprocessing workflow
          • build_workflow()
          • check_deps()
          • get_parser()
          • json_file()
          • main()
    • xcp_d.interfaces package
      • Submodules
        • xcp_d.interfaces.ants module
          • CompositeInvTransformUtil
          • ConvertTransformFile
        • xcp_d.interfaces.bids module
          • BaseDerivativesDataSink
            • BaseDerivativesDataSink.__init__()
            • BaseDerivativesDataSink.out_path_base
          • DerivativesDataSink
            • DerivativesDataSink.out_path_base
        • xcp_d.interfaces.c3 module
          • C3d
        • xcp_d.interfaces.connectivity module
          • ApplyTransformsx
          • ConnectPlot
          • NiftiConnect
        • xcp_d.interfaces.constants module
        • xcp_d.interfaces.filtering module
          • FilteringData
        • xcp_d.interfaces.layout_builder module
          • LayoutBuilder
            • LayoutBuilder.get_list_of_tasks()
            • LayoutBuilder.run()
            • LayoutBuilder.setup()
            • LayoutBuilder.teardown()
            • LayoutBuilder.write_html()
          • ModalContainer
            • ModalContainer.add_image()
            • ModalContainer.add_images()
            • ModalContainer.get_button()
            • ModalContainer.get_container()
            • ModalContainer.get_image_class()
            • ModalContainer.get_modal_id()
            • ModalContainer.get_scripts()
          • ModalSlider
            • ModalSlider.get_container()
            • ModalSlider.get_scripts()
          • Section
            • Section.get_scripts()
            • Section.get_section()
          • TasksSection
            • TasksSection.run()
            • TasksSection.write_bold_gray_row()
            • TasksSection.write_t1_reg_rows()
          • TxSection
            • TxSection.run()
        • xcp_d.interfaces.nilearn module
          • BinaryMath
          • Merge
          • Smooth
        • xcp_d.interfaces.prepostcleaning module
          • CensorScrub
          • ConvertTo32
          • Interpolate
          • RemoveTR
        • xcp_d.interfaces.qc_plot module
          • CensoringPlot
          • QCPlot
        • xcp_d.interfaces.regression module
          • CiftiDespike
          • Regress
        • xcp_d.interfaces.report module
          • AboutSummary
          • FunctionalSummary
          • SubjectSummary
          • SummaryInterface
          • get_space()
        • xcp_d.interfaces.report_core module
          • Report
          • generate_reports()
          • run_reports()
        • xcp_d.interfaces.resting_state module
          • BrainPlot
          • ComputeALFF
          • DespikePatch
          • ReHoNamePatch
          • SurfaceReHo
        • xcp_d.interfaces.surfplotting module
          • BrainPlotx
          • PlotImage
          • PlotSVGData
          • RibbontoStatmap
        • xcp_d.interfaces.workbench module
          • ApplyAffine
          • ApplyWarpfield
          • ChangeXfmType
          • CiftiCorrelation
          • CiftiCreateDenseScalar
          • CiftiParcellate
          • CiftiSeparateMetric
          • CiftiSeparateVolumeAll
          • CiftiSurfaceResample
          • ConvertAffine
          • FixCiftiIntent
          • SurfaceAverage
          • SurfaceGenerateInflated
          • SurfaceSphereProjectUnproject
    • xcp_d.utils package
      • Submodules
        • xcp_d.utils.atlas module
          • get_atlas_cifti()
          • get_atlas_names()
          • get_atlas_nifti()
        • xcp_d.utils.bids module
          • BIDSError
          • BIDSWarning
          • collect_data()
          • collect_participants()
          • collect_run_data()
          • collect_surface_data()
          • get_freesurfer_dir()
          • get_preproc_pipeline_info()
          • write_dataset_description()
        • xcp_d.utils.concatenation module
          • concatenate_derivatives()
          • concatenate_tsv_files()
          • make_dcan_df()
        • xcp_d.utils.confounds module
          • consolidate_confounds()
          • describe_regression()
          • get_confounds_tsv()
          • get_customfile()
          • load_confound()
          • load_confound_matrix()
          • load_motion()
          • motion_regression_filter()
          • readjson()
        • xcp_d.utils.dcan2fmriprep module
          • bbregplot()
          • copyfileobj_example()
          • dcan2fmriprep()
          • dcan2fmriprepx()
          • extractreg()
          • writejson()
        • xcp_d.utils.doc module
          • fill_doc()
        • xcp_d.utils.execsummary module
          • generate_brain_sprite()
          • ribbon_to_statmap()
        • xcp_d.utils.fcon module
          • compute_2d_reho()
          • compute_alff()
          • extract_timeseries_funct()
          • mesh_adjacency()
        • xcp_d.utils.filemanip module
          • binarize_img()
          • check_binary_mask()
          • copyfile()
          • copyfiles()
          • ensure_list()
          • find_and_copy_files()
          • find_one_file()
          • fname_presuffix()
          • get_related_files()
          • hash_infile()
          • hash_timestamp()
          • indirectory()
          • on_cifs()
          • relpath()
          • split_filename()
          • which()
        • xcp_d.utils.hcp2fmriprep module
          • hcp2fmriprep()
          • hcpfmriprepx()
        • xcp_d.utils.modified_data module
          • compute_fd()
          • downcast_to_32()
          • generate_mask()
          • interpolate_masked_data()
        • xcp_d.utils.plot module
          • FMRIPlot
            • FMRIPlot.TR
            • FMRIPlot.confounds
            • FMRIPlot.func_file
            • FMRIPlot.mask_data
            • FMRIPlot.plot()
            • FMRIPlot.seg_data
            • FMRIPlot.spikes
          • confoundplot()
          • confoundplotx()
          • plot_alff_reho_surface()
          • plot_alff_reho_volumetric()
          • plot_carpet()
          • plot_design_matrix()
          • plot_ribbon_svg()
          • plot_svgx()
          • plotimage()
          • surf_data_from_cifti()
        • xcp_d.utils.qcmetrics module
          • compute_dvars()
          • compute_registration_qc()
          • coverage()
          • crosscorr()
          • dc()
          • jc()
        • xcp_d.utils.sentry module
          • before_send()
          • process_crashfile()
          • sentry_setup()
          • start_ping()
        • xcp_d.utils.utils module
          • butter_bandpass()
          • fwhm2sigma()
          • get_bold2std_and_t1w_xforms()
          • get_segfile()
          • get_std2bold_xforms()
          • zscore_nifti()
        • xcp_d.utils.write_save module
          • despikedatacifti()
          • get_cifti_intents()
          • read_gii()
          • read_ndata()
          • run_shell()
          • scalex()
          • write_gii()
          • write_ndata()
    • xcp_d.workflow package
      • Submodules
        • xcp_d.workflow.anatomical module
          • init_anatomical_wf()
          • init_t1w_wf()
        • xcp_d.workflow.base module
          • init_subject_wf()
          • init_xcpd_wf()
        • xcp_d.workflow.bold module
          • init_boldpostprocess_wf()
        • xcp_d.workflow.cifti module
          • init_ciftipostprocess_wf()
        • xcp_d.workflow.connectivity module
          • init_cifti_functional_connectivity_wf()
          • init_nifti_functional_connectivity_wf()
        • xcp_d.workflow.execsummary module
          • init_brainsprite_wf()
          • init_execsummary_wf()
        • xcp_d.workflow.outputs module
          • init_writederivatives_wf()
        • xcp_d.workflow.plotting module
          • init_qc_report_wf()
        • xcp_d.workflow.postprocessing module
          • init_resd_smoothing_wf()
        • xcp_d.workflow.restingstate module
          • init_cifti_reho_wf()
          • init_compute_alff_wf()
          • init_nifti_reho_wf()