API Documentation

• qsirecon.workflows package
  • Subpackages
    • qsirecon.workflows.recon package
      • Reconstruction pipeline nodes
        • Converting between file formats
          • init_mif_to_fibgz_wf()
          • init_fibgz_to_mif_wf()
        • Dipy Reconstruction workflows
          • init_dipy_brainsuite_shore_recon_wf()
          • init_dipy_mapmri_recon_wf()
          • init_dipy_dki_recon_wf()
        • DSI Studio workflows
          • init_dsi_studio_recon_wf()
          • init_dsi_studio_connectivity_wf()
          • init_dsi_studio_export_wf()
          • init_dsi_studio_autotrack_wf()
          • init_dsi_studio_connectivity_wf()
          • init_dsi_studio_export_wf()
        • MRTrix workflows
          • init_mrtrix_csd_recon_wf()
          • init_mrtrix_tractography_wf()
          • init_mrtrix_connectivity_wf()
        • Miscellaneous workflows
          • init_discard_repeated_samples_wf()
          • init_conform_dwi_wf()
      • Submodules
        • qsirecon.workflows.recon.amico module
          • AMICO Reconstruction workflows
            • init_amico_noddi_fit_wf()
          • init_amico_noddi_fit_wf()
        • qsirecon.workflows.recon.anatomical module
          • check_hsv_inputs()
          • init_dwi_recon_anatomical_workflow()
          • init_highres_recon_anatomical_wf()
          • init_output_grid_wf()
          • init_register_fs_to_qsiprep_wf()
        • qsirecon.workflows.recon.build_workflow module
          • init_dwi_recon_workflow()
          • workflow_from_spec()
        • qsirecon.workflows.recon.converters module
          • Converting between file formats
            • init_mif_to_fibgz_wf()
            • init_fibgz_to_mif_wf()
          • init_fibgz_to_mif_wf()
          • init_fod_fib_wf()
          • init_mif_to_fibgz_wf()
          • init_qsirecon_to_fsl_wf()
        • qsirecon.workflows.recon.dipy module
          • Dipy Reconstruction workflows
            • init_dipy_brainsuite_shore_recon_wf()
            • init_dipy_mapmri_recon_wf()
            • init_dipy_dki_recon_wf()
          • external_format_datasinks()
          • infer_deltas()
          • init_dipy_brainsuite_shore_recon_wf()
          • init_dipy_dki_recon_wf()
          • init_dipy_mapmri_recon_wf()
        • qsirecon.workflows.recon.dsi_studio module
          • DSI Studio workflows
            • init_dsi_studio_recon_wf()
            • init_dsi_studio_connectivity_wf()
            • init_dsi_studio_export_wf()
            • init_dsi_studio_autotrack_wf()
            • init_dsi_studio_connectivity_wf()
            • init_dsi_studio_export_wf()
          • init_dsi_studio_autotrack_registration_wf()
          • init_dsi_studio_autotrack_wf()
          • init_dsi_studio_connectivity_wf()
          • init_dsi_studio_export_wf()
          • init_dsi_studio_recon_wf()
          • init_dsi_studio_tractography_wf()
        • qsirecon.workflows.recon.mrtrix module
          • MRTrix workflows
            • init_mrtrix_csd_recon_wf()
            • init_mrtrix_tractography_wf()
            • init_mrtrix_connectivity_wf()
          • init_global_tractography_wf()
          • init_mrtrix_connectivity_wf()
          • init_mrtrix_csd_recon_wf()
          • init_mrtrix_tractography_wf()
        • qsirecon.workflows.recon.pyafq module
          • PyAFQ tractometry and visualization
            • init_pyafq_wf()
          • init_pyafq_wf()
        • qsirecon.workflows.recon.scalar_mapping module
          • Summarize and Transform recon outputs
            • init_scalar_to_bundle_wf()
            • init_scalar_to_atlas_wf()
            • init_scalar_to_template_wf()
            • init_scalar_to_surface_wf()
          • init_scalar_to_atlas_wf()
          • init_scalar_to_bundle_wf()
          • init_scalar_to_surface_wf()
          • init_scalar_to_template_wf()
        • qsirecon.workflows.recon.steinhardt module
          • init_steinhardt_order_param_wf()
        • qsirecon.workflows.recon.tortoise module
          • TORTOISE recon workflows
            • init_tortoise_estimator_wf()
          • init_tortoise_estimator_wf()
        • qsirecon.workflows.recon.utils module
          • Miscellaneous workflows
            • init_discard_repeated_samples_wf()
            • init_conform_dwi_wf()
          • init_conform_dwi_wf()
          • init_discard_repeated_samples_wf()
          • init_gradient_select_wf()
          • init_scalar_output_wf()
          • init_test_wf()
  • Submodules
    • qsirecon.workflows.base module
      • init_qsirecon_wf()
      • init_single_subject_recon_wf()
    • qsirecon.workflows.reports module
      • init_json_preproc_report_wf()
      • init_single_subject_json_report_wf()
• qsirecon.interfaces package
  • Submodules
    • qsirecon.interfaces.amico module
      • Workflows for AMICO
      • AmicoReconInterface
      • NODDI
      • NODDITissueFraction
    • qsirecon.interfaces.anatomical module
      • Image tools interfaces
      • CalculateSOP
      • GetTemplate
      • QSIPrepAnatomicalIngress
      • VoxelSizeChooser
      • calculate_steinhardt()
      • get_l_m()
    • qsirecon.interfaces.ants module
      • ConvertTransformFile
      • ImageMath
    • qsirecon.interfaces.bids module
      • Interfaces for handling BIDS-like neuroimaging structures
      • CopyAtlas
      • DerivativesDataSink
        • DerivativesDataSink.out_path_base
      • ReconDerivativesDataSink
        • ReconDerivativesDataSink.out_path_base
      • get_bids_params()
      • get_entity()
      • get_recon_output_name()
    • qsirecon.interfaces.converters module
      • DSIStudioTrkToTck
      • FIBGZtoFOD
      • FODtoFIBGZ
      • MergeFODGQIFibs
      • NODDItoFIBGZ
      • amico_directions_to_fibgz()
      • amplitudes_to_fibgz()
      • amplitudes_to_sh_mif()
      • combine_gqi_and_csd_fib_files()
      • fast_load_fibgz()
      • fib2amps()
      • get_dsi_studio_ODF_geometry()
      • mif2amps()
      • peaks_to_odfs()
      • popen_run()
    • qsirecon.interfaces.denoise module
      • Interfaces for image denoising
      • SeriesPreprocReport
        • SeriesPreprocReport.__init__()
    • qsirecon.interfaces.dipy module
      • Image tools interfaces
      • BrainSuiteShoreReconstruction
      • DipyReconInterface
      • KurtosisReconstruction
      • KurtosisReconstructionMSDKI
      • KurtosisReconstructionMicrostructure
      • MAPMRIReconstruction
      • TensorReconstruction
    • qsirecon.interfaces.dsi_studio module
      • AggregateAutoTrackResults
      • AutoTrack
      • ChenAutoTrack
      • DSIStudioAtlasGraph
      • DSIStudioConnectivityMatrix
      • DSIStudioCreateSrc
      • DSIStudioExport
      • DSIStudioGQIReconstruction
      • DSIStudioReconstruction
      • DSIStudioTracking
      • FixDSIStudioExportHeader
      • btable_from_bvals_bvecs()
      • stat_txt_to_df()
    • qsirecon.interfaces.freesurfer module
      • FreeSurfer tools interfaces
      • find_fs_path()
    • qsirecon.interfaces.gradients module
      • ExtractB0s
      • GradientSelect
      • RemoveDuplicates
      • concatenate_bvals()
      • concatenate_bvecs()
      • subset_dwi()
    • qsirecon.interfaces.images module
      • Image tools interfaces
      • ConformDwi
      • ValidateImage
      • bvec_to_rasb()
      • to_lps()
    • qsirecon.interfaces.ingress module
      • Interfaces for handling BIDS-like neuroimaging structures
      • QSIPrepDWIIngress
    • qsirecon.interfaces.interchange module
      • ReconAnatomicalData
      • ReconWorkflowInputs
    • qsirecon.interfaces.mrtrix module
      • Image tools interfaces
      • BuildConnectome
      • CompressConnectome2Tck
      • Connectome2Tck
      • Dwi2Response
      • EstimateFOD
      • GenerateMasked5tt
      • GlobalTractography
      • ITKTransformConvert
      • MRTrixAtlasGraph
      • MRTrixGradientTable
      • MRTrixIngress
      • MTNormalize
      • SIFT2
      • SS3TBase
      • SS3TDwi2Response
      • SS3TEstimateFOD
      • TckGen
      • TransformHeader
      • response_function_to_bids()
    • qsirecon.interfaces.pyafq module
      • Interface for running a PyAFQ workflow
      • PyAFQRecon
    • qsirecon.interfaces.qc module
      • createB0_ColorFA_Mask_Sprites()
      • createSprite4D()
      • create_sprite_from_tiles()
      • embed_tiles_in_json_sprite()
      • get_middle_slice_tiles()
      • load_and_reorient()
      • make_a_square()
      • mplfig()
      • mplfigcontour()
      • nearest_square()
      • reorient_array()
      • square_and_normalize_slice()
    • qsirecon.interfaces.recon_scalars module
      • Classes that collect scalar images and metadata from Recon Workflows
      • AMICOReconScalars
        • AMICOReconScalars.scalar_metadata
      • BrainSuite3dSHOREReconScalars
        • BrainSuite3dSHOREReconScalars.scalar_metadata
      • DIPYDKIReconScalars
        • DIPYDKIReconScalars.scalar_metadata
      • DIPYMAPMRIReconScalars
        • DIPYMAPMRIReconScalars.scalar_metadata
      • DSIStudioReconScalars
        • DSIStudioReconScalars.scalar_metadata
      • DisorganizeScalarData
      • OrganizeScalarData
      • ParcellateScalars
      • ParcellationTableSplitterDataSink
      • ReconScalars
        • ReconScalars.scalar_metadata
      • ReconScalarsTableSplitterDataSink
      • TORTOISEReconScalars
        • TORTOISEReconScalars.scalar_metadata
    • qsirecon.interfaces.reports module
      • Interfaces to generate reportlets
      • AboutSummary
      • CLIReconPeaksReport
      • ConnectivityReport
      • InteractiveReport
      • ScalarReport
      • SubjectSummary
      • SummaryInterface
      • plot_scalar_map()
    • qsirecon.interfaces.scalar_mapping module
      • BundleMapper
      • ScalarMapper
      • TemplateMapper
      • calculate_mask_stats()
    • qsirecon.interfaces.tortoise module
      • Wrappers for the TORTOISE programs
      • ComputeADMap
      • ComputeFAMap
      • ComputeLIMap
      • ComputeMAPMRI_NG
      • ComputeMAPMRI_PA
      • ComputeMAPMRI_RTOP
      • ComputeMDMap
      • ComputeRDMap
      • EstimateMAPMRI
      • EstimateTensor
      • TORTOISECommandLine
        • TORTOISECommandLine.run()
      • TORTOISEConvert
      • TORTOISEReconCommandLine
      • make_bmat_file()
    • qsirecon.interfaces.utils module
      • Miscellaneous utilities
      • ConformAtlas
      • ExtractAtlasFiles
      • RecombineAtlasConfigs
      • SplitAtlasConfigs
      • TestReportPlot
      • WarpConnectivityAtlases
      • WriteSidecar
      • label_convert()