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This is the development documentation of brainprep (2.1.0.dev) Switch to stable version (0.0.2)

brainprep 2.1.0.dev documentation
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brainprep 2.1.0.dev documentation
  • Quickstart
  • Examples
    • Tools
      • HTML reporting
      • RST reporting
    • Basic tutorials
      • Interpretability of the image quality metrics
    • Workflows
      • Defacing
      • Quality Assurance
      • Quasi-RAW
      • SBM
      • Sulci Reconstruction
      • VBM
      • fMRI
  • User guide
    • 1. Data Organization Ontology
    • 2. Wrappers for Interface Construction
    • 3. Command Line Interface
    • 4. Quality Assurance Workflow
    • 5. Defacing Workflow
    • 6. QuasiRAW Workflow
    • 7. Voxel Based Morphometry Workflow
    • 8. Surface-Based Morphometry Workflow
    • 9. Sulci Reconstruction and Identification
    • 10. fMRI Pre-Processing Workflow
    • 11. Reporting Workflow
    • 12. Glossary
    • 13. Software Used
  • API References
    • brainprep.cli: Command-line interface (CLI) utilities for BrainPrep workflows.
      • brainprep.cli.main
      • brainprep.cli.make_wrapped
    • brainprep.config: Configuration used by BrainPrep.
      • brainprep.config.Config
    • brainprep.datasets.ibc: Fetcher to download IBC dataset from OpenNeuro.
      • brainprep.datasets.ibc.IBCDataset
    • brainprep.datasets.openms: Fetcher to download the OpenMS dataset from GitHub.
      • brainprep.datasets.openms.OpenMSDataset
    • brainprep.datasets: Module that implements dataset fetchers.
      • brainprep.datasets.IBCDataset
      • brainprep.datasets.OpenMSDataset
      • brainprep.datasets.git_download
      • brainprep.datasets.openneuro_download
    • brainprep.datasets.utils: Dataset creation tools.
      • brainprep.datasets.utils.git_download
      • brainprep.datasets.utils.openneuro_download
    • brainprep.decorators: Defines a hook-driven decorator step with common hooks.
      • brainprep.decorators.BidsHook
      • brainprep.decorators.CoerceparamsHook
      • brainprep.decorators.CommandLineWrapperHook
      • brainprep.decorators.Hook
      • brainprep.decorators.LogRuntimeHook
      • brainprep.decorators.OutputdirHook
      • brainprep.decorators.PythonWrapperHook
      • brainprep.decorators.SaveRuntimeHook
      • brainprep.decorators.SignatureHook
    • brainprep.interfaces.amico: Amico functions.
      • brainprep.interfaces.amico.noddi_fit
    • brainprep.interfaces.ants: ANTs functions.
      • brainprep.interfaces.ants.biasfield
    • brainprep.interfaces.cat12: CAT12 functions.
      • brainprep.interfaces.cat12.cat12vbm_morphometry
      • brainprep.interfaces.cat12.cat12vbm_wf
      • brainprep.interfaces.cat12.write_catbatch
    • brainprep.interfaces.fmriprep: fMRIprep functions.
      • brainprep.interfaces.fmriprep.fmriprep_wf
      • brainprep.interfaces.fmriprep.func_vol_connectivity
    • brainprep.interfaces.freesurfer: FreeSurfer functions.
      • brainprep.interfaces.freesurfer.aparcstats2table
      • brainprep.interfaces.freesurfer.asegstats2table
      • brainprep.interfaces.freesurfer.brainmask
      • brainprep.interfaces.freesurfer.freesurfer_command_status
      • brainprep.interfaces.freesurfer.freesurfer_features_summary
      • brainprep.interfaces.freesurfer.freesurfer_tissues
      • brainprep.interfaces.freesurfer.fsaveragesym_projection
      • brainprep.interfaces.freesurfer.fsaveragesym_surfreg
      • brainprep.interfaces.freesurfer.localgi
      • brainprep.interfaces.freesurfer.mgz_to_nii
      • brainprep.interfaces.freesurfer.mri_convert
      • brainprep.interfaces.freesurfer.mris_apply_reg
      • brainprep.interfaces.freesurfer.nextbrain
      • brainprep.interfaces.freesurfer.reconall
      • brainprep.interfaces.freesurfer.reconall_longitudinal
      • brainprep.interfaces.freesurfer.surfreg
      • brainprep.interfaces.freesurfer.xhemireg
    • brainprep.interfaces.fsl: FSL functions.
      • brainprep.interfaces.fsl.affine
      • brainprep.interfaces.fsl.applyaffine
      • brainprep.interfaces.fsl.applymask
      • brainprep.interfaces.fsl.deface
      • brainprep.interfaces.fsl.dti_fit
      • brainprep.interfaces.fsl.reorient
      • brainprep.interfaces.fsl.scale
    • brainprep.interfaces.geolab: GeoLab functions.
      • brainprep.interfaces.geolab.geolab_parcellation
    • brainprep.interfaces.morphologist: Morphologist functions.
      • brainprep.interfaces.morphologist._get_single_match
      • brainprep.interfaces.morphologist.morphologist_cmd
      • brainprep.interfaces.morphologist.morphologist_morphometry
      • brainprep.interfaces.morphologist.morphologist_move
      • brainprep.interfaces.morphologist.morphologist_wf
    • brainprep.interfaces.mriqc: MRIQC functions.
      • brainprep.interfaces.mriqc.group_level_qa
      • brainprep.interfaces.mriqc.subject_level_qa
    • brainprep.interfaces.mrtrix3: MrTrix3 functions.
      • brainprep.interfaces.mrtrix3.dwi_preproc
    • brainprep.interfaces.plotting: Plotting functions.
      • brainprep.interfaces.plotting.plot_brainparc
      • brainprep.interfaces.plotting.plot_defacing_mosaic
      • brainprep.interfaces.plotting.plot_histogram
      • brainprep.interfaces.plotting.plot_network
      • brainprep.interfaces.plotting.plot_pca
    • brainprep.interfaces.qualcheck: Quality check functions.
      • brainprep.interfaces.qualcheck.euler_numbers
      • brainprep.interfaces.qualcheck.fmriprep_metrics
      • brainprep.interfaces.qualcheck.incremental_pca
      • brainprep.interfaces.qualcheck.mask_overlap
      • brainprep.interfaces.qualcheck.maskdiff
      • brainprep.interfaces.qualcheck.mean_correlation
      • brainprep.interfaces.qualcheck.mriqc_metrics
      • brainprep.interfaces.qualcheck.network_entropy
      • brainprep.interfaces.qualcheck.sulcirec_metrics
      • brainprep.interfaces.qualcheck.vbm_metrics
    • brainprep.interfaces: Module that implements interfaces.
      • brainprep.interfaces.affine
      • brainprep.interfaces.anonfile
      • brainprep.interfaces.aparcstats2table
      • brainprep.interfaces.applyaffine
      • brainprep.interfaces.applymask
      • brainprep.interfaces.asegstats2table
      • brainprep.interfaces.biasfield
      • brainprep.interfaces.brainmask
      • brainprep.interfaces.cat12vbm_morphometry
      • brainprep.interfaces.cat12vbm_wf
      • brainprep.interfaces.copyfiles
      • brainprep.interfaces.deface
      • brainprep.interfaces.dti_fit
      • brainprep.interfaces.dwi_preproc
      • brainprep.interfaces.euler_numbers
      • brainprep.interfaces.fmriprep_metrics
      • brainprep.interfaces.fmriprep_wf
      • brainprep.interfaces.freesurfer_command_status
      • brainprep.interfaces.freesurfer_features_summary
      • brainprep.interfaces.freesurfer_tissues
      • brainprep.interfaces.fsaveragesym_projection
      • brainprep.interfaces.fsaveragesym_surfreg
      • brainprep.interfaces.func_vol_connectivity
      • brainprep.interfaces.geolab_parcellation
      • brainprep.interfaces.group_level_qa
      • brainprep.interfaces.incremental_pca
      • brainprep.interfaces.localgi
      • brainprep.interfaces.mask_overlap
      • brainprep.interfaces.maskdiff
      • brainprep.interfaces.mean_correlation
      • brainprep.interfaces.mgz_to_nii
      • brainprep.interfaces.morphologist_wf
      • brainprep.interfaces.movedir
      • brainprep.interfaces.mri_convert
      • brainprep.interfaces.mriqc_metrics
      • brainprep.interfaces.mris_apply_reg
      • brainprep.interfaces.network_entropy
      • brainprep.interfaces.nextbrain
      • brainprep.interfaces.noddi_fit
      • brainprep.interfaces.plot_brainparc
      • brainprep.interfaces.plot_defacing_mosaic
      • brainprep.interfaces.plot_histogram
      • brainprep.interfaces.plot_network
      • brainprep.interfaces.plot_pca
      • brainprep.interfaces.reconall
      • brainprep.interfaces.reconall_longitudinal
      • brainprep.interfaces.reorient
      • brainprep.interfaces.scale
      • brainprep.interfaces.subject_level_qa
      • brainprep.interfaces.sulcirec_metrics
      • brainprep.interfaces.surfreg
      • brainprep.interfaces.tractseg_parcellation
      • brainprep.interfaces.ungzfile
      • brainprep.interfaces.vbm_metrics
      • brainprep.interfaces.write_catbatch
      • brainprep.interfaces.write_uuid_mapping
      • brainprep.interfaces.xhemireg
    • brainprep.interfaces.tractseg: TractSeg functions.
      • brainprep.interfaces.tractseg.tractseg_parcellation
    • brainprep.interfaces.utils: Utils functions.
      • brainprep.interfaces.utils.anonfile
      • brainprep.interfaces.utils.copyfiles
      • brainprep.interfaces.utils.movedir
      • brainprep.interfaces.utils.ungzfile
      • brainprep.interfaces.utils.write_uuid_mapping
    • brainprep.reporting.html_reporting: Module that implements a HTML reporting tool.
      • brainprep.reporting.html_reporting.HTMLReport
      • brainprep.reporting.html_reporting.generate_qc_report
    • brainprep.reporting: Module that implements reporting tools.
      • brainprep.reporting.RSTReport
      • brainprep.reporting.generate_qc_report
      • brainprep.reporting.trace_module_calls
    • brainprep.reporting.rst_reporting: Module that implements a RST reporting tool.
      • brainprep.reporting.rst_reporting.RSTReport
      • brainprep.reporting.rst_reporting.SingletonReport
      • brainprep.reporting.rst_reporting.trace_module_calls
    • brainprep.reporting.utils: Reporting tools.
      • brainprep.reporting.utils.dataframe_to_html
      • brainprep.reporting.utils.inject_with_jinja
      • brainprep.reporting.utils.png_image_to_base64
    • brainprep.utils.bunch: An extension of dictionaries by enabling values to be accessed by a key or by
      • brainprep.utils.bunch.Bunch
    • brainprep.utils.color: Utility methods to print the results in a terminal using term colors.
      • brainprep.utils.color.print_call
      • brainprep.utils.color.print_category_color
      • brainprep.utils.color.print_color
      • brainprep.utils.color.print_command
      • brainprep.utils.color.print_deprecated
      • brainprep.utils.color.print_error
      • brainprep.utils.color.print_info
      • brainprep.utils.color.print_result
      • brainprep.utils.color.print_stdout
      • brainprep.utils.color.print_subtitle
      • brainprep.utils.color.print_title
      • brainprep.utils.color.print_warn
    • brainprep.utils: Module that implements tools.
      • brainprep.utils.Bunch
      • brainprep.utils.coerce_to_list
      • brainprep.utils.coerce_to_path
      • brainprep.utils.find_first_occurrence
      • brainprep.utils.find_stack_level
      • brainprep.utils.make_run_id
      • brainprep.utils.parse_bids_keys
      • brainprep.utils.print_call
      • brainprep.utils.print_command
      • brainprep.utils.print_deprecated
      • brainprep.utils.print_error
      • brainprep.utils.print_info
      • brainprep.utils.print_result
      • brainprep.utils.print_stdout
      • brainprep.utils.print_subtitle
      • brainprep.utils.print_title
      • brainprep.utils.print_warn
      • brainprep.utils.sidecar_from_file
    • brainprep.utils.utils: Module that contains some utility functions.
      • brainprep.utils.utils.bvecbval_from_file
      • brainprep.utils.utils.check_run_fn
      • brainprep.utils.utils.coerce_to_list
      • brainprep.utils.utils.coerce_to_path
      • brainprep.utils.utils.find_first_occurrence
      • brainprep.utils.utils.find_stack_level
      • brainprep.utils.utils.make_run_id
      • brainprep.utils.utils.parse_bids_keys
      • brainprep.utils.utils.sidecar_from_file
    • brainprep.workflow.defacing: Brain image defacing workflow.
      • brainprep.workflow.defacing.brainprep_defacing
      • brainprep.workflow.defacing.brainprep_group_defacing
    • brainprep.workflow.dmriprep: Diffusion MRI pre-processing workflow.
      • brainprep.workflow.dmriprep.brainprep_dmriprep
    • brainprep.workflow.fmriprep: Functional MRI pre-processing workflow.
      • brainprep.workflow.fmriprep.brainprep_fmriprep
      • brainprep.workflow.fmriprep.brainprep_group_fmriprep
    • brainprep.workflow.quality_assurance: Quality assurance workflow.
      • brainprep.workflow.quality_assurance.brainprep_group_quality_assurance
      • brainprep.workflow.quality_assurance.brainprep_quality_assurance
    • brainprep.workflow.quasiraw: Quasi-RAW workflow.
      • brainprep.workflow.quasiraw.brainprep_group_quasiraw
      • brainprep.workflow.quasiraw.brainprep_quasiraw
    • brainprep.workflow: Available workflows.
      • brainprep.workflow.brainprep_defacing
      • brainprep.workflow.brainprep_fmriprep
      • brainprep.workflow.brainprep_group_defacing
      • brainprep.workflow.brainprep_group_fmriprep
      • brainprep.workflow.brainprep_group_quality_assurance
      • brainprep.workflow.brainprep_group_quasiraw
      • brainprep.workflow.brainprep_group_sbm
      • brainprep.workflow.brainprep_group_sulcirec
      • brainprep.workflow.brainprep_group_vbm
      • brainprep.workflow.brainprep_longitudinal_sbm
      • brainprep.workflow.brainprep_longitudinal_vbm
      • brainprep.workflow.brainprep_quality_assurance
      • brainprep.workflow.brainprep_quasiraw
      • brainprep.workflow.brainprep_sbm
      • brainprep.workflow.brainprep_sulcirec
      • brainprep.workflow.brainprep_vbm
    • brainprep.workflow.sbm: Surface-based morphometry (SBM) workflow.
      • brainprep.workflow.sbm.brainprep_group_sbm
      • brainprep.workflow.sbm.brainprep_longitudinal_sbm
      • brainprep.workflow.sbm.brainprep_sbm
    • brainprep.workflow.sulcirec: Functional MRI pre-processing workflow.
      • brainprep.workflow.sulcirec.brainprep_group_sulcirec
      • brainprep.workflow.sulcirec.brainprep_sulcirec
    • brainprep.workflow.vbm: Voxel-based morphometry (VBM) workflow.
      • brainprep.workflow.vbm.brainprep_group_vbm
      • brainprep.workflow.vbm.brainprep_longitudinal_vbm
      • brainprep.workflow.vbm.brainprep_vbm
    • brainprep.wrappers: Functions for running shell commands.
      • brainprep.wrappers.check_outputs
      • brainprep.wrappers.is_command_installed
      • brainprep.wrappers.is_list_list_str
      • brainprep.wrappers.is_list_str
      • brainprep.wrappers.run_command
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brainprep.workflow.defacing: Brain image defacing workflow.¶

Brain image defacing workflow.

Functions¶

brainprep_defacing(anatomical_file, output_dir)

Defacing pre-processing workflow for anatomical images.

brainprep_group_defacing(modality, output_dir)

Group-level defacing pre-processing.
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  • brainprep.workflow.defacing: Brain image defacing workflow.
    • Functions