Hide navigation sidebar

Hide table of contents sidebar

Skip to content

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

Toggle site navigation sidebar

brainprep 2.1.0.dev documentation

Toggle table of contents sidebar

brainprep 2.1.0.dev documentation

Quickstart
Examples
Toggle navigation of Examples
- Tools
  Toggle navigation of Tools
  - HTML reporting
  - RST reporting
- Basic tutorials
  Toggle navigation of Basic tutorials
  - Interpretability of the image quality metrics
- Workflows
  Toggle navigation of Workflows
  - Defacing
  - Quality Assurance
  - Quasi-RAW
  - SBM
  - Sulci Reconstruction
  - VBM
  - fMRI
User guide
Toggle navigation of User guide
API References
Toggle navigation of API References
- brainprep.cli: Command-line interface (CLI) utilities for BrainPrep workflows.
  Toggle navigation of brainprep.cli: Command-line interface (CLI) utilities for BrainPrep workflows.
  - brainprep.cli.main
  - brainprep.cli.make_wrapped
- brainprep.config: Configuration used by BrainPrep.
  Toggle navigation of brainprep.config: Configuration used by BrainPrep.
  - brainprep.config.Config
- brainprep.datasets.ibc: Fetcher to download IBC dataset from OpenNeuro.
  Toggle navigation of 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.
  Toggle navigation of brainprep.datasets.openms: Fetcher to download the OpenMS dataset from GitHub.
  - brainprep.datasets.openms.OpenMSDataset
- brainprep.datasets: Module that implements dataset fetchers.
  Toggle navigation of brainprep.datasets: Module that implements dataset fetchers.
- brainprep.datasets.utils: Dataset creation tools.
  Toggle navigation of 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.
  Toggle navigation of brainprep.decorators: Defines a hook-driven decorator step with common hooks.
- brainprep.interfaces.amico: Amico functions.
  Toggle navigation of brainprep.interfaces.amico: Amico functions.
  - brainprep.interfaces.amico.noddi_fit
- brainprep.interfaces.ants: ANTs functions.
  Toggle navigation of brainprep.interfaces.ants: ANTs functions.
  - brainprep.interfaces.ants.biasfield
- brainprep.interfaces.cat12: CAT12 functions.
  Toggle navigation of brainprep.interfaces.cat12: CAT12 functions.
- brainprep.interfaces.fmriprep: fMRIprep functions.
  Toggle navigation of brainprep.interfaces.fmriprep: fMRIprep functions.
  - brainprep.interfaces.fmriprep.fmriprep_wf
  - brainprep.interfaces.fmriprep.func_vol_connectivity
- brainprep.interfaces.freesurfer: FreeSurfer functions.
  Toggle navigation of brainprep.interfaces.freesurfer: FreeSurfer functions.
- brainprep.interfaces.fsl: FSL functions.
  Toggle navigation of brainprep.interfaces.fsl: FSL functions.
- brainprep.interfaces.geolab: GeoLab functions.
  Toggle navigation of brainprep.interfaces.geolab: GeoLab functions.
  - brainprep.interfaces.geolab.geolab_parcellation
- brainprep.interfaces.morphologist: Morphologist functions.
  Toggle navigation of brainprep.interfaces.morphologist: Morphologist functions.
- brainprep.interfaces.mriqc: MRIQC functions.
  Toggle navigation of brainprep.interfaces.mriqc: MRIQC functions.
  - brainprep.interfaces.mriqc.group_level_qa
  - brainprep.interfaces.mriqc.subject_level_qa
- brainprep.interfaces.mrtrix3: MrTrix3 functions.
  Toggle navigation of brainprep.interfaces.mrtrix3: MrTrix3 functions.
  - brainprep.interfaces.mrtrix3.dwi_preproc
- brainprep.interfaces.plotting: Plotting functions.
  Toggle navigation of brainprep.interfaces.plotting: Plotting functions.
- brainprep.interfaces.qualcheck: Quality check functions.
  Toggle navigation of brainprep.interfaces.qualcheck: Quality check functions.
- brainprep.interfaces: Module that implements interfaces.
  Toggle navigation of brainprep.interfaces: Module that implements interfaces.
- brainprep.interfaces.tractseg: TractSeg functions.
  Toggle navigation of brainprep.interfaces.tractseg: TractSeg functions.
  - brainprep.interfaces.tractseg.tractseg_parcellation
- brainprep.interfaces.utils: Utils functions.
  Toggle navigation of brainprep.interfaces.utils: Utils functions.
- brainprep.reporting.html_reporting: Module that implements a HTML reporting tool.
  Toggle navigation of 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.
  Toggle navigation of brainprep.reporting: Module that implements reporting tools.
- brainprep.reporting.rst_reporting: Module that implements a RST reporting tool.
  Toggle navigation of brainprep.reporting.rst_reporting: Module that implements a RST reporting tool.
- brainprep.reporting.utils: Reporting tools.
  Toggle navigation of brainprep.reporting.utils: Reporting tools.
- brainprep.utils.bunch: An extension of dictionaries by enabling values to be accessed by a key or by
  Toggle navigation of 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.
  Toggle navigation of brainprep.utils.color: Utility methods to print the results in a terminal using term colors.
- brainprep.utils: Module that implements tools.
  Toggle navigation of brainprep.utils: Module that implements tools.
- brainprep.utils.utils: Module that contains some utility functions.
  Toggle navigation of brainprep.utils.utils: Module that contains some utility functions.
- brainprep.workflow.defacing: Brain image defacing workflow.
  Toggle navigation of 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.
  Toggle navigation of brainprep.workflow.dmriprep: Diffusion MRI pre-processing workflow.
  - brainprep.workflow.dmriprep.brainprep_dmriprep
- brainprep.workflow.fmriprep: Functional MRI pre-processing workflow.
  Toggle navigation of 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.
  Toggle navigation of 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.
  Toggle navigation of brainprep.workflow.quasiraw: Quasi-RAW workflow.
  - brainprep.workflow.quasiraw.brainprep_group_quasiraw
  - brainprep.workflow.quasiraw.brainprep_quasiraw
- brainprep.workflow: Available workflows.
  Toggle navigation of brainprep.workflow: Available workflows.
- brainprep.workflow.sbm: Surface-based morphometry (SBM) workflow.
  Toggle navigation of brainprep.workflow.sbm: Surface-based morphometry (SBM) workflow.
- brainprep.workflow.sulcirec: Functional MRI pre-processing workflow.
  Toggle navigation of 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.
  Toggle navigation of brainprep.workflow.vbm: Voxel-based morphometry (VBM) workflow.
- brainprep.wrappers: Functions for running shell commands.
  Toggle navigation of brainprep.wrappers: Functions for running shell commands.
API Search

Development

Contributing
Continuous integration
Maintenance
Changelog
People
License
Versions

Back to top

View this page

Edit this page

Toggle table of contents sidebar

11. Reporting Workflow¶

…

Made with Sphinx and @pradyunsg's Furo