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

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brainprep 2.1.0.dev documentation

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brainprep 2.1.0.dev documentation

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

Contributing
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Changelog
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`brainprep.interfaces.geolab`: GeoLab functions.¶

GeoLab functions.

Functions¶

geolab_parcellation(tractogram_file, ...)

Superficial white matter (SWM) parcellation.

brainprep.interfaces.geolab.geolab_parcellation

brainprep.interfaces.fsl.scale

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brainprep.interfaces.geolab: GeoLab functions.
- Functions