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  • Tutorials: Getting started
  • How to examples
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  • Bibliography
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  • User Guide
  • Tutorials: Getting started
  • How to examples
  • Developing pyAFQ
  • Bibliography
  • API Reference
  • GitHub
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Section Navigation

  • Getting started with pyAFQ
    • Tutorials: Getting started
      • Getting started with pyAFQ - GroupAFQ
      • Getting started with pyAFQ - ParticipantAFQ
      • Re-running pyAFQ
      • Exporting pyAFQ Results
      • Visualizing AFQ derivatives
      • How pyAFQ uses BIDS
      • Plotting Default Regions of Interest (ROIs) to Understand the Tracts
  • How To
    • How to install pyAFQ
    • How to get help using pyAFQ
    • How to cite our work
    • Organizing your data
    • Re-running pyAFQ
    • How to add custom tissue properties from another pipeline
    • Tractography from other pipelines
    • The pyAFQ docker image
    • The pyAFQ singularity image
    • The pyAFQ Image API
    • Tractography Parameters
    • Segmentation Parameters
    • Cleaning Parameters
    • How to examples
      • How to add new bundles into pyAFQ (Acoustic Radiations Example)
      • How to add new bundles into pyAFQ (SLF 1/2/3 Example)
      • Callosal bundles using AFQ API
      • How to use Free water DTI
      • BabyAFQ : tractometry for infant dMRI data
      • Delineating cerebellar peduncles
      • Using cloudknot to run pyAFQ on AWS batch:
      • AFQ with HCP data
      • How to add new bundles into pyAFQ(Optic Radiations Example)
      • How to track the Optic Tract and Posterior Optic Nerve in pyAFQ
      • Understanding the different stages of tractometry with videos
      • Running pyAFQ using the GPU for tractography
      • Running pyAFQ 2.x defaults in pyAFQ 3.x
      • Using RecoBundles for bundle recognition
      • Using Subject Space ROIs from Freesurfer
      • How to segment out only some bundles
  • Explanations
    • Bundle Orientation
    • Modeling White Matter
    • Profiling
    • Bundle Recognition
    • Tractography
    • What’s new in PyAFQ 3.0
  • Reference Documentation
    • API Reference
      • AFQ
        • AFQ.api
        • AFQ.data
        • AFQ.definitions
        • AFQ.models
        • AFQ.nn
        • AFQ.recognition
        • AFQ.registration
        • AFQ.tasks
        • AFQ.tractography
        • AFQ.utils
        • AFQ.viz
    • Defining Custom Bundle Dictionaries
    • Major Fiber Tracts
    • Tissue Properties in pyAFQ
    • The pyAFQ API methods
    • The pyAFQ API optional arguments
    • Visualization Backends
    • The pyAFQ Mapping API
    • The pyAFQ configuration file
  • User Guide
  • Reference Documentation
  • API Reference

API Reference#

This page contains auto-generated API reference documentation [1].

  • AFQ
    • AFQ.api
      • AFQ.api.bundle_dict
      • AFQ.api.group
      • AFQ.api.participant
      • AFQ.api.utils
    • AFQ.data
      • AFQ.data.fetch
      • AFQ.data.utils
    • AFQ.definitions
      • AFQ.definitions.image
      • AFQ.definitions.mapping
      • AFQ.definitions.utils
    • AFQ.models
      • AFQ.models.QBallTP
      • AFQ.models.asym_filtering
      • AFQ.models.csd
      • AFQ.models.dki
      • AFQ.models.dti
      • AFQ.models.fwdti
      • AFQ.models.msmt
      • AFQ.models.wmgm_interface
    • AFQ.nn
      • AFQ.nn.brainchop
      • AFQ.nn.multiaxial
      • AFQ.nn.synthseg
      • AFQ.nn.utils
    • AFQ.recognition
      • AFQ.recognition.cleaning
      • AFQ.recognition.clustering
      • AFQ.recognition.criteria
      • AFQ.recognition.curvature
      • AFQ.recognition.other_bundles
      • AFQ.recognition.preprocess
      • AFQ.recognition.recognize
      • AFQ.recognition.roi
      • AFQ.recognition.sparse_decisions
      • AFQ.recognition.utils
    • AFQ.registration
    • AFQ.tasks
      • AFQ.tasks.data
      • AFQ.tasks.decorators
      • AFQ.tasks.mapping
      • AFQ.tasks.segmentation
      • AFQ.tasks.structural
      • AFQ.tasks.tissue
      • AFQ.tasks.tractography
      • AFQ.tasks.utils
      • AFQ.tasks.viz
    • AFQ.tractography
      • AFQ.tractography.tractography
      • AFQ.tractography.utils
    • AFQ.utils
      • AFQ.utils.bin
      • AFQ.utils.docs
      • AFQ.utils.docstring_parser
      • AFQ.utils.models
      • AFQ.utils.path
      • AFQ.utils.stats
      • AFQ.utils.streamlines
      • AFQ.utils.volume
    • AFQ.viz
      • AFQ.viz.altair
      • AFQ.viz.fury_backend
      • AFQ.viz.plot
      • AFQ.viz.plotly_backend
      • AFQ.viz.utils
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© Copyright 2018--, The pyAFQ Contributors.

Created using Sphinx 9.1.0.

Please Cite the following papers:
Kruper et al. (2025)
Kruper et al. (2021)