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  • Getting started with pyAFQ
    • Tutorials: getting started with the pyAFQ Python library
      • 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
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    • How to add custom tissue properties from another pipeline
    • Tractography from other pipelines
    • The pyAFQ docker image
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    • 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)
      • 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)
      • Callosal bundles using AFQ API
      • Using RecoBundles for bundle recognition
      • Understanding the different stages of tractometry with videos
      • How to use Free water DTI
      • Running pyAFQ using the GPU for tractography
      • Using Subject Space ROIs from Freesurfer
      • How to segment out only some bundles
  • Explanations
    • AFQ Tractometry Pipeline
    • Bundle Orientation
    • Modeling White Matter
    • Profiling
    • Bundle Recognition
    • Tractography
  • Reference Documentation
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      • AFQ
        • AFQ.api
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        • AFQ.utils
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        • AFQ.registration
    • Defining Custom Bundle Dictionaries
    • Major Fiber Tracts
    • Tissue Properties in pyAFQ
    • The pyAFQ API methods
    • Visualization Backends
    • The pyAFQ Mapping API
    • The pyAFQ configuration file
  • User Guide
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AFQ Tractometry Pipeline#

Click images for explanations!

../_images/tract_modeling2.png ../_images/down_left_arrow.png ../_images/tract_tractography.png ../_images/down_right_arrow.png ../_images/tract_recognition.png ../_images/down_left_arrow.png ../_images/tract_profiling.png ../_images/greencheck.png

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