How to examples

These examples provide details of various advanced and more complex usage of pyAFQ. These are intended to provide a reference and answer questions about the variety of pyAFQ functionality that is available.

• How to add new bundles into pyAFQ (Acoustic Radiations Example)
  • Get dMRI data
  • Define custom BundleDict object
  • Define GroupAFQ object
  • Interactive bundle visualization
  • References
• Creating tract density maps of callosal bundles
  • Get some example data
  • Set segmentation parameters (optional)
  • Initialize a GroupAFQ object:
  • Create tract density maps:
  • Visualizing bundles and tract profiles:
• How to use Free water DTI
  • Get some data
  • Define an AFQ object
  • Compare fwDTI and DTI maps
  • Free-water fraction map
  • Comparing bundle profiles
  • References
• BabyAFQ : tractometry for infant dMRI data
  • Baby dMRI data
  • Initialize a GroupAFQ object:
  • Running the pipeline
  • Viewing the results
  • References
• Delineating cerebellar peduncles
  • References
• Using cloudknot to run pyAFQ on AWS batch:
  • Define the function to use
  • Defining a Knot instance
  • Launching the computation
• AFQ with HCP data
• How to add new bundles into pyAFQ (Optic Radiations Example)
  • Get dMRI data
  • Define custom BundleDict object
  • Define GroupAFQ object
  • Visualize a montage
  • Interactive bundle visualization
  • References
• How to track the Optic Tract and Posterior Optic Nerve in pyAFQ
  • Get dMRI data
  • Define Optic Tract and Optic Nerve BundleDict object
  • Tractography and segmentation parameters
  • Define PVE images for segmentation
  • Define GroupAFQ object
  • References
• Understanding the different stages of tractometry with videos
  • Imports
  • Get data from HBN POD2
  • Visualize the processed dMRI data
  • Visualizing whole-brain tractography
  • Visualize the streamlines
  • Whole brain with waypoints
  • Define the bundles
  • Visualize the arcuate bundle
  • Clean bundle
  • Show the values of tissue properties along the bundle
  • Core of the bundle and tract profile
  • Core of all bundles and their tract profiles
  • Tract profiles as a table
• How to use TRX in pyAFQ
• Running pyAFQ using the GPU for tractography
  • Set tractography parameters
  • Running with the GPU
• Running pyAFQ 2.x defaults in pyAFQ 3.x
  • Tractography parameters in the old way
  • Partial Volume Estimate in the old way
  • VOF / pAF / CST in the old way
  • Callosal bundles in the old way
  • Run GroupAFQ with these parameters
• Using RecoBundles for bundle recognition
  • Defining the segmentation params
  • References
• Using Subject Space ROIs from Freesurfer
  • Get some example data
  • Generate left thalamus ROI from freesurfer segmentation file
  • Set tractography parameters (optional)
  • Define custom BundleDict object
  • Initialize a GroupAFQ object:
• How to segment out only some bundles