How To

This section of the documentation provides guides on various aspects of the software.

• How to install pyAFQ
  • How to install the release version
  • How to install the development version
  • How to install using Docker
  • How to build an Apptainer (Singularity) image
• How to get help using pyAFQ
• How to cite our work
• Organizing your data
  • Example data
  • Preprocessing
• Re-running pyAFQ
  • Method Parameters
  • Examples
• How to add custom tissue properties from another pipeline
• Tractography from other pipelines
• Matlab AFQ to Python AFQ conversion
• The pyAFQ docker image
• The pyAFQ singularity image
• The pyAFQ Image API
• Tractography Parameters
  • Example Usage
  • Tractography Parameter Reference
• Segmentation Parameters
  • Example Usage
  • Segmentation Parameter Reference
• Cleaning Parameters
  • Example Usage
  • Cleaning Parameter Reference
• How to examples
  • How to add new bundles into pyAFQ (Acoustic Radiations Example)
  • Creating tract density maps of callosal bundles
  • 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
  • How to use TRX in pyAFQ
  • 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