pyAFQ

Automated Fiber Quantification ... in Python.

For details, see Documentation

For further analysis of results, see AFQ-Insight

Citing pyAFQ

If you use pyAFQ in a scientific publication, please cite our papers:

Kruper J, Richie-Halford A, Qiao J, Gilmore A, Chang K, Grotheer M, et al. (2025) A software ecosystem for brain tractometry processing, analysis, and insight. PLoS Comput Biol 21(8): e1013323. https://doi.org/10.1371/journal.pcbi.1013323

Kruper, J., Yeatman, J. D., Richie-Halford, A., Bloom, D., Grotheer, M., Caffarra, S., Kiar, G., Karipidis, I. I., Roy, E., Chandio, B. Q., Garyfallidis, E., & Rokem, A. Evaluating the Reliability of Human Brain White Matter Tractometry. DOI:10.52294/e6198273-b8e3-4b63-babb-6e6b0da10669

@article{kruper2025software,
  title={A software ecosystem for brain tractometry processing, analysis, and insight},
  author={Kruper, John and Richie-Halford, Adam and Qiao, Joanna and Gilmore, Asa and Chang, Kelly and Grotheer, Mareike and Roy, Ethan and Caffarra, Sendy and Gomez, Teresa and Chou, Sam and others},
  journal={PLoS computational biology},
  volume={21},
  number={8},
  pages={e1013323},
  year={2025},
  publisher={Public Library of Science San Francisco, CA USA},
  doi=10.1371/journal.pcbi.1013323
}

@article {Kruper2021-xb,
  title     = "Evaluating the reliability of human brain white matter
               tractometry",
  author    = "Kruper, John and Yeatman, Jason D and Richie-Halford, Adam and
               Bloom, David and Grotheer, Mareike and Caffarra, Sendy and Kiar,
               Gregory and Karipidis, Iliana I and Roy, Ethan and Chandio,
               Bramsh Q and Garyfallidis, Eleftherios and Rokem, Ariel",
  journal   = "Apert Neuro",
  publisher = "Organization for Human Brain Mapping",
  volume    =  1,
  number    =  1,
  month     =  nov,
  year      =  2021,
  doi       =  10.52294/e6198273-b8e3-4b63-babb-6e6b0da10669,
}