pyAFQ is an open-source software tool for tractometry of brain white matter in diffusion MRI measurements. It implements a complete and automated data processing pipeline for tractometry, from preprocessed dMRi data to white matter tract identification, as well as quantification of tissue properties along the length of the major long-range brain white matter connections.
The new release includes major advances relative to versions in the 2.X series of the software, including:
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PyAFQ 3.0 now uses T1w images for registration, tissue segmentation, and brain segmentation. When segmentations are not provided, it uses the synthseg software/model (https://pubmed.ncbi.nlm.nih.gov/36857946/).
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Asymmetric ODFs and seeding in the white-matter/gray-matter interface is used by default to better handle the superficial white matter, based on previous work by Poirier and Descoteaux (https://pubmed.ncbi.nlm.nih.gov/38244878/)
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Significant performance improvements include numba-accelerated probalistic tracking, which is used by default and options to use cuda, metal, and webgpu accelerated tracking, based on https://github.com/dipy/GPUStreamlines. Whole-brain tractography in under 1 minute!
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New and improved tract definitions, including sub-bundles of the vertical occipital fasiculus.
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Major documentation overhaul, with many new examples and better organization.
pyAFQ heavily relies on methods implemented in DIPY (https://dipy.org). To learn more about the software and the ecosystem of tools within which it is embedded, please visit https://tractometry.org and read our paper published last year in PLoS Computational Biology; https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1013323.
Demonstrating the range of applications of these tools, recent publications from our group that use pyAFQ include:
- Velioglu et al. Microstructural Alterations of the Cerebellum-Ventral Tegmental Area Pathways in First-Episode Psychosis, Biological Psychiatry: Cognitive Neuroscience and Neuroimaging: in press. https://www.sciencedirect.com/science/article/pii/S2451902226000947
- Luo et al, Two Axes of White Matter Development, Nature Communications 17:1957 Two axes of white matter development | Nature Communications
- Zhou et al. Free water elimination tractometry reveals local and remote white matter alterations in diffuse gliomas. Journal of Neurooncology 176:115 https://link.springer.com/article/10.1007/s11060-025-05370-w
- Chiu et al. Neonatal brain-age models in full-and preterm infants. Preprint. Neonatal brain-age models in full- and preterm infants - PMC
- Zika et al. Cortical and white matter myelination proceed in concert during early infancy. Preprint. https://www.biorxiv.org/content/10.1101/2025.07.07.663449v2
- Roy et al. Development of the arcuate fasciculus is linked to learning gains in reading. Imaging Neuroscience: 3 imag_a_00542. https://doi.org/10.1162/imag_a_00542