XTRACT - Standardised protocols for automated tractography in the human and macaque brain

Neuroimage. 2020 Aug 15;217:116923. doi: 10.1016/j.neuroimage.2020.116923. Epub 2020 May 11.


We present a new software package with a library of standardised tractography protocols devised for the robust automated extraction of white matter tracts both in the human and the macaque brain. Using in vivo data from the Human Connectome Project (HCP) and the UK Biobank and ex vivo data for the macaque brain datasets, we obtain white matter atlases, as well as atlases for tract endpoints on the white-grey matter boundary, for both species. We illustrate that our protocols are robust against data quality, generalisable across two species and reflect the known anatomy. We further demonstrate that they capture inter-subject variability by preserving tract lateralisation in humans and tract similarities stemming from twinship in the HCP cohort. Our results demonstrate that the presented toolbox will be useful for generating imaging-derived features in large cohorts, and in facilitating comparative neuroanatomy studies. The software, tractography protocols, and atlases are publicly released through FSL, allowing users to define their own tractography protocols in a standardised manner, further contributing to open science.

Keywords: Comparative anatomy; Diffusion MRI; Human connectome project; Non-human primate; White matter atlas; White matter tracts.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Atlases as Topic
  • Automation
  • Brain / anatomy & histology
  • Brain / diagnostic imaging*
  • Connectome
  • Databases, Factual
  • Diffusion Magnetic Resonance Imaging
  • Diffusion Tensor Imaging / methods
  • Diffusion Tensor Imaging / standards*
  • Gray Matter / diagnostic imaging
  • Humans
  • Image Processing, Computer-Assisted / methods
  • Image Processing, Computer-Assisted / standards*
  • Macaca mulatta
  • Neural Pathways / diagnostic imaging
  • Software
  • White Matter / anatomy & histology
  • White Matter / diagnostic imaging