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

Abstract

We present a new toolbox and 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.

A Pig White Matter Atlas and Common Connectivity Space Provide a Roadmap for the Introduction of a New Animal Model in Translational Neuroscience

“…All tractography protocols except for those of the cross-hemispheric structures use the sagittal midline as an exclusion mask to prevent streamline propagation into the contralateral hemisphere. These tract protocols allow for reproducible tractography of pigs registered to the common PNI50 space and are compatible with the recently released XTRACT package 21 . The repository we present here provides all 27 tractography protocols, the nal tracts used to construct the connectivity blueprint, and the corresponding data-driven ICAs for each tract 18,27 .…”

“…The volumetric and surface template les are included in the data and code release (https://github.com/neurabenn/pig_connectivity_bp_preprint), opening our data-driven and protocolbased tractography methods to be used by other researchers. All protocols were de ned in the PNI50 and form part of an open resource for pig researchers compatible with FSL's Xtract and autoPtx 20,21 .…”

“…Using anatomical and diffusion-weighted imaging (DWI), we then characterize the white matter structural organization in a subgroup of six pigs in an exploratory data-driven analysis ( Figure 1A) 18,19 . Our exploratory analysis overcomes the scarcity of knowledge regarding the pig's white matter architecture and was used to guide the de nition of hand-drawn tractography protocols in the PNI50 space for automated tractography in FSL autoPTX and Xtract 20,21 . We delineated 27 tracts to include in our WM atlas of the pig, including the projection, cross-hemispheric, association, and limbic tracts.…”

Non-Negative Data-Driven Mapping of Structural Connections in the Neonatal Brain

“…Despite the large potential of diffusion imaging for exploring early developmental stages of the brain, current analysis techniques follow the paradigms that have been established for the adult brain. For instance, dMRI tractography protocols for identifying specific white matter bundles typically rely on delineation of regions of interest (ROIs) that provide a priori anatomical knowledge on the route of the tract; and these ROIs can be defined relative to a template for automated delineation de Groot et al, 2013;Warrington et al, 2019).…”

Pandora: 4-D white matter bundle population-based atlases derived from diffusion MRI fiber tractography

“…Six methods for tractography and virtual bundle dissection were employed on all diffusion datasets in native space (Figure 2, Subjectlevel processing). These included (1) TractSeg [50], (2) Recobundles [45], (3) Tracula [33], (4) XTract [51], (5) Automatic Fibertract Quantification (AFQ) [52], and (6) post-processing of AFQ where only the stem of the bundle was retained, which we call AFQ-clipped.…”