Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Warrington S

PROVIDER: S-EPMC7260058 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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

Warrington Shaun S Bryant Katherine L KL Khrapitchev Alexandr A AA Sallet Jerome J Charquero-Ballester Marina M Douaud Gwenaëlle G Jbabdi Saad S Mars Rogier B RB Sotiropoulos Stamatios N SN

NeuroImage 20200511

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 d ...[more]

PMID: 32407993

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Project description:Introduction: Tractography analysis in group-based studies across large populations has been difficult to implement. We propose Selective Automated Group Integrated Tractography (SAGIT), an automated group tractography software platform that incorporates multiple diffusion magnetic resonance imaging (dMRI) practices which will allow great accessibility to group-wise dMRI. We use a merged tractography approach that permits evaluation of tractography datasets at the group level. We also introduce an image normalized overlap score (NOS) that measures the quality of the group tractography results. We deploy SAGIT to evaluate deterministic and probabilistic constrained spherical deconvolution (CST det , CST prob ) tractography, eXtended Streamline Tractography (XST), and diffusion tensor tractography (DTT) in their ability to delineate different neuroanatomy, as well as validating NOS across these different brain regions. Materials and methods: Magnetic resonance sequences were acquired from 42 healthy adults. Anatomical and group registrations were performed using Automated Normalization Tools. Cortical segmentation was performed using FreeSurfer. Four tractography algorithms were used to delineate six sets of neuroanatomy: fornix, facial/vestibular-cochlear cranial nerve complex, vagus nerve, rubral-cerebellar decussation, optic radiation, and auditory radiation. The tracts were generated both with and without region of interest filters. The generated visual reports were then evaluated by five neuroscientists. Results: At a group level, merged tractography demonstrated that different methods have different fiber distribution characteristics. CST prob is prone to false-positives, and thereby suitable in anatomy with strong priors. CST det and XST are more conservative, but have greater difficulty resolving hemispherical decussation and distant crossing projections. DTT consistently shows the worst reproducibility across the anatomies. Linear regression of rater scores against NOS shows significant (p < 0.05) correlation of the two sets of scores in filtered tractography. However, correlations are not significant (p > 0.05) for unfiltered tractography. Conclusion: The tractography results demonstrated reliable and consistent performance of SAGIT across multiple subjects and techniques. Through SAGIT, we quantifiably demonstrated that different algorithms showed different strengths and weaknesses at a group level. While no single algorithm seems to be suitable for all anatomical tasks, it is useful to consider the use of a mix of algorithms for different anatomical segments. SAGIT appears to be a promising group-wise tractography analysis approach for this purpose.

Project description:Electrocorticography (ECoG), multichannel brain-surface recording and stimulation with probe electrode arrays, has become a potent methodology not only for clinical neurosurgery but also for basic neuroscience using animal models. The highly evolved primate's brain has deep cerebral sulci, and both gyral and intrasulcal cortical regions have been implicated in important functional processes. However, direct experimental access is typically limited to gyral regions, since placing probes into sulci is difficult without damaging the surrounding tissues. Here we describe a novel methodology for intrasulcal ECoG in macaque monkeys. We designed and fabricated ultra-thin flexible probes for macaques with micro-electro-mechanical systems technology. We developed minimally invasive operative protocols to implant the probes by introducing cutting-edge devices for human neurosurgery. To evaluate the feasibility of intrasulcal ECoG, we conducted electrophysiological recording and stimulation experiments. First, we inserted parts of the Parylene-C-based probe into the superior temporal sulcus to compare visually evoked ECoG responses from the ventral bank of the sulcus with those from the surface of the inferior temporal cortex. Analyses of power spectral density and signal-to-noise ratio revealed that the quality of the ECoG signal was comparable inside and outside of the sulcus. Histological examination revealed no obvious physical damage in the implanted areas. Second, we placed a modified silicone ECoG probe into the central sulcus and also on the surface of the precentral gyrus for stimulation. Thresholds for muscle twitching were significantly lower during intrasulcal stimulation compared to gyral stimulation. These results demonstrate the feasibility of intrasulcal ECoG in macaques. The novel methodology proposed here opens up a new frontier in neuroscience research, enabling the direct measurement and manipulation of electrical activity in the whole brain.

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Dataset Information

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

Publications

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

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