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Updated: Jan 30, 2026

Automated Segmentation of Cortical Grey Matter from T1-Weighted MRI Images
Published on: January 7, 2019
Automated Segmentation of Cortical Grey Matter from T1-Weighted MRI Images
Eileanoir B Johnson1, Rachael I Scahill2, Sarah J Tabrizi3
1Huntington's Disease Research Centre, UCL Institute of Neurology; eileanoir.johnson@ucl.ac.uk.
Abstract:
Within neuroimaging research, a number of recent studies have discussed the impact of between-study differences in volumetric findings that are thought to result from the use of different segmentation tools to generate brain volumes. Here, processing pipelines for seven automated tools that can be used to segment grey matter within the brain are presented. The protocol provides an initial step for researchers aiming to find the most accurate method for generating grey matter volumes from T1-weighted MRI scans. Steps to undertake detailed visual quality control are also included in the manuscript. This protocol covers a range of potential segmentation tools and encourages users to compare the performance of these tools within a subset of their data before selecting one to apply to a full cohort. Furthermore, the protocol may be further generalized to the segmentation of other brain regions.
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