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Updated: Sep 10, 2025

Automated Segmentation of Cortical Grey Matter from T1-Weighted MRI Images
Published on: January 7, 2019
QUANTIFYING WHITE MATTER HYPERINTENSITY AND BRAIN VOLUMES IN HETEROGENEOUS CLINICAL AND LOW-FIELD PORTABLE MRI
Pablo Laso1,2, Stefano Cerri1,3, Annabel Sorby-Adams1
1Massachusetts General Hospital, Harvard Medical School, USA.
Abstract:
Brain atrophy and white matter hyperintensity (WMH) are critical neuroimaging features for ascertaining brain injury in cerebrovascular disease and multiple sclerosis. Automated segmentation and quantification is desirable but existing methods require high-resolution MRI with good signal-to-noise ratio (SNR). This precludes application to clinical and low-field portable MRI (pMRI) scans, thus hampering large-scale tracking of atrophy and WMH progression, especially in underserved areas where pMRI has huge potential. Here we present a method that segments white matter hyperintensity and 36 brain regions from scans of any resolution and contrast (including pMRI) without retraining. We show results on eight public datasets and on a private dataset with paired high- and low-field scans (3T and 64mT), where we attain strong correlation between the WMH (ρ=.85) and hippocampal volumes (ρ=.89) estimated at both fields. Our method is publicly available as part of FreeSurfer, at: http://surfer.nmr.mgh.harvard.edu/fswiki/WMH-SynthSeg.
Insights
This study introduces a new method for segmenting brain atrophy and white matter hyperintensity (WMH) from MRI scans, even low-field portable MRI (pMRI). This advance enables widespread tracking of brain injury progression in diverse clinical settings.
Area of Science:
- Neuroimaging
- Radiology
- Medical Image Analysis
Background:
- Brain atrophy and white matter hyperintensity (WMH) are key indicators of brain injury in cerebrovascular disease and multiple sclerosis.
- Current automated segmentation methods require high-resolution MRI with good signal-to-noise ratio (SNR), limiting their use in clinical and portable MRI (pMRI) settings.
- This limitation hinders large-scale tracking of neurodegenerative disease progression, particularly in underserved regions where pMRI is prevalent.
Purpose of the Study:
- To develop a robust method for segmenting WMH and 36 brain regions applicable to MRI scans of any resolution and contrast.
- To enable accurate quantification of brain atrophy and WMH progression using low-field pMRI data.
- To provide a universally applicable tool for neuroimaging analysis without the need for retraining.
Main Methods:
- A novel segmentation method was developed to process MRI scans regardless of resolution or contrast.
- The method was validated on eight public datasets and a private dataset with paired 3T and 64mT scans.
- The approach integrates seamlessly with existing neuroimaging software, such as FreeSurfer.
Main Results:
- The method successfully segmented white matter hyperintensity and 36 distinct brain regions across various MRI qualities.
- Strong correlations were observed between WMH (ρ=.85) and hippocampal volumes (ρ=.89) estimated from both high-field (3T) and low-field (64mT) scans.
- The technique demonstrated high accuracy and reliability across diverse datasets, including challenging pMRI data.
Conclusions:
- The developed method overcomes the limitations of existing techniques by enabling accurate segmentation of brain atrophy and WMH from low-field pMRI.
- This innovation facilitates large-scale tracking of neurodegenerative disease progression, especially in resource-limited settings.
- The publicly available tool enhances accessibility and applicability of advanced neuroimaging analysis in clinical practice and research.
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