AUTHOR=Freeman Holly J. , Atalay Alexander S. , Li Jian , Sobczak Evie , Gilmore Natalie , Snider Samuel B. , Healy Brian C. , Carrington Holly , Selmanovic Enna , Pruyser Ariel , Bura Lisa , Sheppard David P. , Hunt David , Seifert Alan C. , Bodien Yelena G. , Hoffman Jeanne M. , Mac Donald Christine L. , Dams-O'Connor Kristen , Edlow Brian L. 

TITLE=Unsupervised semi-automated MRI segmentation detects cortical lesion expansion in chronic traumatic brain injury

JOURNAL=Frontiers in Neurology

VOLUME=Volume 16 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/neurology/articles/10.3389/fneur.2025.1640514

DOI=10.3389/fneur.2025.1640514

ISSN=1664-2295

ABSTRACT=Traumatic brain injury (TBI) is a risk factor for neurodegeneration and cognitive decline, yet the underlying pathophysiologic mechanisms are incompletely understood. This gap in knowledge is in part related to a lack of reliable and efficient methods for measuring cortical lesions in neuroimaging studies. The objective of this study was to develop a semi-automated lesion detection tool and apply it to an investigation of longitudinal changes in brain structure among individuals with chronic TBI. We identified 24 individuals with chronic moderate-to-severe TBI enrolled in the Late Effects of TBI (LETBI) study who had cortical lesions detected by T1-weighted MRI and underwent two MRI scans at least 2 years apart. Initial MRI scans were performed more than 1 year post-injury, and follow-up scans were performed a median of 3.1 (IQR = 1.7) years later. We leveraged FreeSurfer parcellations of T1-weighted MRI volumes and a recently developed super-resolution technique, SynthSR, to automate the identification of cortical lesions in this longitudinal dataset. Trained raters received the data in a randomized order and manually edited the automated lesion segmentations, yielding a final semi-automated lesion mask for each scan at each time point. Inter-rater variability was assessed in an independent cohort of 10 additional LETBI subjects with cortical lesions. The semi-automated lesion segmentations showed a high level of accuracy compared to “ground truth” lesion segmentations performed via manual segmentation by a separate blinded rater. In a longitudinal analysis of the semi-automated segmentations, lesion volume increased between the two time points with a median volume change of 4.91 (IQR = 12.95) mL (p < 0.0001). Lesion volume significantly expanded in 37 of 61 measured lesions (60.7%), as defined by a longitudinal volume increase that exceeded inter-rater variability. Longitudinal analyses showed similar changes in lesion volume using the ground-truth lesion segmentations. Inter-scan duration was not associated with the magnitude of lesion growth. While the proposed tool requires further refinement and validation, we show that reliable and efficient semi-automated lesion segmentation is feasible in studies of chronic TBI, creating opportunities to elucidate mechanisms of post-traumatic neurodegeneration.