Cross-sectional robustness of 6 freely available software packages for brain volume measurements in multiple sclerosis

Automated segmentation of brain MR images has paved the way for large cohort atrophy studies in multiple sclerosis (MS). A variety of automated software packages is available. Here we aimed to quantify brain volume differences measured by six freely available software packages on data from 21 MS patients all scanned thrice on three different MR scanners. While intra-class correlation coefficients were high, systematic differences between scanners were found for every software. This suggests that direct comparison of volumes acquired with different scanners is not possible and standardization is needed.