Aim of this study was to test two available methods (FSL-SIENAx/SIENA and Icometrix-MSmetrix) used for brain atrophy estimation on MR images of multiple sclerosis (MS) patients for a future clinical use. The accuracy and precision of these methods, as well as their main steps, were evaluated on 3D-T1 and 3DT2-FLAIR sequences of a simulated dataset, MRI of MS patients acquired at different scanners, field strengths, and on longitudinal dataset. From the comparison, SIENAx/SIENA showed a worst image registration, brain extraction and higher dependence on image acquisition quality than MSmetrix software. FSL pipelines showed better accuracy for cross-sectional and longitudinal analysis.
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