Fig. 1

Representative anatomic slice showing segmentation of the cerebral subcortical deep gray matter (DGM) in one patient from 1.5T (left) and 3T (right) MRI scans. This is from a 51 year-old woman with multiple sclerosis and moderate physical disability. The total DGM volume was 28.4 ml at 1.5T and 29.3 ml at 3T. Component DGM structures are shown in different colors. The segmentation maps are overlaid to the original raw 3D T1-weighted images after re-sampling to the axial plane. Segmentation was performed by the fully automated FSL-FIRST pipeline. In the present study, we utilized the FSL-FIRST outputs to assess the volume of the thalamus, caudate, putamen, and globus pallidus (and their sum = total DGM)