Source-based morphometry (SBM) was recently used for non-random “patterns” of gray matter (GM) atrophy or white matter (WM) microstructural damage.

To assess whether and to what extent such patterns may be inter-related in MS.

SBM was applied to images of GM concentration and fractional anisotropy (FA) in MS patients (n = 41, median EDSS = 1) and normal controls (NC, n = 28). The same procedure was repeated on an independent and similar data set (39 MS patients and 13 NC).

We found in MS patterns of GM atrophy and reduced FA (p < 0.05, corrected). Deep GM atrophy was mostly (70%) explained by lesion load in projection tracts and lower FA in posterior corona radiata and thalamic radiation. By contrast, sensorimotor and posterior cortex atrophy was less (50%) dependent from WM damage. All patterns correlated with EDSS (r from −0.33 to −0.56, p < 0.03) while the only cognition-related correlation was between posterior GM atrophy pattern and processing speed (r = 0.45, p = 0.014). Reliability analysis showed similar results.

In relatively early MS, we found a close link between deep GM atrophy pattern and WM damage while sensorimotor and posterior cortex patterns were partially independent from WM damage and perhaps related to primary mechanisms. Patterns were clinically relevant.