Evaluating white matter hyperintensities (WMHs) in neuropsychiatric systemic lupus erythematosus (NPSLE) is a challenging task. Multimodal MRI images in combination with unsupervised machine characterization can provide a powerful tool to investigate the spatial WHM distribution of relevant phenotypes. Automatically segmented WMH maps were spatially allocated to a white matter tract atlas. Cluster analysis was applied on this tract-wise lesion-load map to obtain subtypes with a distinct WMH damage profile. This approach on microstructural changes could help to identify specific progression pattern which may improve the accuracy of NPSLE classification.