Purpose: To investigate the gray matter (GM) atrophy in Progressive supranuclear palsy (PSP) using T1-weighted Fluid-Attenuated Inversion Recovery (FLAIR) images based on voxel based morphometry (VBM) method. Materials and methods: In this study, we firstly modified the conventional VBM method to make it can process the T1-weighted HAIR brain images. Then, we used this method on the 24 PSP patients and 23 healthy age- and sex-matched control subjects to find the local gray matter density changes of PSP patients. Results: Compared with healthy controls, GM reductions of PSP patients mainly located in the thalamus, basal ganglia, pons, midbrain, insular cortex, frontal cortex, temporal lobe, cerebellum, cingulate cortex and hippocampus. Conclusion: We used the modified VBM technique into T1 FLAIR data to study the brain gray matter atrophy in PSP, and found some new atrophy areas, including pallidum, middle and posterior cingulum, lingual, fusiform gyrus and the post part of inferior temporal gyrus. These areas have not been described in the former VBM studies, but they revealed abnormity in the pathologic and other studies on PSP. Our results might be expected to provide significant underlining neurology information and diagnostic value for PSP. (C) 2015 Elsevier B.V. All tights reserved.