Objective To explore the clinical values of voxel-based morphometry(VBM)analysis in magnetic resonance imaging(MRI)for detecting secondary damage to the distant thalamus and substantia nigra in patients with cerebral infarction.Methods A total of nineteen patients with first-time unilateral middle cerebral artery(MCA)ischemic stroke were prospectively recruited.Three-dimensional whole-brain MRI scans were performed at 1 week,1 month,and 3 months after onset.VBM analysis was used to analyze changes in the thalamus and substantia nigra volumes.Results VBM analysis revealed that compared to ipsilateral thalamic volume at 1 week after onset,ipsilateral thalamic volume was significantly reduced at 1 month or 3 months after onset(reduced by 637 mm3 and 1488 mm3,respectively;P<0.01),with the atrophy primarily located in the dorsomedial nucleus of the thalamus.Similarly,compared to ipsilateral substantia nigra volume at 1 week after onset,the ipsilateral substantia nigra volume was significantly reduced at 1 month or 3 months after onset(reduced by 64 mm3 and 76 mm3,respectively;P<0.05).Conclusions VBM technology can be used to evaluate the ipsilateral thalamic and substantia nigra volume reduction in patients with cerebral infarction in the MCA supply area at 1-3 months after stroke,and to detect secondary damage.