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Purpose: Statistical parametric mapping (SPM) and NEUROSTAT (NS) are widely used for intersubject statistical analysis of brain images. We investigated individual anatomical variations after standardization of 18F-fluorodeoxyglucose positron emission tomography (FDG PET) images of normal brain and compared the differences in the standardized images obtained from SPM and NS., Methods: Twenty healthy normal subjects were recruited for FDG PET and magnetic resonance imaging (MRI) studies. Sylvian fissures (SF), cingulate sulci (CingS) and central sulci (CtlS) were marked on the brain surface of each individual's co-registered MR images. Then spatial standardization was performed on each subject's PET images using SPM99 and NS with NS's FDG template image, and each subject's MR images (with the SF, CingS, and CtlS marked in advance) were standardized using the sets of parameters obtained from PET standardization by SPM and NS, respectively. The coordinates of each subject's SF, CingS, and CtlS detected on the MR images standardized by the two methods were measured and compared with those on the template images., Results: The mean individual deviations from the averaged coordinates for the markers on the SF, CingS and CtlS standardized by SPM and by NS were no more than 0.21-1.15 mm. The number of voxels within the brain volume on standardized MR images of all 20 subjects was 88.0% of the total number of brain volume voxels for SPM and 85.3% for NS., Conclusion: This study demonstrates that SPM and NS yield relatively small differences in standardization and that both methods are effective and valid for PET studies in normal subjects.