The VBM output orientation is determined by SPM. While it's likely that's okay, mistakes could happen, and left-right flipping problems happen more often than we would like (see link to prepress paper below). We have tools in align_epi_anat.py with the "-check_flip" option, but that works well for anatomical and EPI datasets. It's not too useful for statistical or computed results. You may want to change the orientation of the input datasets to VBM by left-right flipping it intentionally with 3dLRflip to flip the voxel values or 3drefit -orient to flip the orientation info in the header. Either way creates an incorrect dataset. If the VBM processing results in the same output, then there's likely a problem. If it results in a mirror image, then that is a good and expected result.

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