randomise -i merged.nii.gz -o TBIvsOI -m template_BrainCerebellumMask -d design.mat -t design.con -n 5000 -T -V
The -n option indicates the number of permutations performed and the  -T option indicates the output being corrected for multiple comparisons.
The following code was run to show statistical overlay on the template image to determine whether any differences in cortical thickness were significant.