Thanks Douglas, "mri_convert lesionmap.mgz -at samseg.m3z lesionmap.mni152.mgz" worked fabulously after some tweaks in the command line!

What would be the best approach to compare population-wise lesion heat maps between groups of subjects using the output from SAMSEG? (the full FS pipeline cannot process my data due to brain defects and time restrictions). 

Thanks for all the support for these fantastic tools!