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Hi Mark, Thanks for the response -- I used the costweightmask in flirt and it works great. However, I'm not sure what option to use in fnirt with this mask. I am using the affine matrix outputted from flirt, but I seem to be getting an error when I do this. The code I'm using is: fnirt --ref=MNI152_T1_2mm_brain.nii.gz --in=skullstripped_T1.nii --aff=standard.mat --iout=fnirt_output.nii The error I'm getting is: Warning, Jacobian not within prescribed range. Prescription is 0.01 -- 100 and obtained range is -5.94365 -- 26.3309. I tried the same fnirt code with a subject without a lesion, and it worked great. So what option do I use in fnirt to use the costweightmask? Could my issue be something else? Thanks, Derek