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Hello all, I am trying to transform my WMH lesion masks into standard MNI space using FNIRT but am having a little bit of trouble. When I transform the masks, the lesion volume is drastically reduced (from ~400 to ~ 40). Any help to fix this issue would be greatly appreciated. Commands: flirt -in T1_struc_betted -ref MNI152_T1_1mm_brain -out T1_struc_bettedstandard -omat T1_struc_xfmtostandard -dof 12 -interp trilinear fnirt --in=T1_struc --inmask=lesionmask --aff=T1_struc_xfmtostandard.mat --cout=warp --config=T1_2_MNI152_2mm applywarp --ref=MNI152_T1_1mm_brain --in=lesionmask --warp=warp --out=lesionmask_warped Thanks, Calvin