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Hi all, I am trying to register (linear and no lineat) T1 GM segmented images to MNI space. I have already registered linearly. My steps are as follow: 1. bet image.nii image_brain.nii -B -f 0.4 -g 0 2. fast -t 1 -n 3 -H 0.1 -I 4 -l 20.0 image_brain.nii -o image_brain_seg 3. flirt -in image_brain_pve_1.nii -ref $FSLDIR/data/standard/tissuepriors/avg152T1_gray.hdr -out image_brain_GM_flirt.nii -omat image_brain_GM_flirt.mat 4. fnirt - I don't know which template I can use. Is it correct if I use MNI152_T1_1mm_brain.nii.gz? It is a template for the full brain not only for GM. Would be this correct? fnirt --in image_brain_pve_1.nii -aff image_brain_GM_flirt.mat -ref $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --cout image_brain_GM_flirt_fnirt --iout image_brain_GM_flirt_fnirt Would be better to register to 2mm instead of 1mm? Thanks in advance