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Hi Dana, Almost! Try this: fslmeants -i gray_matter.nii.gz --label=HarvardOxford-cort-maxprob-thr0-2mm.nii.gz The output is a matrix. Each row corresponds to a volume in gray_matter.nii.gz (so, if the input is a 3D file, there is just 1 long line). Each column (there are 48) is for a label. You'd be interested in the 7th column it seems. All the best, Anderson