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I tried both of the options suggested, but neither is working for me. I'm trying to average across all the subjects' functional scans, but with the fslmerge option, I get an error message displaying: Error in size-match along non-concatenated dimension. With the fslmaths option, it does not work either. Let me verify the command line for the fslmaths. Is it fslmaths subject1.nii subject2.nii etc -Tmean mean_subject? Thanks On Wed, Nov 30, 2011 at 5:47 PM, Benjamin Kay <[log in to unmask]> wrote: > My guess is that BET works better on individuals' brains than it does on an > averaged brain, so if you are going to skull strip then you should > probably do > it before averaging. Someone more familiar with BET could give you a better > answer. > > On Wednesday, November 30, 2011 20:40:59 you wrote: > > Thanks Benjamin, would you use the BET version of the brain or does it > not > > matter as much? > > > > On Tue, Nov 29, 2011 at 7:42 PM, Benjamin Kay <[log in to unmask]> > wrote: > > > fslmerge -t subjects.nii subject1.nii subject2.nii subject3.nii > > > fslmaths subjects.nii -Tmean mean_subject.nii > > > > > > Or something like that -- there's more than one way. Obviously, you > will > > > probably want to resample each subject into the same stereotactic space > > > first. > > > > > > On Tuesday, November 29, 2011 22:34:49 you wrote: > > > > Hello, > > > > > > > > I'm trying to average across 10 subjects' brains, but not sure how to > > > > go about doing that. Any help will be greatly appreciated. > > > > > > > > Thanks, > > > > Amy > -- (Amy) Zhong Sheng Zheng UCLA Dept. of Neurosurgery