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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