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Thanks Chris & Udunna,

I will check dcm2nii first since I have used that program before. Chris, I am not sure I understand how your method really works, but if dcm2nii doesn't work, then I will take a shot at SPM's Imcalc.

Best,
Vy

On Wed, Sep 12, 2012 at 2:03 PM, Chris Watson <[log in to unmask]> wrote:
You can use the output of Segmentation in imCalc; e.g. given c{1,2,3}.nii, something like
"i1 + i2 + i3 > 0.9" as the equation should do it.

On 09/12/2012 02:50 PM, Vy Dinh wrote: 
Hi SPMers,

Is there an SPM tool for skull stripping? We have functional images that we would like to skullstrip. I have tried using FSL's Brain Extraction Tool (BET), but when I try to convert BET's output (the skullstripped 4D functional image), none of the conversion programs that I use (SPM's "Expand Image Frames", FSL's fslsplit, an independent Matlab function) work. These programs only give me one output, and the Matlab error messages indicate that the 4D file has only 1 image volume. I may have to consult the FSL forum to see why BET's output (skullstripped 4D image) cannot be converted to 3D, but I thought I should check with the SPM forum first to see if a skullstripping tool works (this would be ideal for us since we are processing our functional data with SPM).

Many thanks in advance,

Vy