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(1) Determine the average FWHM across subjects, this is not the smoothing kernel, but the smoothness of the image. Rather than assuming that the FWHM is the same in all three planes, I usually use 3dFWHMx (afni) to estimate the smoothness using the residuals. For this option, you'd use the first-level model residuals.

(2) Determine the FWHM of the group-level model to estimate the smoothness of the image. Rather than assuming that the FWHM is the same in all three planes, I usually use 3dFWHMx (afni) to estimate the smoothness using the residuals. For this option, you'd use the group-level model residuals.

There has been debate over whether option1 or option2 is better.

With 3dClustSim, don't forget to use a mask.

Best Regards, Donald McLaren
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D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Office: (773) 406-2464
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