Hi Jeni, usually you smooth with surf2surf and include a mask or label to indicate that it should only be smoothed inside the mask/label. mri_glmfit will create a mask from non-zero voxels; if you ask glmfit to smooth, then it will only smooth inside of the mask. If you smooth using surf2surf, then do not smooth using glmfit.
doug





On 7/29/12 11:49 PM, Jeni Chen wrote:
Now I'm confused... So if I included a mask in my GLM analysis (which I did), then I should add the -fwhm option in mri_glmfit? If that's the case, does that mean my -y input file should be unsmoothed to avoid double-smoothing? 

Jeni

On 2012-07-29, at 11:31 PM, Douglas Greve wrote:

Mostly yes. The one in mri_glmfit will also do smoothing within a given mask by default, but basically they do the same thing.
doug

On 7/29/12 11:15 PM, Jeni Chen wrote:
So essentially the  -fwhm option in mri_glmfit does the same thing as mri_surf2surf --fwhm ? Just want to make sure... Thanks again!

Jeni





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