Hi Jeni, you should not smooth with both. If you want to smooth within a given label with surf2surf, pass that label to surf2surf then don't smooth with glmfit. doug

On 07/30/2012 12:46 AM, Jeni Chen wrote:

Hi Doug,

When you say "If you smooth using surf2surf, then do not smooth using glmfit..." are you referring to smoothing the whole hemisphere, or with a label? In other words, if I had asked surf2surf to smooth only inside a label, then no need to smooth again in glmfit. But if I did a smoothing of 10mm in surf2surf on the entire hemisphere instead (i.e. without "--label" option in surf2surf), then I will need to do smoothing in glmfit. Did I get it right?

By the way, thank you for replying- on midnight Sunday! (unless you are in a different time zone...)

Jeni

On 2012-07-30, at 12:04 AM, Douglas Greve wrote:

...

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:

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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:

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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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