I have never masked out out-of-brain voxels. For visualization purposes, I usually mask out in tkmedit by loading the brain.mgz as aux and then applying aux as a mask from the View menu. It is strange that you are getting out-of-brain activation in the group analysis. How close is it to the edge? Remember, that talairach is only "accurate" to an inch or so.

doug

Dan Dillon wrote:

Dear FreeSurfers,

Quick question about masking. I routinely make a brainmask for each subject and include the mask flag in the mkanalysis (see below), but I note that when I run contrasts and plot results—either for individual subjects or for group-level stuff—I get statistical results for voxels outside the brain. I’d like to mask the extra-brain voxels out at the individual level, so that they don’t get included at any point in my group level analyses. How do I do this? More generally, does the brainmask serve only a visual/display function or can I use it to constrain what I’m doing stats on (which is what I want it to do)?

Thanks for your endless help!

Dan Dillon

PS. This is a a typical mkanalysis step . . .

mkanalysis-sess.new -analysis ${analysis} -gammafit 2.25 1.25 -TR 2.5 -paradigm mg_3_7.par -designtype event-related -funcstem fmcs

tcsm6 -nconditions 13 -polyfit 2 -taumax 30 -inorm -mask brain -timeoffset -1.25 -TER .1 -autostimdur -force
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting