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
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