You can try using fsaverage/mri/brainmask.mgz. It will not be in the correct space, so you'll have to resample it. Try

tkregister2 --s fsaverage --fstarg brainmask.mgz --mov LowTrauma/bold/LowTraumaSPMHRF/tal-ffx/Rcue_v_Ncue/h-offset.bhdr --regheader --reg junk

The h-offset should be in reg with the the brian mask. If it is, then:

mri_vol2vol --targ $SUBJECTS/fsaverage/mri/brainmask.mgz --mov LowTrauma/bold/LowTraumaSPMHRF/tal-ffx/Rcue_v_Ncue/h-offset.bhdr --regheader --o brainmask.func.mgz --inv

This will create brainmask.func.mgz that you can pass to volcluster with --mask

doug

Dan Dillon wrote:

Dear FreeSurfers,

I've run some fixed and random effects analyses in Talairach space and would like to constrain the output of mri_volcluster to areas within the brain (e.g., not the eyeballs). How do I create a brainmask that is the same dimensions as the input volume I pass to mri_volcluster? Without a mask, I'm currently getting stats on extra-brain voxels that I do not want, and I can't use the Talairach brainmask.mgz file b/c it doesn't match my input volume.

Any help would be appreciated.

Dan Dillon

PS. The command I'm currently running, sans mask, is as follows:

mri_volcluster --in LowTrauma/bold/LowTraumaSPMHRF/tal-ffx/Rcue_v_Ncue/sig --in_type bfloat --reg LowTrauma/bold/LowTraumaSPMHRF/tal-ffx/register.dat --thmin 3 --minsizevox 12

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