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