Hello-

Can somebody point me towards the best way to make a thresholded binary mask out of a sig.mgh file that comes out of qdec/mri_glmfit? I'd like to take the sig.mgh file and use all values above threshold as a mask for another mri_glmfit analysis. I'm used to functional data in FSL, and could do this lickety-split with fslmaths or fslroi. Does FreeSurfer have a similar set of utilities to be used in manipulating .mgh files?

I've tried to run thresholding within tksurfer, then "Save Overlay As" but that doesn't cut off the sub-threshold values. I'm sure I could draw on the surface to trace my supra-threshold areas and create a mask that way, but I'd prefer to just do it mathematically if possible. Thanks!