You can use mri_binarize, something like

mri_binarize --i sig.mgh --min 3 --o mask.mgh

Note that sig.mgh is a signed quantity. If you want it unsigned, then use --abs above

doug

Miranka Wirth wrote:

Dear Freesurfers,

I would to like to generate a binary surface-based mask from the GLM output file (e.g., sig.mgh) the way that vertices above a certain p threshold are set to 1 and below this threshold to 0. I believe I can use this mask in the mri_glmfit procedure?

Thank you for helpful information Miranka _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer