[Freesurfer] mri_glmfit restricted to a label

Hi, we are trying to run glmfit restricted to a label, with the following commands:

mri_glmfit --y lh.p.thickness.10.mgh --label lh.l.label --fsgd f.fsgd --C C.mtx --surf fsaverage lh --cortex --glmdir lh.p.thickness.10.glmdir

mri_glmfit-sim --glmdir lh.p.thickness.10.glmdir --sim mc-z 10000 1.3 mc-z.abs --sim-sign abs --cache-label lh.l.label --cwpvalthresh .999 --overwrite

but if we check mc-z.abs.sig.masked.mgh and mc-z.abs.sig.cluster.mgh, we found clusters outside the label (see image below).

Are we doing it properly? How can we be sure that both the analysis and the correction are done inside the label?

thanks! Gari

[image: Inline image 1]