[Freesurfer] Intersection of labels with other labels or volumes

Hello-

Is there a simple way to obtain the intersection of two labels, output into a third label? Or the intersection of a label and an .mgh file output by mri_surfcluster?

For instance, I have a cluster defined by mri_glmfit/mri_surfcluster that spans multiple anatomical regions, and I want to investigate the values from subsections of the cluster. That is to say, I want to run mris_anatomical_stats on only the section of my cluster that covers, say, precentral cortex but not caudal middle frontal or pars opercularis.

I've tried several strategies without success. The most promising seemed to be just having mri_surfcluster output an aparc file, and then pass that aparc file into mris_anatomical_stats. However, that aparc just puts the very first region definition to every vertex. The same happens if I run mri_label2aparc on the labels output by mri_surfcluster. This happens no matter which LUT or ctab I use, i.e., with aparc.annot.ctab the whole volume gets labeled "bankssts" and with FreeSurferColorLUT.txt every vertex in the cluster volume gets labeled "Left-Cerebral-Exterior."

I guess there are a few issues in this email, but the most important one to me is being able to run mris_anatomical_stats on the union of a cluster file and the individual regions from the standard aparc atlas.

Any suggestions?

Thanks in advance, --------- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota