Yes, you will need to choose an index and then pass the color table to mri_segstats with --ctab to make sure it appears in the output.

Hi Rotem

sorry, we don't label the pineal gland, but yes you can label it in the volume yourself using freeview. I think if you add it to the color lut file it will be included in the stats, but perhaps Doug can comment
Bruce


On Fri, 4 Aug 2017, Rotem Saar wrote:

Dear Freesurfer experts,

I wondered if its possible to extract the volume of the pineal gland using the
basic cortical + sub-cortical segmentation (recon-all)?

I could not find the volume of this ROI in the output.

If the volume output for this ROI is available - please guide me where to look
(maybe I missed it?)

If not - does manual ROI drawing and following,volume calculation is possible
using freesurfer?

Thanks !

Rotem Saar-Ashkenazy

Department of Brain and Cognitive Science
Ben Gurion University of the Negev, Beer-Sheva, 84105

School of Social Work
Ashkelon Academic College, Ashkelon, 78211 

Israel

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer