In principle you can, but it might require a lot of work. You can use something like mri_binarize --i aparc+aseg.mgz --replaceonly X Y --replaceonly X2 Y ... where X is the seg no for a given cortical segmentation and Y is the seg no for the lobe it belongs to. You would do this for all segments/lobes in a single command line. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Platten, Michael MPLATTEN@mgh.harvard.edu Sent: Tuesday, October 6, 2020 10:28 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Lobe segmentation

Hi,

I have a question regarding lobe (temporal, frontal, parietal, and occipital) segmentation. I have already completed a recon-all for all subjects. I have seen that the surface stream has a -lobesStrict function which parcellates the lobes. I have also seen that you can convert the surface to a volume through mri_surf2vol. This, I believe, would in the end get me what I'm after; which are the lobe segmentations.

My plan is to overlay a lesion mask and extract the lesions based on, among other things, which lobe they belong to.

I was wondering if there was a way to use the segmentation outputs from FreeSurfer to get lobe segmentation directly, i.e. by adding up various segmentation volumes? Or do I have to go through the Surface stream?

Is my above-stated method the easiest and best way to get lobe segmentations in order to extract the lesion load per lobe?

Thank you for your time and help!

Best, Michael