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
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
freesurfer@nmr.mgh.harvard.edu