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Hi Bruce,

Again, so sorry if this message has been spammed to the mailing list; I kept getting messages that the body of the message was too big whenever I tried to send it with the attachments, so I'm instead sending along a dropbox link to the requested files from a subject with the described problem: https://secure-web.cisco.com/1bc6MB5a_uvCZt5sOF35dk1a-glsFH3pnjNrc9AoxTGiIkn...

Thank you for your insight and assistance with this!

Sincerely, Jee Won ________________________________________

Message: 2 Date: Tue, 21 Dec 2021 15:31:42 +0000 From: "Fischl, Bruce" BFISCHL@mgh.harvard.edu Subject: Re: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: BY5PR04MB6614B1B44ADDBBB00C9E7109EF7C9@BY5PR04MB6614.namprd04.prod.outlook.com

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Hi Jee Won

Can you send us the recon-all.log file? And ideally an example orig.mgz that we can try things on

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Kang, Jee Won Sent: Tuesday, December 21, 2021 9:19 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter

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Hello all,

I found a very common error in our data while I was correcting recons. The lateral ventricles (usually the horns) are being misclassified as white matter in aseg.mgz. This happened in around 1/3 of our 108 subjects.

We were able to fix this issue by manually filling in the ventricles in aseg.presurf.mgz and re-running Freesurfer with the command autorecon2-noaseg -autorecon3, but this is obviously quite a labor-intensive fix for a substantial portion of our data. This was also the only way to fix the segmentation - filling in the mislabeled areas as 255 in the wm.mgz did not fix the problem. I'm not sure why Freesurfer is having issues here, as the areas it is mislabeling have very distinct intensity boundaries - the T1 intensity is usually between 20 and 45 in the areas that are being mislabeled. I've attached a screenshot of a subject's aseg.presurf.mgz who had this ventricle segmentation issue, and you can see that a large portion of the right ventricle has just not been segmented properly; the intensity of the area in the aseg.presurf.mgz and wm.mgz volumes is just 0, and it was 41 (R cerebral white matter) in aseg.mgz.

Would you be able to provide some insight into why this might have been happening, and what we could do in the future to prevent such extensive manual editing in the future? I can also say that this data was processed with a T2 image as well, and supplying that flag didn't help with the segmentation issue.

Thank you,

Jee Won