Dear Douglas,

This is just a friendly reminder concerning the data I send you. I'd much appreciate if there is any advice on how to advance our pial surfacing other than manual editing.

Thanks!

Johann


From: Rusche, Johann
Sent: Monday, January 07, 2019 1:03 PM
To: Freesurfer support list
Subject: RE: [Freesurfer] Pial surface error (failing dura removal)

Hi Douglas,

Thanks for your swift reply. I just shared a link to a Partners Dropbox folder with you as our group (lazargp) does not have a folder in /cluster/outgoing.

No T2 or FLAIR unfortunately. Other than MPRAGE T1 we only have fMRI and DTI scans.

Thanks,
Johann

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. [DGREVE@mgh.harvard.edu]
Sent: Monday, January 07, 2019 11:05 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Pial surface error (failing dura removal)

Do you have a T2 or a FLAIR? Can you upload the subject so we can take a look?

On 1/6/19 6:20 PM, Rusche, Johann wrote:
Dear Freesurfers,

I have been processing my T1 dataset through the longitudinal pipeline with the -3T flag (scanned at Martinos). Unfortunately in 50% of all subjects large areas of dura are being included in the pial surface.

Both gcut and adjustment of watershed parameters (down to 5) did not bring significant improvements. I understand intensity characteristics are very similar for GM and dura. However, I wonder whether you can recommend a more elegant solution than painfully recon-editing all brainmasks by hand.

Attached is a screenshot depicting the issue with and without gcut. I am using stable v6.0. Thanks for your time!

Best,
Johann

__________________
Johann Rusche

Graduate Research Student, Lazar Lab
Department of Psychiatry – Neurosciences
Massachusetts General Hospital


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