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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. [dgr...@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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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