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
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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
Rusche, Johann