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
