Hi Carol
the bigventricles stuff works much better in the upcoming 6.0 and dev than it did in 5.3. You might try downloading dev and trying it out
cheers Bruce On Wed, 31 Aug 2016, Carol Nguyen wrote:
Hello FreeSurfer Developers, I am attempting to segment a brain with large ventricles. I was able to create a decent brainmask.mgz but the aseg segmentation after running autorecon2 and autorecon3 is neglecting a part of one hemisphere (see a picture attached). I tried to readjust the talairach parameters with tkregister without success. Running autorecon2 with "-bigventricles" flag did yield a similar result as running without it. Lastly, for your information, I use FS v5.3. I am also attaching the recon-all.log from the most recent attempt.
Can you please advise me how to get the correct segmentation of such a brain?
Thank you!
Best regards,
Carol
Carol NguyenUniversity of Minnesota, Twin Cities Researcher | Department of Pediatrics Division of Neuropsychology nguy1903@umn.edu