Hi FreeSurfer experts,
We recently finished a twin study with 450 participants. Most of the FreeSurfer issues have been common and fixable. However, we have two sessions that have a similar issue that I have not been able to find a solution to using the forums. Could you please advise us on how to correct these problems?
Please see attached screenshots:
114147 - aparc+aseg and brainmask are grabbing the cerebellum
116336 - aparc+aseg is over grabbing the brainstem when tracing the cerebellum (the brainmask is fine on this one). I made edits to aparc+aseg and aseg and reprocessed with no change, however, since these are not common edits the processor may not have uploaded/taken these edits correctly.
We use a service at the university Center for Computational Imaging called XNAT. The lab who runs this processor writes spiders for us to process everything so I have limited access to the scripts. However, on past projects I have used terminal for FreeSurfer processing. If I can fix this problem with a terminal script, then upload it to XNAT for normal FreeSurfer processing, it may correct the issue. I haven't been able to figure out a correct terminal script to correct the issue on my own though.
Any help is appreciated.
Sincerely,
Leah Burgess
Leah Burgess Research Analyst Department of Psychology Vanderbilt University 219 Wilson Hall 111 21st Avenue South Nashville, TN 37240 (615) 343-1446tel:%28615%29%20343-1446
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