I tried to send the email below on May 10, 2017 with screenshots but received
an email stating:
Your mail to 'Freesurfer' with the subject
Freesurfer Cerebellum Overgrab
Is being held until the list moderator can review it for approval.
The reason it is being held:
Message body is too big: 2086938 bytes with a limit of 1000 KB
I have not received anything since, so I'm not sure if it is still under review
or not. Could someone please look into this please, and let me know if there is
a better way to send screenshots so you are able to see the cerebellum issues?
Thanks!
Sincerely,
Leah Burgess
Leah Burgess
Research Analyst
Department of Psychology
Vanderbilt University
219 Wilson Hall
111 21st Avenue South
Nashville, TN 37240
(615) 343-1446<tel:%28615%29%20343-1446>
NOTE: This e-mail transmission, including any attachments, is intended only for
the named recipient(s) and may contain information that is privileged,
confidential and/or exempt from disclosure under applicable law. If you have
received this transmission in error, or are not the named recipient(s), please
notify the sender immediately by return e-mail and permanently delete this
transmission, including any attachments.
________________________________
From: Burgess, Leah Lanette
Sent: Wednesday, May 10, 2017 2:55 PM
To: Freesurfer support list [freesurfer@nmr.mgh.harvard.edu]
Subject: Freesurfer Cerebellum Overgrab
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) 343-1446<tel:%28615%29%20343-1446>
NOTE: This e-mail transmission, including any attachments, is intended only for
the named recipient(s) and may contain information that is privileged,
confidential and/or exempt from disclosure under applicable law. If you have
received this transmission in error, or are not the named recipient(s), please
notify the sender immediately by return e-mail and permanently delete this
transmission, including any attachments.
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