External Email - Use Caution
Hi Freesurfer team,
I am new to FreeSurfer and am currently doing QC using FreeSurfer (v.8). I wanted to check what the best approach is to correcting the following participant (screenshot attached).
It appears that the participant had very large ventricles (?), which have been misclassified (as indicated by FreeSurfer drawing the white and pial surfaces around them). My initial thought was to add control points or manually fill the ventricles in WM.mgz, but I wanted to check first, since this issue is widespread across the brain volumes.
Many thanks for your help!
Sincerely, Rachel
External Email - Use Caution
Hi
Have you tried running with the -bigventricles flag? ________________________________ From: Ran Yan rachyan@umich.edu Sent: Monday, September 1, 2025 6:57 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Fixing Misclassified Ventricles During QC
External Email - Use Caution
Hi Freesurfer team,
I am new to FreeSurfer and am currently doing QC using FreeSurfer (v.8). I wanted to check what the best approach is to correcting the following participant (screenshot attached).
It appears that the participant had very large ventricles (?), which have been misclassified (as indicated by FreeSurfer drawing the white and pial surfaces around them). My initial thought was to add control points or manually fill the ventricles in WM.mgz, but I wanted to check first, since this issue is widespread across the brain volumes.
Many thanks for your help!
Sincerely, Rachel -- Ran (Rachel) Yan She/her Ph.D. Candidate in Developmental Psychology University of Michigan 530 Church St. | East Hall 2048 | Ann Arbor, MI | 48109-1043
. WARNING - This email originated from outside of the UCI Health email system. Do not click any links and do not open attachments unless you can confirm the sender. PLEASE FORWARD SUSPICIOUS EMAILS TO: security@hs.uci.edu .
External Email - Use Caution
The image looks a lot better with the flag! Thank you.
Sincerely, Rachel
On Mon, Sep 1, 2025 at 9:54 PM Taylor, Lisa ltaylor2@hs.uci.edu wrote:
External Email - Use CautionHi
Have you tried running with the -bigventricles flag?
*From:* Ran Yan rachyan@umich.edu *Sent:* Monday, September 1, 2025 6:57 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Fixing Misclassified Ventricles During QC
External Email - Use CautionHi Freesurfer team,
I am new to FreeSurfer and am currently doing QC using FreeSurfer (v.8). I wanted to check what the best approach is to correcting the following participant (screenshot attached).
It appears that the participant had very large ventricles (?), which have been misclassified (as indicated by FreeSurfer drawing the white and pial surfaces around them). My initial thought was to add control points or manually fill the ventricles in WM.mgz, but I wanted to check first, since this issue is widespread across the brain volumes.
Many thanks for your help!
Sincerely, Rachel -- *Ran (Rachel) Yan* She/her Ph.D. Candidate in Developmental Psychology University of Michigan 530 Church St. | East Hall 2048 | Ann Arbor, MI | 48109-1043
. *WARNING - This email originated from outside of the UCI Health email system. Do not click any links and do not open attachments unless you can confirm the sender. *PLEASE FORWARD SUSPICIOUS EMAILS TO: security@hs.uci.edu . _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu
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Ran Yan -
Taylor, Lisa