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Hello all,
Apologies for the delay in response!
For the applications in my group's work, we are looking at ventricular volume,
as well as white matter volume. To that degree, we are interested in whether
there are any processing steps earlier in the pipeline that we can implement
just to minimize the manual editing required - just anecdotally, there have
been cases where lateral ventricle volume increases over 5% after making manual
edits, and I was unable to identify if there was a common element to the
subjects with ventricle problems.
Thank you for your work on this! We really appreciate it.
Thank you,
Jee Won
________________________________________
Message: 2
Date: Tue, 4 Jan 2022 22:11:53 +0000
From: "Nadar, Priyanka (NIH/CC/OCRTME) [F]" <priyanka.na...@nih.gov>
Subject: Re: [Freesurfer] [EXTERNAL] Re: Ventricle segmentation issue
- ventricle mislabeled as white matter
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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I am not part of Jee Won's team: just generally interested. For my work, I am
looking at ventricular volume and so it would be good to not have to manually
correct a large number of my scans.
________________________________
From: Douglas N. Greve <dgr...@mgh.harvard.edu>
Sent: Tuesday, January 4, 2022 1:19 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] Ventricle segmentation issue - ventricle
mislabeled as white matter
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Hi Jee Won and Priyanka, there are several things going on here. First, the
original aseg (aseg.presurf.mgz) has these areas labeled as nothing (0); they
show up as WM in aseg.mgz and aparc+aseg.mgz. Obviously, it would be good to
have them properly labeled, but is this critical to your applications? Eg, are
you looking at ventricular volume?
On 12/21/2021 9:19 AM, Kang, Jee Won wrote:
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Hello all,
I found a very common error in our data while I was correcting recons. The
lateral ventricles (usually the horns) are being misclassified as white matter
in aseg.mgz. This happened in around 1/3 of our 108 subjects.
We were able to fix this issue by manually filling in the ventricles in
aseg.presurf.mgz and re-running Freesurfer with the command autorecon2-noaseg
-autorecon3, but this is obviously quite a labor-intensive fix for a
substantial portion of our data. This was also the only way to fix the
segmentation - filling in the mislabeled areas as 255 in the wm.mgz did not fix
the problem. I'm not sure why Freesurfer is having issues here, as the areas it
is mislabeling have very distinct intensity boundaries - the T1 intensity is
usually between 20 and 45 in the areas that are being mislabeled. I've attached
a screenshot of a subject's aseg.presurf.mgz who had this ventricle
segmentation issue, and you can see that a large portion of the right ventricle
has just not been segmented properly; the intensity of the area in the
aseg.presurf.mgz and wm.mgz volumes is just 0, and it was 41 (R cerebral white
matter) in aseg.mgz.
Would you be able to provide some insight into why this might have been
happening, and what we could do in the future to prevent such extensive manual
editing in the future? I can also say that this data was processed with a T2
image as well, and supplying that flag didn't help with the segmentation issue.
Thank you,
Jee Won
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