On 10/29/2021 10:46 AM, Kang, Jee Won wrote:
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Hello all,
There are two topics I would appreciate your expert advice on:
Topic 1: Aseg and wm edits
I was going through the wiki and the archive of past inquiries and was
unable to find a clear answer to whether you can make aseg edits and
wm edits, and then re-run in Freesurfer at the same time. Furthermore,
I was just a little unclear as to how exactly to perform aseg edits.
According to this post:
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are supposed to edit aseg.manedit.mgz, and only make edits to wm.mgz
if segmentation is still incorrect after re-running. The command
suggested to be used is recon-all -s subject -autorecon2 -nogcareg
-nocanorm -nocareg -autorecon3.
However, according to this post:
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the wiki page it references here:
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https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations,
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you are supposed to edit aseg.presurf.mgz, and doesn't mention whether
aseg edits are compatible with wm.mgz edits. The command these posts
say you should run is recon-all -autorecon2-noaseg -autorecon3 -s
subject, and this is also listed in the "OtherUsefulFlags" table.
My questions are:
1) Does it matter which volume, aseg.presurf.mgz or aseg.manedit.mgz
that you edit?
manedit does not exist in version 7, so that is where the confusion
comes from
2) What is the proper command to use for re-running with aseg edits?
If you are editing the aseg to help fix the surfaces, then use
-autorecon2-noaseg -autorecon3
3) Can you make edits to wm.mgz and aseg edits and re-run with both
edits being taken into account?
Yes, both will be taken into account
For some background into why I've been looking into editing aseg
segmentations, we have a sizeable portion of our data for whom the
lateral ventricles are being mislabeled as wm (for some this is quite
mild, for others it is pretty extensive). I know the -big-ventricles
flag is an option, but we are not looking to re-run all of our subject
with it at this time, as we have 100+ subjects.
Topic 2: White/pial overlap near subcortical structures
Sometimes, the pial surface near the subcortical structures will "pull
back" too much, I've attached an example image. This "pull back"
sometimes appears after I've re-run the subject after making wm edits,
when it was not present in before re-running. In the attached example
image, the original pial surface before re-running is in blue, the new
pial surface is in red. The original white surface is in green, the
new white surface is in yellow. I have the aparc+aseg.mgz and wm.mgz
visible. As shown in the image, this "pull back" will often end up
exclude a chunk of voxels from the aseg and aparc+aseg, even if there
are wm.mgz voxels filled in that area.
How important is it to fix errors in this area in general, and would
aseg edits be appropriate since wm edits don't seem to address the
problem?
It is hard to tell what is going on there from the pictures that you
have sent. That spot may just be part of the medial wall, in which case
it can be ignored
Thank you for your insight into these topics!
Sincerely,
Jee Won
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