Hi Qi
it is not obvious from that one image that something is wrong there. What
does a saggital view look like with the cursor on that region? Also, can
you send an image of the rh.inflated.nofix in 3D mode? Sometime XL
defects are fixable automatically, which may be the case for your
subjects with very large ventricles, but sometimes not
cheers
Bruce
On Tue, 5 May 2020,
Zeng, Qi wrote:
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Hi Douglas,
Compared to the ones without error, the subject surface misses including
left parietal lobe. Is that correct? Attached the comparison.
Thank you so much!
Best,
Qi
On Tue, May 5, 2020 at 1:58 PM Douglas N. Greve <dgr...@mgh.harvard.edu>
wrote:
You should load that volume along with the orig.nofix hemisphere
that is giving you problems and look for a large area that
should not be within the surface
On 5/5/2020 1:23 PM, Zeng, Qi wrote:
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Hi Douglas,
The cerebrum is removed and with no skull attached.
However, compared to others that run normally, it may have
problems with white matter segmentation and missing brainstem
(no clear). Attached the comparison below. Can you help figure
it out?
Thank you so much!
Best,
Qi
On Tue, May 5, 2020 at 11:36 AM Douglas N. Greve
<dgr...@mgh.harvard.edu> wrote:
You should look at the wm.mgz to see where the
defect is. Probably cerebellum is still attached or
maybe a big piece of skull.
On 5/4/2020 11:19 PM, Zeng, Qi wrote:
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Hi,
I've conducted longitudinal T1 recon-all. One
subject's last-scan ran into error in the first
independent recon all step: " recon-all -s SUBJ1
-SUBJ1.nii -all'.
Error: "CORRECTING DEFECT 0 (vertices=14101, convex
hull=2297, v0=1419) XL defect detected...". Log file
attached below.
I've increased the memory usage limit as some
suggestions did, but no help. Also T1.nii looks
fine, same parameter setting as first scan, also
attached below. Subject first scan and all the other
subjects were finished without errors. Can you help
figure out what has caused it?
Thank you so much!
Best,
Qi
--
Ph.D. candidate
Icahn School of Medicine at Mount Sinai
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Icahn School of Medicine at Mount Sinai
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Icahn School of Medicine at Mount Sinai
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