Hi Martin
we are happy to take a look, but can't really tell much from a screenshot.
Feel free to upload the subject to our ftp site if you want us to help
cheers
Bruce
On Tue, 12 Dec 2017, Loeffler, Martin wrote:
Dear Bruce,
thanks for the quick reply! You are right, of course. I do find errors in
lh.inflated.nofix.
I have attached a screenshot of the biggest errors I found..
Can you maybe guide me a little how to fix the issue? Do I just cancel the
running recon-all process, and set control points and run again? Investing some
time in manual editing would be fine as it's a case study...
Thanks for your help,
Martin
________________________________________
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce
Fischl [fis...@nmr.mgh.harvard.edu]
Gesendet: Montag, 11. Dezember 2017 22:47
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
Hi Martin
a defect that large means that something big went wrong (skull or
dura attached, etc...). Try looking at the ?h.orig.nofix and/or the
?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find
defect 9
cheers
Bruce
On Mon, 11 Dec 2017, Loeffler, Martin wrote:
Dear FreeSurfer team,
For a case report I’m running recon-all on a patient with a giant arachnoid
cyst in the left
hemisphere. It gets stuck at this point (last message):
CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
XL defect detected...
It is stuck here since a whole day now, so I’m not expecting it to advance…
Following this post:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I
looked at the wm.mgz, but did not find huge errors.
Do you have any ideas what the problem might be or what I can do to work around
it?
Thanks,
Martin
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