Hi Daniel
you can load the ?h.defect_labels as an overlay on either the
inflated.nofix or orig.nofix surface and use it to find the location of
that defect. Usually this means something big is wrong - it should be
obvious looking at the inflated.nofix I would think. If you can't find it,
upload the subject to our ftp site and I'll take a look
Bruce
On Tue, 9 May 2017, Weisholtz, Daniel S.,M.D. wrote:
Hello Freesurfer Developers,
I am trying to run recon-all -all and the procedure is freezing while trying
to correct what appears to be a large defect (vertices=36706). The source T1
image is not great quality due to rippling artifact, but I have inspected
brainmask.mgz, wm.mgz, and aseg.mgz and I cannot identify a large defect.
The dura was not completely removed, and I tried improving this by using
various watershed thresholds as well as using gcut. I also tried manually
removing the remaining dura, but none of this was helpful. I also tried
using -T2FLAIR, but this did not seem helpful either.
I am attaching the recon-all.log. This does not include the edits I made to
brainmask.mgz. That was done on a separate attempt. This does include the
-T2FLAIR, as you can see in the recon-all.log file.
1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
2) Platform: OS X Yosemite 10.10.5
3) recon-all.log attached
I very much appreciate any assistance you can provide. Happy to send any of
the data if it would be helpful.
Sincerely,
Dan Weisholtz
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