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