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