Dear Bruce,
Thank you so much for your suggestions. Unfortunately, I was not able to open lh.defect_labels in freeview. When I try, Freeview crashes. There are no rh surfaces in the surf folder, so I presume this means the problem occurred in the left hemisphere. I was able to view the inflated.nofix and orig.nofix but I’m still not exactly sure what the problem is, and I would be grateful if you could take a look at the subject folder. I will upload it to the ftp site. It is called s117.
Thank you!
Best, Dan
On May 10, 2017, at 10:43 AM, freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 9 Date: Tue, 9 May 2017 15:54:12 -0400 (EDT) From: Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all freezes while CORRECTING DEFECT 60 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1705091553090.16219@door.nmr.mgh.harvard.edumailto:alpine.LRH.2.20.1705091553090.16219@door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-15"
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