do you mean they finished with an error? If so, what was it? On Fri, 8 Feb 2013, Jonathan Holt wrote:
Basically, I had a bunch of recon-all's terminate without finishing. Do I need to run recon-all -s <subjid> -make all, or can I run as usual?
jon On Feb 6, 2013, at 9:35 PM, Jonathan Holt wrote:
Just had a cluster of computers lock up, unfortunately resulting in several freesurfer jobs terminating prior to completion. It's possible I may have a ton of this same error come tomorrow. Two questions
is there a way to tell if a surface is out of date without starting up tkmedit?
last time I ran -make all, the command line disappeared until the job completed. This never happens when I run recon-all with autorecon2&3. Anyway to avoid this?
jon On Feb 1, 2013, at 1:28 PM, Jonathan Holt wrote:
OK, good deal! The first time I ran recon-all it exited with errors. That must be the issue.
thanks, jon
Hi Jon
that means that one of the surfaces is out of date, usually because you edited and reran but not to completion. Try running
recon-all -s <subject> -make all
cheers Bruce
p.s. ignore the "can't find file" thing. It really means it tried to read it, but found it wasn't the same topology as the other surface and that's what it is complaining about
On Fri, 1 Feb 2013, Jonathan Holt wrote:
Experts,
Having an issue with this error. It's complaining about rh.pial not matching rh.white, indicates there's no such file or directory and that mrisReadTriangleFile failed, and then proceeds to load without rh.pial. I tried loading rh.pial manually, but upon loading it immediately removes every surface on the LH. Wasn't an issue before I ran recon-all. Worth noting this brain was generated from a particularly low contrast MRI scan, and freesurfer had trouble generating correct surfaces from the get go.
Jon
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