did you run
recon-all -s <subject name> -make all
?
I don't see it in the log On Tue, 31 Jul 2018, Rockers, Elijah D. wrote:
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Oh, yep, sorry about that. I copy the list on this e-mail, and attach the log. I think the list blocks attachments, but if anyone wants to see full log I can send it.
Thanks to all,
-Eli
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Tuesday, July 31, 2018 2:03:05 PM To: Rockers, Elijah D. Subject: Re: Surface editing: recon-all exited with errors can you cc the list on these emails so others can help? On Tue, 31 Jul 2018, Rockers, Elijah D. wrote:
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The recon-all -make all command finished relatively quickly, still with errors. It's still showing the same errors, and I have attached the new recon-all.log.
_
From: Rockers, Elijah D. Sent: Tuesday, July 31, 2018 12:32:11 PM To: Bruce Fischl Subject: Re: Surface editing: recon-all exited with errors
Odd. I assumed the individual recon-all commands in the log are just what is reported by the
general
pipeline, since I definitely did not issue all those commands separately. I just used the
recon-all
-make all command after editing. In anycase, I will run it again to see if anything changes, but I think that would be surprising.
Thanks again
- Eli
_
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Tuesday, July 31, 2018 11:52:59 AM To: Rockers, Elijah D. Subject: Re: Surface editing: recon-all exited with errors Hi Eli
it's hard for me to tell since you have so many individual recon-all commands, but it looks like you didn't recreate all the surfaces after editing. Errors like thiss one:
mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn't match ../surf/lh.white.preaparc
typically mean something hasn't been recreated properly. Try running recon-all -make all
cheers Bruce
On Tue, 31 Jul 2018, Rockers, Elijah D. wrote:
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Hi Bruce,
I have attached the recon-all.log, regarding an exit with ERRORS that occured after manually
editing
the surface. Thanks for taking a look.
Also, I double checked - the original recon-all command finished with no errors. So it seems the message occurs after surface editing. But the new reconstructed surfaces appear accurate, at
least
with respect to gray and white matter boundaries. Let me know if there's anything else you need.
Thanks again,
- Eli
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