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that means that one of the surfaces is out of date, usually because you edited and reran but not to completion.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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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
1) is there a way to tell if a surface is out of date without starting up tkmedit?
2) 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that means that one of the surfaces is out of date, usually because you edited and reran but not to completion.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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Hi Jon
I'm not sure what this means, but -make all is the thing to do in this case.
cheers Bruce
On Wed, 6 Feb 2013, 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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No, the computers they were running on had to be rebooted before they finished. On Feb 8, 2013, at 1:19 PM, 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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so they might have finished properly if you hadn't done so? Try running -make all again. In theory it's only supposed to reru what is needed.
Bruce
On Fri, 8 Feb 2013, Jonathan Holt wrote:
No, the computers they were running on had to be rebooted before they finished. On Feb 8, 2013, at 1:19 PM, 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Also note that there are "IsRunning" files created in the scripts folder. If those still exist, then it will come back saying to delete them first. doug
On 2/8/13 3:13 PM, Bruce Fischl wrote:
so they might have finished properly if you hadn't done so? Try running -make all again. In theory it's only supposed to reru what is needed.
Bruce
On Fri, 8 Feb 2013, Jonathan Holt wrote:
No, the computers they were running on had to be rebooted before they finished. On Feb 8, 2013, at 1:19 PM, 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 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > >
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-
Bruce Fischl -
Douglas Greve -
Jonathan Holt