Re: [Freesurfer] mrisReadTriangleFile failed
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 Two questions 1) is there a way to tell if a surface is out of date without starting up tkmedit? 2) last time I ran -make all, the command line disappeared until the job completed.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 autorecon23. 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 thanks, jon Hi Jon that means that one of the surfaces is out of date, usually because you edited and reran but not to completion.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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mrisReadTriangleFile failed
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 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 autorecon23. 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 ___ 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
Re: [Freesurfer] mrisReadTriangleFile failed
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 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 autorecon23. 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 ___ 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
Re: [Freesurfer] mrisReadTriangleFile failed
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 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 autorecon23. 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 ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mrisReadTriangleFile failed
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 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 autorecon23. 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 ___ 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 ___ 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
Re: [Freesurfer] mrisReadTriangleFile failed
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 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 autorecon23. 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mrisReadTriangleFile failed
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 autorecon23. 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
Re: [Freesurfer] mrisReadTriangleFile failed
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.
Re: [Freesurfer] mrisReadTriangleFile failed
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
