Hello FreeSurfers,
I am trying to run a group analysis with Qdec following this tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freevi...
I got a series of errors when I ran: recon-all -s <subjid> -qcache
.... ERROR: number of vertices in /home/subiculum/Desktop/local_recons/OCD_analysis/3662/surf/lh.volume does not match surface (126049,126592) ERROR: reading curvature file ...
mri_concat ./tmp.mris_preproc.6022/3662.1.mgh --o lh.volume.fsaverage.mgh mghRead(./tmp.mris_preproc.6022/3662.1.mgh, -1): could not open file ninputs = 1 Checking inputs ERROR: reading ./tmp.mris_preproc.6022/3662.1.mgh ...
Reading source surface reg /home/subiculum/Desktop/local_recons/OCD_analysis/fsaverage/surf/lh.sphere.reg Loading source data ERROR: could not read lh.volume.fsaverage.mgh as type 3 Linux subiculum-Precision-T1650 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 3662 exited with ERRORS at Thu Jan 23 15:22:21 EST 2014
One of the errors says "number of vertices in... does not match surface." I found an older post where someone else was complaining about the same error and Doug suggested running "recon-all -surfvolume ..." https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-September/025737....
I did that and then I ran -qcache again but I got the same errors. It also seems to be a problem with fsaverage. I do have a copy of fsaverage in the subject's directory of this study. I am attaching the log file with details about the errors.
Can someone help me sort this out?
Thank you, Mihaela
Hi Mihaela
usually that means the subject was partially but not completely rerun. You can try using recon-all -s <subject> -make all
and see if it fixes it cheers Bruce On Thu, 23 Jan 2014, Mihaela Stefan wrote:
Hello FreeSurfers, I am trying to run a group analysis with Qdec following thistutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnal ysis_freeview
I got a series of errors when I ran: recon-all -s <subjid> -qcache
.... ERROR: number of vertices in /home/subiculum/Desktop/local_recons/OCD_analysis/3662/surf/lh.volume does not match surface (126049,126592) ERROR: reading curvature file ...
mri_concat ./tmp.mris_preproc.6022/3662.1.mgh --o lh.volume.fsaverage.mgh mghRead(./tmp.mris_preproc.6022/3662.1.mgh, -1): could not open file ninputs = 1 Checking inputs ERROR: reading ./tmp.mris_preproc.6022/3662.1.mgh ...
Reading source surface reg/home/subiculum/Desktop/local_recons/OCD_analysis/fsaverage/surf/lh.sphere. reg Loading source data ERROR: could not read lh.volume.fsaverage.mgh as type 3 Linux subiculum-Precision-T1650 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 3662 exited with ERRORS at Thu Jan 23 15:22:21 EST 2014
One of the errors says "number of vertices in... does not match surface." I found an older post where someone else was complaining about the same error and Doug suggested running "recon-all -surfvolume ..." https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-September/025737 .html
I did that and then I ran -qcache again but I got the same errors. It also seems to be a problem with fsaverage. I do have a copy of fsaverage in the subject's directory of this study. I am attaching the log file with details about the errors.
Can someone help me sort this out?
Thank you, Mihaela
Hi Bruce,
I used that command and I got the same errors when I ran -qcache again. I also found that my colleague, who did the edits, used the same command after she manually edited the recons. I re-ran the subject with the following command recon-all -autorecon2-cp -autorecon3 -subjid <subject> and, when it was done, I ran -qcache again. It finished without errors.
I am not sure what is going on.
Best, Mihaela
On Thu, Jan 23, 2014 at 6:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Mihaela
usually that means the subject was partially but not completely rerun. You can try using recon-all -s <subject> -make all
and see if it fixes it cheers Bruce
On Thu, 23 Jan 2014, Mihaela Stefan wrote:
Hello FreeSurfers,
I am trying to run a group analysis with Qdec following thistutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnal ysis_freeview
I got a series of errors when I ran: recon-all -s <subjid> -qcache
.... ERROR: number of vertices in /home/subiculum/Desktop/local_recons/OCD_analysis/3662/surf/lh.volume does not match surface (126049,126592) ERROR: reading curvature file ...
mri_concat ./tmp.mris_preproc.6022/3662.1.mgh --o lh.volume.fsaverage.mgh mghRead(./tmp.mris_preproc.6022/3662.1.mgh, -1): could not open file ninputs = 1 Checking inputs ERROR: reading ./tmp.mris_preproc.6022/3662.1.mgh ...
Reading source surface reg/home/subiculum/Desktop/ local_recons/OCD_analysis/fsaverage/surf/lh.sphere. reg Loading source data ERROR: could not read lh.volume.fsaverage.mgh as type 3 Linux subiculum-Precision-T1650 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 3662 exited with ERRORS at Thu Jan 23 15:22:21 EST 2014
One of the errors says "number of vertices in... does not match surface." I found an older post where someone else was complaining about the same error and Doug suggested running "recon-all -surfvolume ..." https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012- September/025737 .html
I did that and then I ran -qcache again but I got the same errors. It also seems to be a problem with fsaverage. I do have a copy of fsaverage in the subject's directory of this study. I am attaching the log file with details about the errors.
Can someone help me sort this out?
Thank you, Mihaela
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.
it's possible that the timestamps on your system are wrong I guess. Did -make all run anything? On Fri, 24 Jan 2014, Mihaela Stefan wrote:
Hi Bruce, I used that command and I got the same errors when I ran -qcache again. I also found that my colleague, who did the edits, used the same command after she manually edited the recons. I re-ran the subject with the following command recon-all -autorecon2-cp -autorecon3 -subjid <subject> and, when it was done, I ran -qcache again. It finished without errors.
I am not sure what is going on.
Best, Mihaela
On Thu, Jan 23, 2014 at 6:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Mihaela
usually that means the subject was partially but not completely rerun. You can try using recon-all -s <subject> -make all and see if it fixes it cheers Bruce On Thu, 23 Jan 2014, Mihaela Stefan wrote: Hello FreeSurfers, I am trying to run a group analysis with Qdec followingthistutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroup Anal ysis_freeview I got a series of errors when I ran: recon-all -s <subjid> -qcache .... ERROR: number of vertices in /home/subiculum/Desktop/local_recons/OCD_analysis/3662/surf/lh.volume does not match surface (126049,126592) ERROR: reading curvature file ... mri_concat ./tmp.mris_preproc.6022/3662.1.mgh --o lh.volume.fsaverage.mgh mghRead(./tmp.mris_preproc.6022/3662.1.mgh, -1): could not open file ninputs = 1 Checking inputs ERROR: reading ./tmp.mris_preproc.6022/3662.1.mgh ... Reading source surfacereg/home/subiculum/Desktop/local_recons/OCD_analysis/fsaverage/surf/lh.sphe re. reg Loading source data ERROR: could not read lh.volume.fsaverage.mgh as type 3 Linux subiculum-Precision-T1650 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 3662 exited with ERRORS at Thu Jan 23 15:22:21 EST 2014 One of the errors says "number of vertices in... does not match surface." I found an older post where someone else was complaining about the same error and Doug suggested running "recon-all -surfvolume ..."https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-September/025737
.html I did that and then I ran -qcache again but I got the same errors. It also seems to be a problem with fsaverage. I do have a copy of fsaverage in the subject's directory of this study. I am attaching the log file with details about the errors. Can someone help me sort this out? Thank you, MihaelaThe 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.
Yes, -make all ran for about 7 hours and it exited without errors. How should I fix this?
What about -qcache after recon-all -autorecon2-cp -autorecon3 -subjid <subject>? Can I use that if it exited without errors? Can I assume that the subject has all the correct files and continue my analysis?
Thanks! Mihaela
On Fri, Jan 24, 2014 at 8:01 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
it's possible that the timestamps on your system are wrong I guess. Did -make all run anything?
On Fri, 24 Jan 2014, Mihaela Stefan wrote:
Hi Bruce,
I used that command and I got the same errors when I ran -qcache again. I also found that my colleague, who did the edits, used the same command after she manually edited the recons. I re-ran the subject with the following command recon-all -autorecon2-cp -autorecon3 -subjid <subject> and, when it was done, I ran -qcache again. It finished without errors.
I am not sure what is going on.
Best, Mihaela
On Thu, Jan 23, 2014 at 6:00 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Mihaela
usually that means the subject was partially but not completely rerun. You can try using recon-all -s <subject> -make all and see if it fixes it cheers Bruce On Thu, 23 Jan 2014, Mihaela Stefan wrote: Hello FreeSurfers, I am trying to run a group analysis with Qdec followingthistutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroup Anal ysis_freeview
I got a series of errors when I ran: recon-all -s <subjid> -qcache .... ERROR: number of vertices in /home/subiculum/Desktop/local_recons/OCD_analysis/3662/surf/lh.volume does not match surface (126049,126592) ERROR: reading curvature file ...
mri_concat ./tmp.mris_preproc.6022/3662.1.mgh --o lh.volume.fsaverage.mgh mghRead(./tmp.mris_preproc.6022/3662.1.mgh, -1): could not open file ninputs = 1 Checking inputs ERROR: reading ./tmp.mris_preproc.6022/3662.1.mgh ... Reading source surfacereg/home/subiculum/Desktop/local_recons/OCD_analysis/fsaverage/surf/lh.sphe re. reg Loading source data ERROR: could not read lh.volume.fsaverage.mgh as type 3 Linux subiculum-Precision-T1650 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 3662 exited with ERRORS at Thu Jan 23 15:22:21 EST 2014 One of the errors says "number of vertices in... does not match surface." I found an older post where someone else was complaining about the same error and Doug suggested running "recon-all -surfvolume ..."https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012- September/025737
.html I did that and then I ran -qcache again but I got the same errors. It also seems to be a problem with fsaverage. I do have a copy of fsaverage in the subject's directory of this study. I am attaching the log file with details about the errors. Can someone help me sort this out? Thank you, MihaelaThe 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.
yes, although why -make all didn't fix things is a mystery to me. On Fri, 24 Jan 2014, Mihaela Stefan wrote:
Yes, -make all ran for about 7 hours and it exited without errors. How should I fix this? What about -qcache after recon-all -autorecon2-cp -autorecon3 -subjid <subject>? Can I use that if it exited without errors? Can I assume that the subject has all the correct files and continue my analysis?
Thanks! Mihaela
On Fri, Jan 24, 2014 at 8:01 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: it's possible that the timestamps on your system are wrong I guess. Did -make all run anything? On Fri, 24 Jan 2014, Mihaela Stefan wrote:
Hi Bruce, I used that command and I got the same errors when I ran -qcache again. I also found that my colleague, who did the edits, used the same command after she manually edited the recons. I re-ran the subject with the following command recon-all -autorecon2-cp -autorecon3 -subjid <subject> and, when it was done, I ran -qcache again. It finished without errors. I am not sure what is going on. Best, Mihaela On Thu, Jan 23, 2014 at 6:00 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Mihaela usually that means the subject was partially but not completely rerun. You can try using recon-all -s <subject> -make all and see if it fixes it cheers Bruce On Thu, 23 Jan 2014, Mihaela Stefan wrote: Hello FreeSurfers, I am trying to run a group analysis with Qdec followingthistutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ QdecGroup Anal ysis_freeview I got a series of errors when I ran: recon-all -s <subjid> -qcache .... ERROR: number of vertices in /home/subiculum/Desktop/local_recons/OCD_analysis/3662/surf/lh.volume does not match surface (126049,126592) ERROR: reading curvature file ... mri_concat ./tmp.mris_preproc.6022/3662.1.mgh --o lh.volume.fsaverage.mgh mghRead(./tmp.mris_preproc.6022/3662.1.mgh, -1): could not open file ninputs = 1 Checking inputs ERROR: reading ./tmp.mris_preproc.6022/3662.1.mgh ... Reading sourcesurfacereg/home/subiculum/Desktop/local_recons/OCD_analysis/fsaverage/surf/ lh.sphe re. reg Loading source data ERROR: could not read lh.volume.fsaverage.mgh as type 3 Linux subiculum-Precision-T1650 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 3662 exited with ERRORS at Thu Jan 23 15:22:21 EST 2014 One of the errors says "number of vertices in... does not match surface." I found an older post where someone else was complaining about the same error and Doug suggested running "recon-all -surfvolume ..."https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-September/025737
.html I did that and then I ran -qcache again but I got the same errors. It also seems to be a problem with fsaverage. I do have a copy of fsaverage in the subject's directory of this study. I am attaching the log file with details about the errors. Can someone help me sort this out? Thank you, Mihaela 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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Mihaela Stefan