Hi,
A serious error was encountered in running recon-all with option -qcache. The error occurred during execution of mri_surf2surf and the message was:
number of vertices in ....../subjectID/surf/lh.thickness does not match surface (141969,131763).
It means the number of vertices in lh.sphere.reg does not match the number in lh.thickness.
I traced the course of this error and that is causing me serious troubles. What happened? I edited the wm voxels and then invoked another call to recon-all by issueing the command recon-all -autorecon2-wm. Looking at the dates of the files in the surf directory I noticed that the file lh.sphere.reg was not updated, so it was still the same file as before editing the wm voxels. The lh.thickness was correctly updated as expected.
What can I do to use the -qcache option?
Ed
Hi Ed, that subject is out-of-synch (maybe it got aborted). You'll need to re-run some portion of recon-all depending upon where in the stream it aborted.
doug
Ed Gronenschild wrote:
Hi,
A serious error was encountered in running recon-all with option -qcache. The error occurred during execution of mri_surf2surf and the message was:
number of vertices in ....../subjectID/surf/lh.thickness does not match surface (141969,131763).
It means the number of vertices in lh.sphere.reg does not match the number in lh.thickness.
I traced the course of this error and that is causing me serious troubles. What happened? I edited the wm voxels and then invoked another call to recon-all by issueing the command recon-all -autorecon2-wm. Looking at the dates of the files in the surf directory I noticed that the file lh.sphere.reg was not updated, so it was still the same file as before editing the wm voxels. The lh.thickness was correctly updated as expected.
What can I do to use the -qcache option?
Ed
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Indeed, you are right, I forgot to run recon-all -autorecon3.
It is not well documented that after running -autorecon2-wm one should also run -autorecon3. I had the impression that this portion was executed automatically by -autorecon2-wm.
Ed
On 2 Feb 2011, at 18:03, Douglas N Greve wrote:
Hi Ed, that subject is out-of-synch (maybe it got aborted). You'll need to re-run some portion of recon-all depending upon where in the stream it aborted.
doug
Ed Gronenschild wrote:
Hi,
A serious error was encountered in running recon-all with option -qcache. The error occurred during execution of mri_surf2surf and the message was:
number of vertices in ....../subjectID/surf/lh.thickness does not match surface (141969,131763).
It means the number of vertices in lh.sphere.reg does not match the number in lh.thickness.
I traced the course of this error and that is causing me serious troubles. What happened? I edited the wm voxels and then invoked another call to recon-all by issueing the command recon-all -autorecon2-wm. Looking at the dates of the files in the surf directory I noticed that the file lh.sphere.reg was not updated, so it was still the same file as before editing the wm voxels. The lh.thickness was correctly updated as expected.
What can I do to use the -qcache option?
Ed
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Thanks for the suggestion Ed. I've just added the text below to http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Troubleshooting. If you know of another place where it would be useful, please let us know.
doug
"Note that after you run recon-all with the -autorecon2-wm flag, you will still need to run it with the -autorecon3 flag. You can run it with both -autorecon2-wm and -autorecon3, though if the changes you made did not fix the problem, then the time spent running autorecon3 will be wasted."
Ed Gronenschild wrote:
Hi Doug,
Indeed, you are right, I forgot to run recon-all -autorecon3.
It is not well documented that after running -autorecon2-wm one should also run -autorecon3. I had the impression that this portion was executed automatically by -autorecon2-wm.
Ed
On 2 Feb 2011, at 18:03, Douglas N Greve wrote:
Hi Ed, that subject is out-of-synch (maybe it got aborted). You'll need to re-run some portion of recon-all depending upon where in the stream it aborted.
doug
Ed Gronenschild wrote:
Hi,
A serious error was encountered in running recon-all with option -qcache. The error occurred during execution of mri_surf2surf and the message was:
number of vertices in ....../subjectID/surf/lh.thickness does not match surface (141969,131763).
It means the number of vertices in lh.sphere.reg does not match the number in lh.thickness.
I traced the course of this error and that is causing me serious troubles. What happened? I edited the wm voxels and then invoked another call to recon-all by issueing the command recon-all -autorecon2-wm. Looking at the dates of the files in the surf directory I noticed that the file lh.sphere.reg was not updated, so it was still the same file as before editing the wm voxels. The lh.thickness was correctly updated as expected.
What can I do to use the -qcache option?
Ed
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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@nmr.mgh.harvard.edu
-
Douglas N Greve -
Ed Gronenschild