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 >> gr...@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 > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
