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 <fis...@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 <fis...@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, >> 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 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.
