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 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. >
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