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
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