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 <fischl@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




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