Re: [Freesurfer] -qcache / fsaverage / number of vertices errors

yes, although why -make all didn't fix things is a mystery to me. On Fri, 24 Jan 2014, Mihaela Stefan wrote:

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 fischl@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
        <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 sourcesurfacereg/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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