consult this page: http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems

typically the problem is resolved by upgrading the nvidia driver (assuming you have such a graphics card).

n.

On Fri, 2010-09-17 at 15:17 -0700, Pradeep wrote:

Hello Nick,

The data_check program works after some minor fixes.

I now a have problem with tksurfer on our server

The recon-all step ran with out any errors

But tksurfer AD_C165 lh smoothwm displays only a part of the image and dose not give any error messages.

Machine Details: x86_64 GNU/Linux FreeSurefer Version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0

So i downloaded the images to another computer and the display is good here.

Machine Details: i686 GNU/Linux FreeSurfer Version: freesurfer-Linux-centos4-stable-pub-v5.0.0

Any suggestions on this would be greately appreciated.

Thanks, Pradeep

On Thu, Sep 16, 2010 at 5:32 PM, Pradeep tpradeep@gmail.com wrote: Thanks for letting us know.

    Is there any other way to do the QA in batch ?

    Thanks,
    Pradeep

    On Thu, Sep 16, 2010 at 3:52 PM, Nick Schmansky

    <nicks@nmr.mgh.harvard.edu> wrote:
    > sorry, this is no longer supported.  it was created by an ra
    who left
    > the center a few years ago.  i suppose i should have
    mentioned that in
    > my original email.
    >
    > n.
    >
    > On Thu, 2010-09-16 at 15:51 -0700, Pradeep wrote:
    >> Hell Nick,
    >>
    >> Looks like the recon_checker has some problems to fix
    >>
    >> Below is my log file.
    >>
    >> ############
    >> surf/rh.sphere surf/rh.sphere.reg surf/rh.lh.sphere.reg
    >> surf/rh.avg_curv label/rh.aparc.annot stats/rh.aparc.stats
    >> label/rh.aparc.a2005s.annot mri/aparc+aseg
    >> .mgz
    >> check to see if all files exist...
    >> AD_C165 missing output files
    >> AD_C165 has no surf/lh.rh.sphere.reg
    >>
    >> In recon_all_status_log_checker
    >>
    >>
    WARNING: /working/pthiyyagura/freesurfer/data_checker/data_checker/sample-recon-all-status.log
    >> does not exist. Skipping this
    >> complete status log file...
    >>
    >> #############
    >>
    >>
    >> Its looking for lh.rh.sphere.reg. which would not exist.
    >> Could you please look into this.
    >>
    >> Thanks,
    >> Pradeep
    >>
    >> P.S also please chage
    >> set scriptsDir =
    >>
    >>
    >>
    >>
    >>
    >>
    >>
    >> On Thu, Sep 16, 2010 at 11:41 AM, Nick Schmansky
    >> <nicks@nmr.mgh.harvard.edu> wrote:
    >> > see also this page:
    >> >
    >> > http://surfer.nmr.mgh.harvard.edu/fswiki/QATools
    >> >
    >> > On Thu, 2010-09-16 at 14:13 -0400, Bruce Fischl wrote:
    >> >> Hi Avram,
    >> >>
    >> >> that all souds reasonable to me.
    >> >>
    >> >> cheers
    >> >> Bruce
    >> >> On Thu, 16 Sep 2010, Avram Holmes wrote:
    >> >>
    >> >> > All,
    >> >> >
    >> >> > I'm setting up a processing stream for a sizable
    dataset and I'd like
    >> >> > to use .tcl scripts to save out images for some
    preliminary quality
    >> >> > control checks. It was my intention to output images
    of the the
    >> >> > curvature and structural parcelation overlaid on the
    inflated surface
    >> >> > (6 views for each hemi) and the lh/rh.white and
    aseg.mgz segmentation
    >> >> > overlaid on the volume (a midline coronal, sagital,
    and axial slice).
    >> >> > The idea would be that then we could go through and
    quickly check
    >> >> > which subjects may need manual intervention.
    >> >> >
    >> >> > I wanted to double check that the images I am saving
    out are
    >> >> > consistent with the checks that other folks are doing
    and I'd love to
    >> >> > get some feedback on what else I should look save.
    >> >> >
    >> >> > Thanks,
    >> >> > Avram
    >> >> >
    >> >> >
    >> >> _______________________________________________
    >> >> Freesurfer mailing list
    >> >> Freesurfer@nmr.mgh.harvard.edu
    >> >>
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    >> >>
    >> >>
    >> >
    >> > _______________________________________________
    >> > Freesurfer mailing list
    >> > Freesurfer@nmr.mgh.harvard.edu
    >> >
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    >> >
    >> >
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    >





    --
    Pradeep Thiyyagura
    Research Assistant
    School of Mathematical and Statistical Sciences
    Graduate Student
    Computational Biosciences
    Arizona State University
    Tempe, AZ 85287-1804
    Pradeep.Thiyyagura@asu.edu

-- Pradeep Thiyyagura Research Assistant School of Mathematical and Statistical Sciences Graduate Student Computational Biosciences Arizona State University Tempe, AZ 85287-1804 Pradeep.Thiyyagura@asu.edu