The XQuartz website you linked makes it sound like it is identical to X11, is it different in some way?  I have X11 already and it works flawlessly with other applications such as AFNI and FSL.  

On Mon, Oct 28, 2013 at 12:36 PM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:

Mike,

You need to install XQuartz:
http://xquartz.macosforge.org/landing/

Also see the following troubleshooting page:
http://ftp.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_troubleshooting

-Zeke

On 10/28/2013 03:17 PM, Michael Datko wrote:

Hi Anastasia,
I've attached my configuration file, and below is pasted the contents of
the error log.  Below that, I've pasted the last few lines of the
trac-all log (not the error log), because it says something about a
"dyld" that cannot be loaded...might be related to the problem.

Thanks,
Mike

from error log:

------------------------------
SUBJECT 226A
DATE Tue Oct 15 18:38:18 PDT 2013
USER mdatko
HOST captain-cosine.local
PROCESSOR i386
OS Darwin
Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun
  7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
$Id: trac-preproc,v 1.17.2.8 2013/02/16 20:57:05 ayendiki Exp $
/Applications/freesurfer/bin/trac-preproc
PWD /Users/mdatko/Desktop
CMD mri_probedicom --i /Users/mdatko/Desktop/226A/dti/i00001.CFMRI.1

Last few lines from non-error log:

mri_probedicom --i /Users/mdatko/Desktop/226A/dti/i00001.CFMRI.1 >
/Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dcminfo.dat
dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib
   Referenced from: /Applications/freesurfer/bin/mri_probedicom
   Reason: image not found
Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun
  7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386

trac-preproc exited with ERRORS at Tue Oct 15 18:38:18 PDT 2013






On Tue, Oct 22, 2013 at 8:04 AM, Anastasia Yendiki

<ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> wrote:


    Hi Mike - I'll need to see the configuration file and trac-all.log.

    Thanks,
    a.y

    On Mon, 21 Oct 2013, Michael Datko wrote:

        Hello,I am running into a tracula error very early in the
        preprocessing steps.

          I have data that was already somewhat preprocessed
        (reconstruction, eddy
        correction and magnetic field inhomogeneity correction) that I'm
        trying to use
        as an input.  I have turned off those steps in the tracula
        configuration file.
          Tracula seems to find these files and starts making a few of
        the dwi output
        files in the subject's freesurfer/dmri folder.  However, it then
        says
        something about not having the correct "frames" and it can't
        find the file
        dwi_frames.nii.gz.  I'm not sure what this error is referring
        to.  I attempted
        to run the same subject's data from their raw dicoms instead of the
        slightly-preprocessed file and also ran into errors.  If it makes a
        difference, the subject had recon-all performed with freesurfer
        version 5.0
        and I am now using version 5.3.  Perhaps the subject is missing
        some necessary
        recon-all output that is only created with 5.3?  Any advice?

        Thanks,
        Mike Datko





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