Re: [Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

Im of the understanding that X11 and XQuartz will not conflict. Many users running Mac OSX Snow Leopard have both applications installed on their systems. But if you are extremely weary of potential issues than I suppose you could create a symbolic link from /opt/X11 to /usr/X11. Additional symlinks may be required tho, which should be easily determined based on the error message obtained.

-Zeke

On 10/28/2013 03:52 PM, Michael Datko wrote:

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 mailto:zkaufman@nmr.mgh.harvard.edu> wrote:

Mike,

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

Also see the following troubleshooting page:
http://ftp.nmr.mgh.harvard.__edu/fswiki/freesurfer_GUIs___troubleshooting
<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>
    <mailto: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





         The information in this e-mail is intended only for the
    person to
         whom it is
         addressed. If you believe this e-mail was sent to you in
    error and
         the e-mail
         contains patient information, please contact the Partners
    Compliance
         HelpLine at
    http://www.partners.org/____complianceline
    <http://www.partners.org/__complianceline>

         <http://www.partners.org/__complianceline
    <http://www.partners.org/complianceline>> . If the e-mail was
    sent to
         you in error
         but does not contain patient information, please contact
    the sender
         and properly
         dispose of the e-mail.




    _________________________________________________
    Freesurfer mailing list
    Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
    https://mail.nmr.mgh.harvard.__edu/mailman/listinfo/__freesurfer
    <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>