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> 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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