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 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> . 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.
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