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 <zkauf...@nmr.mgh.harvard.edu > <mailto:zkauf...@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 > <ayend...@nmr.mgh.harvard.edu > <mailto:ayend...@nmr.mgh.harvard.edu> > <mailto:ayend...@nmr.mgh.__harvard.edu > <mailto:ayend...@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> > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
