Hello, I installed XQuartz and the processing gets a little bit farther than it did before. However, I now run into an error about not being able to move the bvecs file. To my knowledge I specified the bvecs file correctly (in the same log file I attached previously), and it is in a format that has worked with other FSL programs in the past. Just in case, I have attached my bvecs and bvals files here if you want to verify. Any advice? Here are the last few lines of the log file before it quits:
fslswapdim /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dwi_orig.nii.gz x -y -z /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dwi_orig_flip.nii.gz mv -f /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dwi_orig_flip.mghdti.bvecs /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/bvecs mv: rename /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dwi_orig_flip.mghdti.bvecs to /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/bvecs: No such file or directory 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 Mon Oct 28 14:13:00 PDT 2013 On Mon, Oct 28, 2013 at 12:52 PM, Michael Datko <mikeda...@gmail.com> 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>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<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 >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >
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