Hi Michael - Two things: First, in the dmrirc that you attached
previously, the bvecfile and bvalfile lines are commented out. Second,
these files need to be in column, not row format, as shown in the
tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps,
a.y
On Mon, 28 Oct 2013, Michael Datko wrote:
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/
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
<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
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