Re: [Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

2013-10-28 Thread Anastasia Yendiki
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

Re: [Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

2013-10-28 Thread Z K
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 sym

Re: [Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

2013-10-28 Thread Michael Datko
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 h

Re: [Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

2013-10-28 Thread Michael Datko
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 wrote: > Mike, > > You need to install XQuartz: > http://xquart

Re: [Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

2013-10-28 Thread Z K
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,

Re: [Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

2013-10-28 Thread Michael Datko
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

Re: [Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

2013-10-22 Thread Anastasia Yendiki
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 mag

[Freesurfer] Tracula preprocessing error: cannot find dwi_frames.nii.gz

2013-10-21 Thread Michael Datko
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 configu