Can you tell us which build of freesurfer you're using (should be in trac-all.log) and what version of OSX you have this installed in?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
Awesome. I overlooked that. It worked but now I get this error/image not found. Should I attach something else?
fslswapdim /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz x z -y /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz fslorient -forceradiological /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz tkregister2 --mov /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat_orig.nii.gz --targ /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anatorig2anat.mat --reg /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/anat2anatorig.dat dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer//tktools/tkregister2.bin Reason: image not found Trace/BPT trap ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 4:19 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - The files should be one row per DWI volume. See example here, under "Specify the diffusion-encoding gradient table" and "Specify the b-value table": http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps, a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
I attached the file above.
For the configuration problem, I actually just installed freesurfer onto one of our newer macs and it seemed to work fine. I was running it on an older linux version of freesurfer. Still couldnt figure the issue on the linux though for the config file. ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:35 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - My guess is that it's something about the file dmri/dwi_orig.mghdti.bvals that's causing the error. Could you please send along that file?
Also, how did you fix your previous configuration file problem? Letting the list know about the resolution of the issue would help other users, who may have the same issue in the future and search the list archives. It'll also help me figure out if there are any checks I could add to trac-all to preclude this.
Thanks! a.y
On Tue, 9 Jul 2013, Gundran, Andrew wrote:
Helo all,
I was finally able to figure out my configuration file problem. But when I run the first step of pre-processing I receive an error about freesurfer being unable to read a certain dwi_frame file.
ln -sf /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi.nii.gz /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.nii.gz awk: can't open file 1000 source line number 1 mri_concat --i /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz --mean --o /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.nii.gz niiRead(): error opening file /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_frame.nii.gz Darwin Wayne-Feng-s-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
I have also attached the trac-all log.
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