New subject: Tracula problem in pre-processing

16 Jul 2013


      Yes. Does the file $FREESURFER_HOME/bin/flirt.fsl exist?
On Tue, 16 Jul 2013, Gundran, Andrew wrote:
...
I've been doing that but I still get that same error...
source $FREESURFER_HOME/SetUpFreeSurfer.csh right?
-----Original Message-----
From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu]
Sent: Tuesday, July 16, 2013 4:42 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Tracula problem in pre-processing
You're very welcome. The error is for flirt.fsl, which is a copy of flirt included in the freesurfer distribution. So if you want to use that, you'll need to source the freesurfer setup script as usual. (You wouldn't need to if you were using flirt from the fsl distribution.)
On Tue, 16 Jul 2013, Gundran, Andrew wrote:
...
And that worked. Great news...another error this time with FSL's flirt. I'm a bit confused on that one since I use FSL a bit within a terminal. I didnt think I had to setenv for it?
flirt.fsl -ref
/Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bb
register.34704/fslregister/refvol.fslregister.nii -in
/Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bb
register.34704/fslregister/movvol.fslregister.nii -bins 256 -cost
corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90
-verbose 0 -omat
/Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bb
register.34704/fslregister/fslmat0.trans.mat -schedule
/usr/local/fsl/etc/flirtsch/xyztrans.sch -init
/Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/tmp.bb
register.34704/reg.init.dat.fsl.mat0
flirt.fsl: Command not found.
ERROR: flirt
Thanks so much for your patience!

From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu]
Sent: Tuesday, July 16, 2013 11:28 AM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Tracula problem in pre-processing
Hi Andrew - Try installing XQuartz:
       http://xquartz.macosforge.org/landing/
a.y
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
...
build-stamp.txt: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
________________________________________
From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 5:20 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Tracula problem in pre-processing
Can you please check for a line that says "build-stamp" in the log
that tells you which freesurfer build you used?
On Mon, 15 Jul 2013, Gundran, Andrew wrote:
...
From the log I found this
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
And mac osx 10.6.8
________________________________________
From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu]
Sent: Monday, July 15, 2013 4:51 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Tracula problem in pre-processing
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_an
at_orig.nii.gz x z -y
/Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_an
at.nii.gz fslorient -forceradiological
/Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_an
at.nii.gz
tkregister2 --mov
/Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_an
at_orig.nii.gz --targ
/Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/brain_an
at.nii.gz --regheader --noedit --fslregout
/Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/ana
torig2anat.mat --reg
/Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/xfms/ana
t2anatorig.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.ni
> i.gz
> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/data.n
> ii.gz
> awk: can't open file 1000
> source line number 1
> mri_concat --i
> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_fr
> ame.nii.gz --mean --o
> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/lowb.n
> ii.gz
> niiRead(): error opening file
> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_fr
> ame.nii.gz
> ninputs = 1
> Checking inputs
> ERROR: reading
> /Users/WayneFeng/Desktop/JG005/JG005/JG005/freesurfer/dmri/dwi_fr
> ame.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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