Hm, it seems like all FSL commands give you a shared library error. Were
you able to run FSL commands properly before updating freesusrfer?
On Thu, 18 Aug 2011, Carolina Valencia wrote:
Hi,After update the FS version to 5.1, I follow the Tracula tutorial and run
the command
trac-all -prep -c
$TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject
It starts to run but finish with errors:
writing
to/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial/Diff001/dmri/dwi_orig.nii.gz...
Saving bvals and bvecs
mri_probedicom
--i/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial//Diff001/orig/6-1.dcm
>/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial/Diff001/dmri/dcminfo.dat
flip4fsl/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial/Diff001/dmri/dwi_orig.nii.gz/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial/Diff001/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 8
fslswapdim/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial/Diff001/dmri/dwi_orig.nii.gz x -y
z/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial/Diff001/dmri/dwi_orig_flip.nii.gz
fslorient
-forceradiological/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial/Diff001/dmri/dwi_orig_flip.nii.gz
fslorient: error while loading shared libraries: libnewimage.so: cannot open
shared object file: No such file or directory
INFO:
found/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial/Diff001/dmri/dwi_orig.mghdti.bvals, converting to FSL format
INFO:
found/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial/Diff001/dmri/dwi_orig.mghdti.bvecs, converting to FSL format
mv -f/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial/Diff001/dmri/dwi_orig_flip.mghdti.bvecs/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial/Diff001/dmri/bvecs
mv -f/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial/Diff001/dmri/dwi_orig_flip.mghdti.bvals/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial/Diff001/dmri/bvals
eddy_correct/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial/Diff001/dmri/dwi_orig_flip.nii.gz/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto
rial/Diff001/dmri/dwi.nii.gz 0
fslroi: error while loading shared libraries: libnewimage.so: cannot open
shared object file: No such file or directory
fslsplit: error while loading shared libraries: libnewimage.so: cannot open
shared object file: No such file or directory
fslmerge: error while loading shared libraries: libnewimage.so: cannot open
shared object file: No such file or directory
/bin/rm: no se puede
borrar«/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tut
orial/Diff001/dmri/dwi_tmp????.*»: No existe el fichero o el directorio
/bin/rm: no se puede
borrar«/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tut
orial/Diff001/dmri/dwi_ref*»: No existe el fichero o el directorio
Linux cvalencia-Precision-WorkStation-T3400 2.6.35-30-generic-pae #56-Ubuntu
SMP Mon Jul 11 21:51:12 UTC 2011 i686 GNU/Linux
trac-preproc exited with ERRORS at jue ago 18 10:54:43 COT 2011
any suggestions??
Thanks,
Carolina
2011/8/16 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>
Hi Carolina - There's info on the new release and how to install
it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
a.y
On Tue, 16 Aug 2011, Carolina Valencia wrote:
Hi FS'users,
I'm trying to do the Tracula tutorial but after set the
configuration file I
run the command trac-all
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/Tracula_Tutoria
l
_Public/diffusion_tutorial> trac-all -help
trac-all: Command not found.
I have the version:
freesurfer-Linux-centos4-stable-pub-v5.0.0.
How I update the to version 5.1? What I have to fix to run
trac-all command?
Thanks,
Best regards
Carolina
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