If you just run bet2 (ie, /usr/lib/fsl/5.0/bin/bet2) outside of FS, do you still get the error? Can you use any of the other FSL commands?
On 07/04/2014 06:26 AM, Alan Lee wrote:
Hello freesurferers,
I ran this command (33333 is my subject name):
selxavg3-sess -a Retinotopy.33333.lh -s 33333
and got this error message:
# ---------- Using FSL's BET to Extract Brain------------------ # /usr/local/freesurfer/subjects/Retinotopy/33333/Retinotopy bet.fsl /tmp/mkbrainmask_14781/in.nii /tmp/mkbrainmask_14781/brain -m -f 0.1 /usr/lib/fsl/5.0/bin/bet2: error while loading shared libraries: libfslvtkio.so: cannot open shared object file: No such file or directory
It seems that something is wrong with the file libfslvtkio.so, or perhaps some path problem (I've manually set $FSLDIR to /usr/lib/fsl/5.0/). Any feedback would be greatly appreciated.
Below are the versions of software I'm using: Linux debian 3.2.0-4-486 #1 Debian 3.2.57-3+deb7u1 i686 GNU/Linux (run in virtualbox with a Windows 8 Host) FSL 5.0.6 freesurfer-Linux-centos4-stable-pub-v5.3.0
Many thanks, Alan
-- Alan Lee sites.google.com/site/alanlflee/ http://sites.google.com/site/alanlflee/
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