# ---------- Using FSL's BET to Extract Brain------------------ #
/media/sf_fMRI_data/scans/33333/func/retino/preprocessed/Retinotopy/33333/Retinotopy
bet.fsl /tmp/mkbrainmask_7812/in.nii /tmp/mkbrainmask_7812/brain -m -f 0.1
/usr/share/fsl/5.0/bin/bet2: error while loading shared libraries: libfslvtkio.so: cannot open shared object file: No such file or directory
mri_binarize --i /tmp/mkbrainmask_7812/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7812/brain_mask.nii
niiRead(): error opening file /tmp/mkbrainmask_7812/brain_mask.nii
It seems that there's a problem running bet2. I tried typing bet2 in the terminal and got this error message:
bet2: error while loading shared libraries: libfslvtkio.so: cannot open shared object file: No such file or directory
I looked through some FSL/FreeSurfer forum messages and it seems to be a problem related to $FSLDIR. My $FSLDIR has been set to (I got this when I echo $FSLDIR):
/usr/share/fsl/5.0
Is this correct? Or do I need to set some other variables? Or the problem is actually something else? I also found some message about a varibale called LD_LIBRARY_PATH, which I don't know is relevant or not...
Any help would be greatly appreciated!
Thanks,
Alan
