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Hello all, In order to get fsl5.0 to work on my Ubuntu 12.04 OS, I need to type fsl5.0- prior to any command (e.g. fsl5.0-fsl, fsl5.0-bet2, etc). Otherwise I get errors. When just using FSL, this isn't really a problem, but when I use a program that calls for FSL, such as Freesurfer, then I run into errors for loading shared libraries. I am attempting to processes fMRI data in Freesurfer, but keep getting this error: /usr/share/fsl/5.0/bin/bet2: error while loading shared libraries: libmeshclass.so: cannot open shared object file: No such file or directory. Below is my command line and the output until the first error. Any suggestions? Thanks, Corinna mkbrainmask-sess -maskstem brain -fsd bold -s lindsay_functional -d /usr/local/freesurfer/subjects/symmetry/functional -rlf symm_runs /usr/local/freesurfer/subjects/symmetry/functional/lindsay_functional Tue Apr 16 16:09:17 EDT 2013 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_12548 /usr/local/freesurfer/subjects/symmetry/functional/lindsay_functional/bold mri_convert template.nii.gz /tmp/mkbrainmask_12548/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_12548/in.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996119, -0.0108587, 0.0873391) j_ras = (0.000562893, 0.991553, 0.129698) k_ras = (0.0880098, -0.129244, 0.9877) writing to /tmp/mkbrainmask_12548/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /usr/local/freesurfer/subjects/symmetry/functional/lindsay_functional/bold bet.fsl /tmp/mkbrainmask_12548/in.nii /tmp/mkbrainmask_12548/brain -m -f 0.1 /usr/share/fsl/5.0/bin/bet2: error while loading shared libraries: libmeshclass.so: cannot open shared object file: No such file or directory mri_binarize --i /tmp/mkbrainmask_12548/brain_mask.nii --min .01 --o /tmp/mkbrainmask_12548/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_12548/brain_mask.nii