Hi Corinna, I hate to pass the buck, but I think you'll have to contact the FSL people to get it sorted out.
doug

On 4/16/13 9:31 AM, Corinna Bauer wrote:

Yes, if I just type bet2 I still get: libmeshclass.so: cannot open shared object file: No such file or directory.

On Fri, Apr 12, 2013 at 4:07 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Hi Corinna, if you just run bet2 at the command line, do you get the
same error?
doug

On 04/12/2013 03:56 PM, Corinna Bauer wrote:
> Hello all, when running preproc-sess, I got this error message:
> ERROR: could not determine file for
> /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold/masks/brain
> Try running mkbrainmask-sess with -per-run
>
> I then ran the mkbrainmask-sess as follows (kbrainmask-sess -s . -d .
> -fsd bold
> m) and got the output below, which shows a problem with a shared library?
>
> Any suggestions?
>
> Corinna
>
> ------------------------------------------------
> /usr/local/freesurfer/subjects/symmetry/lindsay/first_test
> Fri Apr 12 15:53:14 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_9634
> /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
> mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii
> mri_convert template.nii.gz /tmp/mkbrainmask_9634/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_9634/in.nii...
> # ---------- Using FSL's BET to Extract Brain------------------ #
> /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
> bet.fsl /tmp/mkbrainmask_9634/in.nii /tmp/mkbrainmask_9634/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_9634/brain_mask.nii --min .01 --o
> /tmp/mkbrainmask_9634/brain_mask.nii
> niiRead(): error opening file /tmp/mkbrainmask_9634/brain_mask.nii
>
> $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
> cwd /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
> cmdline mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min
> .01 --o /tmp/mkbrainmask_9634/brain_mask.nii
> sysname  Linux
> hostname lotfi
> machine  x86_64
> user     bauer
>
> input      /tmp/mkbrainmask_9634/brain_mask.nii
> frame      0
> nErode3d   0
> nErode2d   0
> output     /tmp/mkbrainmask_9634/brain_mask.nii
> Binarizing based on threshold
> min        0.01
> max        +infinity
> binval        1
> binvalnot     0
>
>
>

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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