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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
