That's alright. I had to add these lines to my .bashrc file # get FSL config loaded if [ -f /usr/share/fsl/5.0/etc/fslconf/fsl.sh ]; then . /usr/share/fsl/5.0/etc/fslconf/fsl.sh; fi
but now, I get this error when running preproc-sess -per-run -fwhm 3 -force -so up -surface self lhrh -s . -d . -fsd bold -rlf symm_runs /usr/local/freesurfer/subjects/symmetry/functional mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/functional/lindsay_functional/mri/brainmask lindsay_functional/bold/006/tmp.bbregister.7574/fslregister/refvol.fslregister.nii On Tue, Apr 16, 2013 at 12:07 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>wrote: > 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 < > gr...@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 >> > >> > >> > >> > _______________________________________________ >> > 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. >> >> > >
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