actually, on closer look, adding those lines to the FSL config did not fix the problem. However, if I call bet2 by typing fsl5.0-bet2, then it works. I am not sure why, but to call anything from fsl I have to first put fsl5.0- first.
On Tue, Apr 16, 2013 at 2:40 PM, Corinna Bauer <corinna...@gmail.com> wrote: > 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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