If you just run bet2 (ie, /usr/lib/fsl/5.0/bin/bet2) outside of FS, do you still get the error? Can you use any of the other FSL commands?
On 07/04/2014 06:26 AM, Alan Lee wrote: > Hello freesurferers, > > I ran this command (33333 is my subject name): > > selxavg3-sess -a Retinotopy.33333.lh -s 33333 > > and got this error message: > > # ---------- Using FSL's BET to Extract Brain------------------ # > /usr/local/freesurfer/subjects/Retinotopy/33333/Retinotopy > bet.fsl /tmp/mkbrainmask_14781/in.nii /tmp/mkbrainmask_14781/brain -m > -f 0.1 > /usr/lib/fsl/5.0/bin/bet2: error while loading shared libraries: > libfslvtkio.so: cannot open shared object file: No such file or directory > > > It seems that something is wrong with the file libfslvtkio.so, or > perhaps some path problem (I've manually set $FSLDIR to > /usr/lib/fsl/5.0/). Any feedback would be greatly appreciated. > > Below are the versions of software I'm using: > Linux debian 3.2.0-4-486 #1 Debian 3.2.57-3+deb7u1 i686 GNU/Linux (run > in virtualbox with a Windows 8 Host) > FSL 5.0.6 > freesurfer-Linux-centos4-stable-pub-v5.3.0 > > > Many thanks, > Alan > > > > -- > Alan Lee > sites.google.com/site/alanlflee/ <http://sites.google.com/site/alanlflee/> > > > _______________________________________________ > 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.
