I think that there must be a problem with your FSL install. I hate to pass the buck, but did you contact the FSL list? doug
On 07/13/2014 01:36 PM, Alan Lee wrote: > Hi Doug, > > When I run the following: > /usr/lib/fsl/5.0/bin/bet2 > > it gives me the following error: > bet2: error while loading shared libraries: libfslvtkio.so: cannot > open shared object file: No such file or directory > > When I run > fsl > > it says > fsl: Command not found. > > However, the command > fslview > > works and brings up a FSLviewer GUI, though it's the version of 4.0.1 > (not 5.0). > > I tried typing "fsl" then hit the TAB key, and it seems that there're > a lot of available commands that need to be run as > fsl5.0-___ > > e.g., when I run > fsl5.0-bet2 > > It shows the help for the bet2 function (because I didn't run it with > the correct arguments, I suppose): > > Part of FSL (build 506) > BET (Brain Extraction Tool) v2.1 - FMRIB Analysis Group, Oxford > > Usage: > bet2 <input_fileroot> <output_fileroot> [options] > > Optional arguments (You may optionally specify one or more of): > -o,--outlinegenerate brain surface outline overlaid onto original image > -m,--maskgenerate binary brain mask > -s,--skullgenerate approximate skull image > -n,--nooutputdon't generate segmented brain image output > -f <f>fractional intensity threshold (0->1); default=0.5; smaller > values give larger brain outline estimates > -g <g>vertical gradient in fractional intensity threshold (-1->1); > default=0; positive values give larger brain outline at bottom, > smaller at top > -r,--radius=<r>head radius (mm not voxels); initial surface sphere is > set to half of this > -w,--smooth=<r>smoothness factor; default=1; values smaller than 1 > produce more detailed brain surface, values larger than one produce > smoother, less detailed surface > -c <x y z>centre-of-gravity (voxels not mm) of initial mesh surface. > -t,--threshold-apply thresholding to segmented brain image and mask > -e,--meshgenerates brain surface as mesh in vtk format > -v,--verboseswitch on diagnostic messages > -h,--helpdisplays this help, then exits > > All these make me think that there's something wrong with my FSL > installation. Should I uninstall it and reinstall it again? Any advice > on this? > > Thanks, > Alan > > > > > > -- > Alan Lee > sites.google.com/site/alanlflee/ <http://sites.google.com/site/alanlflee/> > > > On Mon, Jul 7, 2014 at 5:40 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > 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/> > <http://sites.google.com/site/alanlflee/> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto: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. > > > > > _______________________________________________ > 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
