Hi Alan, I can guess there are several problems here with your fsl installation. Are you on Neurodebian? For some historical reasons fsl5.0-command format for usual fsl commands were used so that when people wanted to use both fsl 4 and 5 at the time there wouldn't be any confusion. Anyway you can make the prefix of 'fsl5.0' go away by this command
source /usr/share/fsl/5.0/etc/fslconf/fsl.sh If it works put it in your .bashrc file. Hope this helps, Arman On Mon, Jul 14, 2014 at 9:55 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > 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 >
_______________________________________________ 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.
