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 greve@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/%3E
On Mon, Jul 7, 2014 at 5:40 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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>
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