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,--outline generate brain surface outline overlaid onto original image -m,--mask generate binary brain mask -s,--skull generate approximate skull image -n,--nooutput don'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,--mesh generates brain surface as mesh in vtk format -v,--verbose switch on diagnostic messages -h,--help displays 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/
On Mon, Jul 7, 2014 at 5:40 PM, Douglas N Greve 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/%3E
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