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
> -o,--outlinegenerate brain surface outline overlaid onto original image
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):
> -m,--maskgenerate binary brain mask> -n,--nooutputdon't generate segmented brain image output
> -s,--skullgenerate approximate skull image
> -f <f>fractional intensity threshold (0->1); default=0.5; smaller> -t,--threshold-apply thresholding to segmented brain image and mask
> 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.
> -e,--meshgenerates brain surface as mesh in vtk format
> -v,--verboseswitch on diagnostic messages
> -h,--helpdisplays this help, then exits
>> sites.google.com/site/alanlflee/ <http://sites.google.com/site/alanlflee/>
> 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
>
>
> On Mon, Jul 7, 2014 at 5:40 PM, Douglas N Greve
> <mailto:Freesurfer@nmr.mgh.harvard.edu>> <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
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> 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>
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> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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> Outgoing:> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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
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