The commands in .bash_profile need to be run before you try to execute any of the FSL commands. Assuming you've checked to make sure that a new shell isn't correctly configured (start a new shell and see if, say, Feat works) then you need to copy the FSL setup lines into your shell's startup file so it is run for each new shell. That should do it.

On 27 Sep 2011, at 16:53, Supreet kaur wrote:

> Hi Dave,
>                  I just entered . .bash_profile in my terminal window, then a fish-bone window popped up
> and then changed into FSLVIEW (3.1.8) plane window with file, tools, window on top..
> Is it the actual fsl window ?? is it ready to go now?
>
> I'll appreciate your feedback on this.
> Thanks
> Supreet kaur
> Biomedical engineer,
> Nationwide Childrens Hospital,
> Columbus, OH
> (614)355-3509
>
> On Tue, Sep 27, 2011 at 11:41 AM, David Flitney <[log in to unmask]> wrote:
> Perhaps your .bash_profile isn't being sourced during your login? Try the following:
>
> . .bash_profile
>
> Note. That is "dot space dot bash_profile"
> then try...
>
> fslview
>
>
> On 27 Sep 2011, at 16:38, Supreet kaur wrote:
>
> > Hello Kay,
> >                    Thanks for your prompt reply. When I try to input the commands in the terminal window for fsl GUI, it doen't
> > open up the FSL GUI (with the fish bone). Please see my commands below:
> >
> > [fsl@localhost fsldoc]$ fslview
> > bash: fslview: command not found
> > [fsl@localhost fsldoc]$
> >  your help will be appreciated.
> > Thanks,
> > Supreet
> >
> > On Tue, Sep 27, 2011 at 11:34 AM, Benjamin Kay <[log in to unmask]> wrote:
> > On Tuesday, September 27, 2011 11:15:01 you wrote:
> > > Dear fsl experts,
> > >                           I am having a FSL installation problem and have
> > > been struggling hard since last week..
> > > I have downloaded the VMware virtual environment. And it has installed
> > > fsl-4.1.8-centos5_32.tar.gz file and fsl installer.sh
> > > its desktop. But once i try to install the FSL , it gives me an error
> > > commands as shown:
> > >
> > > [fsl@localhost fsldoc]$ bash fsl_installer.sh
> > > FSL install script
> > > ==================
> > >
> > > Looking for FSL tarball in the current directory...
> > > ***************************************************************
> > > No FSL tarball specified, assuming you want me to install
> > > /home/fsl/Desktop/fsldoc/fsl-4.1.8-centos5_32.tar.gz
> > > from the current directory.
> > > ***************************************************************
> > >
> > > Where would you like to install FSL to? [/usr/local] /home/fsl/
> > >
> > > Checking OS release ...
> > > [OK]
> > > Checking CPU type...
> > > [OK]
> > > Checking install file...(this may take several minutes)
> > > [Skipped]
> > > Installing FSL from /home/fsl/Desktop/fsldoc/fsl-4.1.8-centos5_32.tar.gz
> > > into /home/fsl/...
> > > [OK]
> > > Patching environment
> > > .bash_profile already contains a FSLDIR definition which is wrong.\nFixing
> > > FSLDIR configuration...
> > > '/home/fsl/.bash_profile' updated with new FSLDIR definition.
> > > [fsl@localhost fsldoc]$
> > > Your help will be highly appreciated
> >
> > It looks like installation failed during a previous attempt but worked this
> > time. Have you tried running any fsl commands to see if they work? If you
> > simply run "fsl" from the commandline you ought to get an GUI.
> >
> >
> >
> > --
> > Sincerely,
> >
> > Supreet kaur
> >
>
> --
> Dave Flitney, IT Manager
> Oxford Centre for Functional MRI of the Brain
> E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717
> URL: http://www.fmrib.ox.ac.uk/~flitney
>
>
>
> --
> Sincerely,
>
> Supreet kaur
>

--

Dave Flitney, IT Manager
Oxford Centre for Functional MRI of the Brain
E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717
URL: http://www.fmrib.ox.ac.uk/~flitney