Hi Anna,
the instructions are correct, both FSLDIR and PATH get exported with
the 'export FSLDIR PATH' later...
Wrt to your and other people's problems:
on my system, bash runs both as the shell for terminal.app and as the
shell in xterm. You can check what shell you are running by typing
'echo $SHELL' in a new terminal.app or xterm window. Also, on my
system, /bin/sh is identical to /bin/bash
Once you establish that bash is running 2 things can happen:
if you run bash as a login shell the file .bash_profile should be
sourced automatically - if bash cant find .bash_profile it will
try .profile instead
if you run bash as a non-login shell, it should be also be
reading .bashrc
You should be able to test what shell is being sourced by simply
adding bogus environment variables (e.g. add export IN_BASH_PROFILE
to .bash_profile ) and checking if these exist after you launched a
shell ( env | grep BASH )
Provided this works correctly, you should then check (i) if FSLDIR
exists and is correct, (ii) if FSLDIR/etc/fslconf/fsl.sh was sourced
correctly ( "env | grep FSL" should return a long list of environment
variables) and (iii) if the PATH contains FSDLIR/bin ( echo $PATH )
If you want to run the GUIs, you'll also need to make sure that X11
runs correctly (after starting X11, open a shell and see if "xeyes"
works).
hope this helps
Christian
On 10 Aug 2006, at 18:14, Anna Barnes wrote:
> Hi
> I'm trying to install FSL on an apple cluster running OSX4.7
> configured with Inquiry (Bioteam.net) and I'm having problems.
>
> Can I confirm these install instructions for the .bash_profile in
> OSX.4.7
>
> FSLDIR=/usr/local/fsl
> . ${FSLDIR}/etc/fslconf/fsl.sh
> PATH=${FSLDIR}/bin:${PATH}
> export FSLDIR PATH
> export DISPLAY=localhost:0.0
>
> Shouldn't it read
>
> export FSLDIR=/usr/local/fsl
> . ${FSLDIR}/etc/fslconf/fsl.sh
> PATH=${FSLDIR}/bin:${PATH}
> export FSLDIR PATH
> export DISPLAY=localhost:0.0
>
> Has anyone had a problem running in bash on X11 OSX. I can get FSL
> to work in tcsh but not bash I just get a command not found error.
>
> The answer I guess is just to run in tcsh but I just was wondering
> why it wouldn't work.
>
> thanks
> Anna
>
>
>
>
> Anna Barnes, PhD
> fMRI Research Laboratory
> Department of Radiology
> Columbia University College of Physicians and Surgeons
> 710 W168th St
> New York, NY10032
> USA
> +1212 342 0293
>
>
--
Christian F. Beckmann
Oxford University Centre for Functional
Magnetic Resonance Imaging of the Brain,
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/~beckmann/
Phone: +44(0)1865 222551 Fax: +44(0)1865 222717
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