I am curious what OS requires you to type 'module load' before an executable
file name. You can just type fslmaths, or fslstats by themselves. If you
get a command not found, this means you have not sourced the FSL config file
yet. You should add the following to your .bashrc file:
FSLDIR=/usr/local/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
Make sure the first line points to where you actually installed FSL. I am
guessing this was already done, since the terminal recognizes 'fsl,' but I
add it just in case.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of RUSSELL JARVIS
Sent: Saturday, May 23, 2009 6:56 PM
To: [log in to unmask]
Subject: [FSL] fsl utilities from BASH shell
Hi Matt and Liam,
Using '&' to fork Linux, provided some slightly different and interesting
behavior, but I don't think it has solved the problem. typing $fsl& frees up
the terminal for future use and launches the fsl GUI as well, but any
commands typed after fsl& are not understood by BASH.
I also tried having other shell tabs open in case the processes where
diverted to other tabs.
Here is an example:
user@tux:~$ fsl&
[1] 5648
user@tux:~$ fsl module avil&
[2] 7528
user@tux:~$ module avil&
[3] 8183
user@tux:~$ bash: module: command not found
user@tux:~$ module load fslmaths&
[1] 5661
user@tux:~$ fsl module load fsl-4.1&
[1] 14158
I checked to see different terminal tabs but they were not giving output or
recognising commands other than simple '$fsl&' or '$fsl'
user@tux:~$ module load fslstats
bash: module: command not found
user@tux:~$
I installed FSL using apt-get. Perhaps apt-get configured and installed
everything to an extent but fell short of setting up the local bash
environment.
I wonder if anyone knows how to set up BASH manually, so it recognises
utility commands?
Thanks for previous help or any future help.
Russell.
------------------------------
Try
fsl&
Liam.
------------------------------
You don't need to type fsl to use the utilities. If you want to do this
anyway, you can type fsl & which will send the fsl process to the background
and allow you to continue typing commands.
Peace,
Matt.
-------------------------------
Hello everyone,
I am using FSL on Ubuntu Linux.
I try to open fsl from the BASH prompt, not with the intention of using the
GUI but to use utilities such as FSL maths and FSL statistics.
However when I type fsl at the prompt the GUI automatically loads up, and
the shell becomes useless (you can't type in further commands - like
>load module etc).
Does anyone know how to make it so that you can continue to type in commands
after the GUI has loaded up in BASH on Linux?
Any help is appreciated.
Thanks.
Russell.
------------------------------
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