[Neurodebian-users] Configuring FSL

[Chuck Theobald]

Hello Assal,

Synaptics is a front-end for the apt family of package management 
programs, so FSL should be installed in /usr/lib/fsl. If you have not 
gotten FSL working, post the results of these commands:

ls -l /usr/bin/fsl4.1-fsl
ls -ld /usr/lib/fsl/4.1

Chuck


On 2/10/12 5:33 PM, Chuck Theobald wrote:
> Hello Assal,
>
> Did you log out and back in again after you updated your 
> .bash_profile? Doing so would be the simplest way to activate your 
> changes.
>
> It is possible the synaptics installed FSL to a different location. I 
> will have to look into this later.
>
> Regards,
> Chuck
>
>
> On 2/10/12 1:16 PM, Assal Habibi wrote:
>> Hi Chuck,
>>
>>
>> Thank you for getting back to me. I installed FSL from Synaptic 
>> Package Manager. I added your lines of code to the .bash_profile. The 
>> file only had this information.. Is that the right fie? I still have 
>> trouble with starting FSL after adding the code and saving it.. It is 
>> still complaining that command is not found.
>>
>> ######################################################################### 
>>
>> #         .bash_profile: Personal initialisation file for 
>> bash          #
>> ######################################################################### 
>>
>>
>> # This script file is executed by bash(1) for login shells.  By default,
>> # it does nothing, as ~/.bashrc is already sourced by /etc/profile.
>> #
>> # [JNZ] Modified 23-Sep-2004
>> #
>> # Written by John Zaitseff and released into the public domain.
>>
>>
>> If you have any other tips, I would really appreciate it. I am pretty 
>> new to Linux .
>>
>> Thank you,
>> assal
>>
>> ----- Original Message -----
>> From: Chuck Theobald<chuckt at uoregon.edu>
>> Date: Friday, February 10, 2012 11:40 am
>> Subject: Re: [Neurodebian-users] Configuring FSL
>> To: neurodebian-users at lists.alioth.debian.org, Assal.Habibi at usc.edu
>>
>>> Hello Assal,
>>>
>>> If you have installed from the NeuroDebian repository, FSLDIR is
>>> set by /etc/fsl/fsl.sh. Here is what I put into each user's
>>> .bash_profile:
>>> # Check for NeuroDebian-style installation of FSL.
>>> if [ -e /etc/fsl/fsl.sh ]; then
>>>   . /etc/fsl/fsl.sh
>>>   export FSLPARALLEL=1
>>>   echo "==>  FSL is installed ..."
>>> # Else check for manual installation.
>>> elif [ -d /usr/local/fsl ]; then
>>>   case `hostname | cut -f1 -d'.'` in
>>>     bleu) export FSLVERSION=3.2 ;;
>>>     *) export FSLVERSION=4.1.8 ;;
>>>   esac
>>>   export FSLDIR=/usr/local/fsl-${FSLVERSION}
>>>   export PATH=${FSLDIR}/bin:${PATH}
>>>   . ${FSLDIR}/etc/fslconf/fsl.sh
>>>   echo "==>  Welcome to FSL ${FSLVERSION} ..."
>>> else
>>>   echo "FSL is not installed"
>>> fi
>>>
>>> The above supports both NeuroDebian and my older method of manual
>>> installation to /usr/local. The elif clause is going away when my
>>> last Gentoo machines die from lack of use.
>>>
>>> Hope this helps,
>>> Chuck
>>>
>>>
>>> On 2/10/12 11:34 AM, Assal Habibi wrote:
>>>> Hi,
>>>>
>>>> I have downloaded (using synaptic package manager) and installed
>>> FSL but having trouble with configuration.
>>>> As instructed on FSL website, I copied and pasted the following
>>> lines of commands  in the shell setup files. I tried .bashrc,
>>> .profile, .cshrc but none of them worked.  The error line is: fsl:
>>> command not found. Does anyone know hot to fix it?
>>>>
>>>> FSLDIR=/usr/local/fsl
>>>> . ${FSLDIR}/etc/fslconf/fsl.sh
>>>> PATH=${FSLDIR}/bin:${PATH}
>>>> export FSLDIR PATH
>>>>
>>>> Thank you,
>>>> Assal
>>>>
>>>>
>>>> _______________________________________________
>>>> Neurodebian-users mailing list
>>>> Neurodebian-users at lists.alioth.debian.org
>>>> http://lists.alioth.debian.org/cgi-
>>> bin/mailman/listinfo/neurodebian-users
>>>>
>>>
>>> -- 
>>> Chuck Theobald
>>> System Administrator
>>> The Robert and Beverly Lewis Center for Neuroimaging
>>> University of Oregon
>>> P: 541-346-0343
>>> F: 541-346-0345
>>>
>>>
>
>


-- 
Chuck Theobald
System Administrator
The Robert and Beverly Lewis Center for Neuroimaging
University of Oregon
P: 541-346-0343
F: 541-346-0345