[Neurodebian-users] Configuring FSL

[Chuck Theobald]

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