Could you send the output of:
ls ~/.bash*
ls ~/.profile
set | grep FSL
echo $PATH
There are several files that might hide the .bash_profile file. Did you not run the fsl_installer script (which does this setup automatically for you)?
Duncan
> On 21 Feb 2016, at 14:51, novice imaging <[log in to unmask]> wrote:
>
> Dear Prof. Smith
>
> Yes, I have opened a new terminal window after editing bash file, and type 'fsl', but in vain.
> Why not working?
>
> Thank you in advance.
>
> Lee K.
>
>
> 2016-02-21 23:40 GMT+09:00 Stephen Smith <[log in to unmask]>:
> Hi - did you open up that terminal AFTER you had edited the bash setup file? You need to.
> Cheers.
>
>
>> On 21 Feb 2016, at 14:35, novice imaging <[log in to unmask]> wrote:
>>
>> Dear David
>>
>> I appreciate your help.
>> According to your guidance and online FSL page, I've tried the followings:
>>
>> In a terminal, I typed
>> > gedit ~/.bash_profile
>>
>> and copied and pasted the following 4 lines (blue) at the bottom of the pages, as shown in the below:
>>
>> # .bash_profile
>>
>> # Get the aliases and functions
>> if [ -f ~/.bashrc ]; then
>> . ~/.bashrc
>> fi
>>
>> # User specific environment and startup programs
>>
>> PATH=$PATH:$HOME/bin
>>
>> export PATH
>>
>> FSLDIR=/usr/local/fsl
>> . ${FSLDIR}/etc/fslconf/fsl.sh
>> PATH=${FSLDIR}/bin:${PATH}
>> export FSLDIR PATH
>>
>>
>>
>> Then I saved and exited bash_profile, and typed 'fsl' in a terminal; however, no FSL GUI appeared and the following message came up agian (bash: fsl: command not found).
>> How can I solve it?
>>
>> Pleas be patient with a novice's query.
>> Thank you again.
>>
>> L K
>>
>> 2016-02-21 1:09 GMT+09:00 David V. Smith <[log in to unmask]>:
>> Hi Lee,
>>
>> You may find this page (or similar pages) helpful:
>> http://unix.stackexchange.com/questions/129143/what-is-the-purpose-of-bashrc-and-how-does-it-work
>>
>> Basically, I'm suggesting that you add the commands you listed to your bash startup file so that they are executed each time you open a new terminal. Detailed instructions can be found here: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/ShellSetup
>>
>> Hope this helps.
>>
>> Cheers,
>> David
>>
>>
>>
>>> On Feb 20, 2016, at 10:22 AM, novice imaging <[log in to unmask]> wrote:
>>>
>>> Dear Dr. David
>>>
>>> Thank you for the quick response.
>>> It is regrettable that I cannot figure out what you have mentioned.
>>> Would you please explain in more detail (which commands must I do ?)
>>> I'm also a novice in Linux.
>>>
>>> Thank you again.
>>>
>>> LK
>>>
>>> 2016-02-21 0:04 GMT+09:00 David V. Smith <[log in to unmask]>:
>>> Hi Lee,
>>>
>>> Did you put those lines in your ~/.bash_profile or ~/.bashrc file? Any commands on those files will be executed each time open a new terminal window. (You might have to create the file if it doesn't exist.)
>>>
>>> Cheers,
>>> David
>>>
>>>> On Feb 20, 2016, at 9:45 AM, novice imaging <[log in to unmask]> wrote:
>>>>
>>>> Hi experts
>>>>
>>>> This is my first time to try installing FSL on a CentOS 6.7 desktop.
>>>> I've installed FSL according to the online guideline with no problem.
>>>> At the final step, I've configured my shell script using the following 4 command lines:
>>>> FSLDIR=/usr/local/fsl
>>>> . ${FSLDIR}/etc/fslconf/fsl.sh
>>>> PATH=${FSLDIR}/bin:${PATH}
>>>> export FSLDIR PATH
>>>> Just after this, when I typed 'fsl' in the same terminal, fsl GUI correctly appeared, and all modules seemed to work well.
>>>> However, when I opened new terminal window and typed again 'fsl', the following message came up (bash: fsl: command not found) and no fsl GUI appeared.
>>>>
>>>> What command did I miss?
>>>>
>>>> Apologies with a novice's silly question.
>>>> Thank you in advance for your hints.
>>>>
>>>> Lee K
>>>
>>>
>>
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Head of Analysis, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
> Stop the cultural destruction of Tibet
>
>
>
>
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>
--
Duncan Mortimer
Senior Informatics Officer, FMRIB Centre, University of Oxford
John Radcliffe Hospital, Oxford, UK
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