Hi,
What system are you running on? (e.g. CentOS, Mac, etc. and include the version number of the OS)
What happens if you type:
echo $FSLDIR
in a terminal window?
And what happens if you type:
echo $FSLOUTPUTTYPE
in a terminal window?
Do you have any other neuroimaging software installed that might use FSL (e.g. FreeSurfer)?
All the best,
Mark
On 14 Aug 2013, at 20:21, Mojdeh Zamyadi <[log in to unmask]> wrote:
> Thanks Wolf :)
>
> yea! I do the following:
> FSLOUTPUTTYPE=NIFTI_GZ
> export FSLOUTPUTTYPE
>
> this is so annoying! I've searched my whole file system and there are two fsl.sh files, one in: /usr/loca/fsl/etc/fslconf and one in: ~/Programs/fsl/etc/fslconf
> and FSLOUTPUTTYPE is set to NIFTI_GZ in both versions!!!! I have no clue what's causing this!
>
> does anyone else has any idea what might be going wrong here?!
>
> -M
>
>
>
> On 08/14/2013 01:51 PM, wolf zinke wrote:
>> Hi,
>>
>> When setting the FSLOUTPUTTYPE in your .bashrc and .bash_profile files, do you also export them? If you do this at the end of these files, and it does not work, I have no idea what is causing it.
>>
>> It might be something specific to the operating system, for example when running NeuroDebian, the configuration files are found elsewhere (e.g. /etc/fsl/5.0/fsl.sh).
>>
>> good luck,
>> wolf
>>
>>
>> On 14/08/13 19:39, Mojdeh Zamyadi wrote:
>>> Thanks for the reply Wolf. I don't seem to have a ~/.fslconf/ directory!!! anywhere else to look?
>>>
>>>
>>> On 08/14/2013 01:01 PM, wolf zinke wrote:
>>>> Hi,
>>>>
>>>> Another place to look might be ~/.fslconf/fsl.sh
>>>>
>>>> Depending when you set the Variable in your .bashrc and .bash_profile files relative to sourcing /usr/local/fsl/etc/fslconf/fsl.sh , it might be the last configuration read in, and thus could cause this reset.
>>>>
>>>> I hope this helps,
>>>> wolf
>>>>
>>>> On 14/08/13 18:02, Mojdeh Zamyadi wrote:
>>>>> Hi all,
>>>>>
>>>>> I have a problem with permanantly setting my FSLOUTPUTTYPE to NII_GZ. I've set the variable in both .bashrc and .bash_profile and I've checked the /usr/local/fsl/etc/fslconf/fsl.sh and it's set to NII_GZ there as well. But every time I open a new bash shell, the FSLOUTPUTTYPE is set to ANALYZE and I have to manually change it back to NII_GZ. Does anyone know where else I should look?
>>>>>
>>>>> Thanks,
>>>>> -Mojdeh
>>>
>>
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