Hi Mark,
Thanks for the reply. I have Fedora and this is what I get:
echo $FSLDIR
/usr/local/fsl
echo $FSLOUTPUTTYPE
ANALYZE
yes, I have FreeSurfer, is there any other place I should check then?
Thanks,
-Mojdeh
On 08/15/2013 04:50 AM, Mark Jenkinson wrote:
> 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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