Great! I moved "export FSLOUTPUTTYPE" to the end of my .bashrc file and
this solved the problem :)
Thanks again,
-M
On 08/16/2013 04:00 AM, Mark Jenkinson wrote:
> Hi,
>
> I would check whether you've got a FreeSurfer setting that is interfering.
> If you look at your .bashrc and/or .bash_profile files then it might help to shift your FSL configuration to after your FreeSurfer one, or to explicitly put in FSLOUTPUTTYPE=NIFTI_GZ and export FSLOUTPUTTYPE _after_ any other settings are performed.
>
> All the best,
> Mark
>
>
> On 15 Aug 2013, at 16:08, Mojdeh Zamyadi<[log in to unmask]> wrote:
>
>> 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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