Hi,
I just want to add, that we had the same experience here. Snow
Leopard/FSL seems to not recognize the Atlases.
We will test the work around later today.
Andrej
David Flitney wrote:
> Okay. I think that perhaps the atlas code isn't picking up that your
> installation is in /Applications/fsl instead of the recommended
> /usr/local/fsl. I'll look into that ASAP. In the meantime another test,
> and possible short term workaround, is to put a symbolic link in. Could
> you try:
>
> cd /usr/local
> ln -s /Applications/fsl .
>
> If the atlas tools start working then it'd lend more evidence for a
> mistake in the atlas code base.
>
> On 26 Oct 2009, at 04:13, Hal Hinkle wrote:
>
>> Thanks for your help on this:
>>
>> _Set | grep FSL
>> _
>> FSLCONFDIR=/Applications/fsl/config
>> FSLDIR=/Applications/fsl
>> FSLLOCKDIR=
>> FSLMACHINELIST=
>> FSLMACHTYPE=
>> FSLMULTIFILEQUIT=TRUE
>> FSLOUTPUTTYPE=NIFTI_GZ
>> FSLREMOTECALL=
>> FSLTCLSH=/Applications/fsl/bin/fsltclsh
>> FSLWISH=/Applications/fsl/bin/fslwish
>>
>> _ls $FSLDIR/data/atlases
>>
>> Cerebellum Juelich
>> Cerebellum_MNIflirt.xml Juelich.xml
>> Cerebellum_MNIfnirt.xml MNI
>> HarvardOxford MNI.xml
>> HarvardOxford-Cortical.xml Talairach
>> HarvardOxford-Subcortical.xml Talairach.xml
>> JHU Thalamus
>> JHU-labels.xml Thalamus.xml
>> JHU-tracts.xml
>> _
>>
>>
>> On 10/24/09 4:09 AM, "Dave Flitney" <[log in to unmask]
>> <mailto:[log in to unmask]>> wrote:
>>
>>> Please email the output of "set | grep FSL" and "ls
>>> $FSLDIR/data/atlases/".
>>>
>>> Dave Flitney, IT Manager
>>> University of Oxford, FMRIB Centre
>>> JR Hospital, Oxford OX3 9DU
>>> T: 01865 222713 F: 01865 222717
>>>
>>> On 24 Oct 2009, at 04:21, Hal Hinkle <[log in to unmask]
>>> <mailto:[log in to unmask]>> wrote:
>>>
>>>> David – Thanks for that. I think our environmental variables (as
>>>> far as I can see) are set right. Nothing else in the FSL suite has
>>>> any problems running.
>>>> Here’s what’s in the bash profile:
>>>>
>>>> # FSL Configuration
>>>> FSLDIR=/Applications/fsl
>>>> PATH=${FSLDIR}/bin:${PATH}
>>>> . ${FSLDIR}/etc/fslconf/fsl.sh
>>>> export FSLDIR PATH
>>>>
>>>> Still the problem remains. FSLView works fine in every regard,
>>>> except when the Atlas tool has been invoked, no Atlas or structures
>>>> show in the tool box, the Atlas tool does not list or access any
>>>> atlases and the Structure’s button crashes FSLView. Please advise.
>>>>
>>>> Thanks.
>>>>
>>>>
>>>>
>>>>
>>>> On 10/22/09 4:44 AM, "David Flitney" <[log in to unmask]
>>>> <mailto:[log in to unmask]>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> In general multiple copies of FSL should be able to coexist. The
>>>>> important thing for FSLView/Atlas tools being that FSLDIR must
>>>>> point to the matching FSL installation. See if you have FSLDIR set
>>>>> in your environment and, if so, that it's value is consistent.
>>>>>
>>>>> Regards
>>>>> Dave
>>>>>
>>>>> On 20 Oct 2009, at 18:05, William Hinkle wrote:
>>>>>
>>>>>> We have recently installed FSL on a Mac 10.6.1 with FSLView_3.1.4.
>>>>>> All works fine
>>>>>> except accessing the atlases or structures from the gui buttons
>>>>>> within the "Atlas tools".
>>>>>> the "Atlases" button comes up blank. "Structures" button will
>>>>>> crash fslview. We also
>>>>>> have an older version of FSLView installed. Before 10.6.1 both
>>>>>> would run with no conflict.
>>>>>> Now we can access files through the Atlas buttons and the
>>>>>> Structure button crashes. Must
>>>>>> we deinstall the older FSL View? Can you please advise?
>>>>>
>>>>>
>>>>
>>>
>>
>
> --
> Dave Flitney, IT Manager
> Oxford Centre for Functional MRI of the Brain
> E:[log in to unmask]
> <mailto:[log in to unmask]> W:+44-1865-222713 F:+44-1865-222717
> URL: http://www.fmrib.ox.ac.uk/~flitney
>
>
>
--
Andrej Schoeke
Mather Lab Research Assistant
Phone: (213) 740-7208
USC, Gerontology Department
3715 McClintock Avenue, Rm 341
Los Angeles, CA 90089-019
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