Dear Alessandro,
Could you please upload the file to here? You should have just received an
email with a link and some instructions.
Thanks!
All the best,
Anderson
On 7 January 2015 at 13:56, Alessandro Bellini <[log in to unmask]> wrote:
> Hello,
> I've updated FSL to the new version (5.0.8) and my problem shows up again!
>
> analisi@analisi-hp-linux ~/Ale/TBSS/CIS/prova/Proc/stats $ autoaq -i
> tbss_tfce_corrp_tstat2.nii.gz -t 0.95 -o report.txt -a "JHU White-Matter
> Tractography Atlas"
> /usr/lib/fsl/5.0/autoaq: riga 143: 4437 Segmentation fault
> ${FSLDIR}/bin/atlasquery -a "${ATLAS}" -m ${TMPNAME}_${cstr} >> ${NEWOUT}
>
> Thanks for your help!
>
> 2014-12-11 16:15 GMT+01:00 Anderson M. Winkler <[log in to unmask]>:
>
>> Hi Alessandro,
>>
>> That line, containing "tmp_${RNDSTR}_${cstr}" has been changed in the
>> version that is now included in FSL, so it looks you were really using the
>> previous version from the website. Nonetheless, a segmentation fault has to
>> be a problem with the atlasquery (i.e. the binary backend), so my
>> recommendation is really to update to 5.0.8 and, if the problem persists,
>> please let us know.
>>
>> Thanks!
>>
>> All the best,
>>
>> Anderson
>>
>>
>> On 11 December 2014 at 14:51, Alessandro Bellini <[log in to unmask]>
>> wrote:
>>
>>> I try to use directly atlasquery and I have the following message
>>>
>>> analisi@analisi-hp-linux ~/Ale/TBSS/CIS/Proc/stats $ *atlasquery -a
>>> "JHU White-Matter Tractography Atlas" -m tbss_tfce_corrp_tstat2.nii.gz *
>>> Anterior thalamic radiation L:1.33074
>>> Anterior thalamic radiation R:0.893303
>>> Corticospinal tract L:0.778339
>>> Corticospinal tract R:0.555696
>>> Cingulum (cingulate gyrus) L:0.315727
>>> Cingulum (cingulate gyrus) R:0.0544736
>>> Cingulum (hippocampus) L:0.153622
>>> Cingulum (hippocampus) R:0.163147
>>> Forceps major:1.01173
>>> Forceps minor:2.53899
>>> Inferior fronto-occipital fasciculus L:1.66984
>>> Inferior fronto-occipital fasciculus R:1.71571
>>> Inferior longitudinal fasciculus L:1.41508
>>> Inferior longitudinal fasciculus R:1.02592
>>> Superior longitudinal fasciculus L:1.45333
>>> Superior longitudinal fasciculus R:0.883632
>>> Uncinate fasciculus L:0.592347
>>> Uncinate fasciculus R:0.311303
>>> Superior longitudinal fasciculus (temporal part) L:0.701945
>>> Superior longitudinal fasciculus (temporal part) R:0.38773
>>> *Segmentation fault*
>>>
>>>
>>>
>>>
>>> 2014-12-11 9:58 GMT+01:00 Alessandro Bellini <[log in to unmask]>:
>>>
>>>> Hi
>>>>
>>>> I'm using FSL version 5.0.7.4 and I'm using the script that comes with
>>>> it.
>>>>
>>>> Thanks
>>>>
>>>> Alessandro
>>>>
>>>> 2014-12-10 18:00 GMT+01:00 Anderson M. Winkler <[log in to unmask]>
>>>> :
>>>>
>>>> Hi Alessandro,
>>>>>
>>>>> The autoaq has been integrated into FSL. Please, make sure that you
>>>>> are using the latest FSL (5.0.8) and that you are invoking the script that
>>>>> comes with it, that is, ${FSLDIR}/bin/autoaq. This version supersedes the
>>>>> previous version of autoaq that was available at brainder.org.
>>>>>
>>>>> All the best,
>>>>>
>>>>> Anderson
>>>>>
>>>>>
>>>>> On 10 December 2014 at 16:17, Alessandro Bellini <[log in to unmask]>
>>>>> wrote:
>>>>>
>>>>>> Hi all,
>>>>>> I'm trying to use autoaq for the first time on my TBSS data. I have
>>>>>> an error while using autoaq.
>>>>>>
>>>>>> autoaq -i tbss_tfce_corrp_tstat2.nii.gz -t 0.95 -o report.txt -a "JHU
>>>>>> White-Matter Tractography Atlas"
>>>>>>
>>>>>> /usr/lib/fsl/5.0/autoaq: riga 151: 6386 Segmentation fault
>>>>>> ${FSLDIR}/bin/atlasquery -a "${ATLAS}" -m tmp_${RNDSTR}_${cstr} >> ${OUT}
>>>>>>
>>>>>> I've downloaded the last autoaq script from the web.
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
