[Neurodebian-users] Problem with atlasquery?

[Jonathan Brooks]

Dear All,

I’m trying to run autoaq.sh (http://brainder.org/tag/autoaq/) using FSL 5.0.6 installed on Ubuntu 14.04 Trusty.

The script (attached) accesses common FSL tools to try to assign labels to the clusters detected from e.g. fMRI group
stats in MNI space.

I have previously had problems with atlasquery failing to run, but on this install it seems to work….up to a point. I.e.
I can type

$ atlasquery —dumpatlases

and it will provide me with the list of available/installed atlases. So far so good.

However, when this program gets called through autoaq.sh I get the following error:

$ autoaq.sh -i thresh_zstat1.nii.gz -t 2.3 -o report.txt -a "Harvard-Oxford Cortical Structural Atlas"
*** Error in `/usr/share/fsl/5.0/bin/atlasquery': corrupted double-linked list: 0x00000000014499f0 ***
/usr/local/bin/autoaq.sh: line 151: 11842 Aborted                 (core dumped) ${FSLDIR}/bin/atlasquery -a "${ATLAS}" -m tmp_${RNDSTR}_${cstr} >> ${OUT}

We have a slightly peculiar install environment, where we also need fsl to “appear” to be installed in /usr/local/fsl

To achieve this we created a symbolic link (ln -s /usr/share/fsl/5.0 /usr/local/fsl)

However, even if I remove this link and get back to the vanilla neurodeb FSL install I still get this problem.

Any advice or ideas would be much much appreciated.

Yours,

Jon
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--
Jonathan Brooks (PhD) - Senior Research Fellow
CRiCBristol, University of Bristol, St Michael's Hill, Bristol, UK
T: +44(0)117-342-1512 W: http://www.cricbristol.ac.uk