[Neurodebian-users] fslview atlases problem

Hidayath Ansari hidayath at gmail.com
Wed Aug 1 19:15:32 UTC 2012 

Thank you for helping me walk through this! Here are the outputs:



$ ls -l /srv/chroots/squeeze/usr/share/fsl/data/atlases/
total 20
lrwxrwxrwx 1 root root 48 Jul 31 15:47 Cerebellum ->
../../../data/bangor-cerebellar-atlas/Cerebellum
lrwxrwxrwx 1 root root 61 Jul 31 15:47 Cerebellum_MNIflirt.xml ->
../../../data/bangor-cerebellar-atlas/Cerebellum_MNIflirt.xml
lrwxrwxrwx 1 root root 61 Jul 31 15:47 Cerebellum_MNIfnirt.xml ->
../../../data/bangor-cerebellar-atlas/Cerebellum_MNIfnirt.xml
lrwxrwxrwx 1 root root 50 Jul 31 15:47 HarvardOxford ->
../../../data/harvard-oxford-atlases/HarvardOxford
lrwxrwxrwx 1 root root 63 Jul 31 15:47 HarvardOxford-Cortical.xml ->
../../../data/harvard-oxford-atlases/HarvardOxford-Cortical.xml
lrwxrwxrwx 1 root root 66 Jul 31 15:47 HarvardOxford-Subcortical.xml ->
../../../data/harvard-oxford-atlases/HarvardOxford-Subcortical.xml
lrwxrwxrwx 1 root root 43 Jul 31 15:47 JHU ->
../../../data/jhu-dti-whitematter-atlas/JHU
lrwxrwxrwx 1 root root 43 Jul 31 16:28 JHU_bak ->
../../../data/jhu-dti-whitematter-atlas/JHU
lrwxrwxrwx 1 root root 54 Jul 31 15:47 JHU-labels.xml ->
../../../data/jhu-dti-whitematter-atlas/JHU-labels.xml
lrwxrwxrwx 1 root root 54 Jul 31 15:47 JHU-tracts.xml ->
../../../data/jhu-dti-whitematter-atlas/JHU-tracts.xml
lrwxrwxrwx 1 root root 48 Jul 31 15:47 Juelich ->
../../../data/juelich-histological-atlas/Juelich
lrwxrwxrwx 1 root root 52 Jul 31 15:47 Juelich.xml ->
../../../data/juelich-histological-atlas/Juelich.xml
lrwxrwxrwx 1 root root 38 Jul 31 15:47 MNI ->
../../../data/mni-structural-atlas/MNI
lrwxrwxrwx 1 root root 42 Jul 31 15:47 MNI.xml ->
../../../data/mni-structural-atlas/MNI.xml
lrwxrwxrwx 1 root root 46 Jul 31 15:47 Talairach ->
../../../data/talairach-daemon-atlas/Talairach
lrwxrwxrwx 1 root root 50 Jul 31 15:47 Talairach.xml ->
../../../data/talairach-daemon-atlas/Talairach.xml
lrwxrwxrwx 1 root root 57 Jul 31 15:47 Thalamus ->
../../../data/oxford-thalamic-connectivity-atlas/Thalamus
lrwxrwxrwx 1 root root 61 Jul 31 15:47 Thalamus.xml ->
../../../data/oxford-thalamic-connectivity-atlas/Thalamus.xml



$ schroot -c squeeze -- ls -l /usr/share/fsl/data/atlases/
total 20
lrwxrwxrwx 1 root root 48 Jul 31 20:47 Cerebellum ->
../../../data/bangor-cerebellar-atlas/Cerebellum
lrwxrwxrwx 1 root root 61 Jul 31 20:47 Cerebellum_MNIflirt.xml ->
../../../data/bangor-cerebellar-atlas/Cerebellum_MNIflirt.xml
lrwxrwxrwx 1 root root 61 Jul 31 20:47 Cerebellum_MNIfnirt.xml ->
../../../data/bangor-cerebellar-atlas/Cerebellum_MNIfnirt.xml
lrwxrwxrwx 1 root root 50 Jul 31 20:47 HarvardOxford ->
../../../data/harvard-oxford-atlases/HarvardOxford
lrwxrwxrwx 1 root root 63 Jul 31 20:47 HarvardOxford-Cortical.xml ->
../../../data/harvard-oxford-atlases/HarvardOxford-Cortical.xml
lrwxrwxrwx 1 root root 66 Jul 31 20:47 HarvardOxford-Subcortical.xml ->
../../../data/harvard-oxford-atlases/HarvardOxford-Subcortical.xml
lrwxrwxrwx 1 root root 43 Jul 31 20:47 JHU ->
../../../data/jhu-dti-whitematter-atlas/JHU
lrwxrwxrwx 1 root root 54 Jul 31 20:47 JHU-labels.xml ->
../../../data/jhu-dti-whitematter-atlas/JHU-labels.xml
lrwxrwxrwx 1 root root 54 Jul 31 20:47 JHU-tracts.xml ->
../../../data/jhu-dti-whitematter-atlas/JHU-tracts.xml
lrwxrwxrwx 1 root root 43 Jul 31 21:28 JHU_bak ->
../../../data/jhu-dti-whitematter-atlas/JHU
lrwxrwxrwx 1 root root 48 Jul 31 20:47 Juelich ->
../../../data/juelich-histological-atlas/Juelich
lrwxrwxrwx 1 root root 52 Jul 31 20:47 Juelich.xml ->
../../../data/juelich-histological-atlas/Juelich.xml
lrwxrwxrwx 1 root root 38 Jul 31 20:47 MNI ->
../../../data/mni-structural-atlas/MNI
lrwxrwxrwx 1 root root 42 Jul 31 20:47 MNI.xml ->
../../../data/mni-structural-atlas/MNI.xml
lrwxrwxrwx 1 root root 46 Jul 31 20:47 Talairach ->
../../../data/talairach-daemon-atlas/Talairach
lrwxrwxrwx 1 root root 50 Jul 31 20:47 Talairach.xml ->
../../../data/talairach-daemon-atlas/Talairach.xml
lrwxrwxrwx 1 root root 57 Jul 31 20:47 Thalamus ->
../../../data/oxford-thalamic-connectivity-atlas/Thalamus
lrwxrwxrwx 1 root root 61 Jul 31 20:47 Thalamus.xml ->
../../../data/oxford-thalamic-connectivity-atlas/Thalamus.xml




$ grep -H . ~/.qt/fsl*
/home/ansari/.qt/fslviewrc:[geometry]
/home/ansari/.qt/fslviewrc:height=945
/home/ansari/.qt/fslviewrc:width=756
/home/ansari/.qt/fslviewrc:x=69
/home/ansari/.qt/fslviewrc:y=104




On Wed, Aug 1, 2012 at 1:56 PM, Yaroslav Halchenko <yoh at dartmouth.edu>wrote:

> ok -- I just did all the steps in NeuroDebian VM -- seems to work as
> expected...  what is the output of following commands?
>
>  ls -l /srv/chroots/squeeze/usr/share/fsl/data/atlases/
>  schroot -c squeeze -- ls -l /usr/share/fsl/data/atlases/
>  grep -H . ~/.qt/fsl*
>
> P.S. Mention the corrected address in CC for the neurodebian-users
> mailing list.  You can subscribe at
> http://lists.alioth.debian.org/mailman/listinfo/neurodebian-users
>
> On Wed, 01 Aug 2012, Hidayath Ansari wrote:
>
> >    In response to your question, yes I followed those instructions
> exactly. I
> >    installed fsl-atlases as root within the schroot environment.
>
> >      �Hi
> >      I followed the instructions at
> >      [1]
> http://neuro.debian.net/blog/2011/2011-12-12_schroot_fslview.html to
> >      set up a chroot-ed environment in which to run fslview using an
> older
> >      version of Debian. I've also installed the fsl-atlases package in
> that
> >      environment and I can see the atlas data in
> /usr/share/fsl/data/atlases
> >      . When I fire up fslview though, the atlases toolbar is empty!
> >      Additionally, when I click on the Structures button in that
> toolbar, the
> >      whole thing just dies:
> >      QComboBox::setCurrentItem: (m_atlasSelection) Index 1 out of range
> >      fslview: /usr/include/boost/smart_ptr/shared_ptr.hpp:418: T*
> >      boost::shared_ptr< <template-parameter-1-1> >::operator->() const
> [with
> >      T = Atlas]: Assertion `px != 0' failed.
> >      [1]+ �Aborted � � � � � � � � (core dumped) fslview
> >      Any ideas?
> >      Thanks!
> >      M. Hidayath Ansari
> >      Graduate Student
> >      University of Wisconsin-Madison
>
> > References
>
> >    Visible links
> >    1. http://neuro.debian.net/blog/2011/2011-12-12_schroot_fslview.html
>
> --
> Yaroslav O. Halchenko
> Postdoctoral Fellow,   Department of Psychological and Brain Sciences
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
> WWW:   http://www.linkedin.com/in/yarik
>
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