[Neurodebian-users] fslview atlases problem

Yaroslav Halchenko debian at onerussian.com
Wed Aug 1 19:28:32 UTC 2012 

grrr...

ok -- may be permissions somehow wrong:

  schroot -c squeeze -- ls -lL /usr/share/fsl/data/atlases/

those should be readable by everyone... if this is not it -- please
install in chroot 'strace' tool (apt-get install strace) and then run

  schroot -c squeeze -p -- strace -fF -o /tmp/strace-output.txt /usr/bin/fslview /usr/share/fsl/data/standard/avg152T1.nii.gz

by when it opens it should try to sense all the atlases so just quit and 

  grep atlas /tmp/strace-output.txt 

to see if it did... e.g. it should look like

10275 open("/usr/share/fsl/data/atlases//Thalamus/Thalamus-prob-2mm.nii.gz", O_RDONLY) = 46
10275 open("/usr/share/fsl/data/atlases//Thalamus/Thalamus-prob-2mm.mnc", O_RDONLY) = -1 ENOENT (No such file or directory)
10275 open("/usr/share/fsl/data/atlases//Thalamus/Thalamus-prob-2mm.mnc.gz", O_RDONLY) = -1 ENOENT (No such file or directory)

where = 46 says that it did find and opened atlas file (at failed to
alternative extensions)

On Wed, 01 Aug 2012, Hidayath Ansari wrote:

>    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 <[1]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
>      [2]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][3]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.
>      [4]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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