[Neurodebian-users] condor problem with tbss_2_reg

[Michael Hanke]

Hi,

On Thu, Jul 26, 2012 at 02:47:57PM +0200, Michael Hanke wrote:
> On Thu, Jul 26, 2012 at 06:25:10AM +0000, Knut Jørgen Bjuland wrote:
> > Data
> > http://www.fmrib.ox.ac.uk/fslcourse/fsl_course_data2.tar.gz
> > tutorials
> > http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/fdt/index.htm
> > 
> > ./etc/fsl/fsl.sh 
> > export FSLPARALLEL=condor
> > tbss_2_reg -T
> 
> Thanks a lot! This should allow me to track it down. I won't be able to
> dive into it before I'll go on vacation, but it is on my TODO for when I
> get back.

I think I found the reason for the initial failure and filed a bug

http://bugs.debian.org/684879

Could you please make the proposed change to your /usr/bin/condor_qsub
and check whether it works for you? If you are also using other
components of FSL, please also check whether it has any undesired
side-effects on them.

I quickly checked FEAT and it seems to work, but more testing would be
good.

There seems to be a second bug, though. If I just rerun the tbss_2_reg
command again, it can't find the .commands file, because fsl_sub is
looking into the wrong path. However, I'm not sure whether this is
"intended", i.e. only an issue with the tutorial data. In any case,
already the call to fsl_sub from within TBSS seems wrong, so this would
probably be an FSL issue and not Condor-related.

Thanks for your patience,

Michael


-- 
Michael Hanke
http://mih.voxindeserto.de