What files end up in the output folder?
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Mark J. Pearrow
Sent: Wednesday, November 04, 2009 11:36 AM
To: [log in to unmask]
Subject: [FSL] find_the_biggest results in core file
Hi all,
We are using FDT Diffusion, and the process terminates in error and
leaves a core file. I'm not exactly sure where to begin looking, but
here are the details.
We are running the Debian packaged version of FSL from the following
repository:
http://apsy.gse.uni-magdeburg.de/debian jaunty main non-free
This is running on the 64-bit, desktop distribution of Ubuntu 9.04.
The system has 8 cores and 32GB of memory. Sun Grid Engine is
configured and SGE-aware FSL jobs get automatically submitted to the
correct queue.
Our job gets submitted from the FSL GUI as follows:
=
=
=
=======================================================================
FSL --> FDT Diffusion
single mask: /study/dti.bedpostX/right-amy.nii.gz
seed space is not diffusion: /study/dti.bedpostX/registerlowb2orig.dat
Classification target: rh.pericalcarine.nii.gz and rh.fusiform.nii.gz
=
=
=
=======================================================================
Once submitted, the job appears in the queue, runs for a while, and
then terminates with a core file. SGE reports that the job has
completed successfully, even though it has only run for a minute at
most.
`file core` returns the following:
core: ELF 64-bit LSB core file x86-64, version 1 (SYSV), SVR4-style,
from '/usr/share/fsl/bin/find_the_biggest seeds_to_* biggest'
Loading the core image into GDB isn't particularly illuminating - here
are the last lines of output:
Core was generated by `/usr/share/fsl/bin/find_the_biggest seeds_to_*
biggest'.
Program terminated with signal 6, Aborted.
[New process 3979]
#0 0x00002b8769643fb5 in raise () from /lib/libc.so.6
Can anyone offer some pointers to help diagnose the issue? My gut is
telling me that there is something about the classification targets
causing the problem, but I don't know how to find better diagnostic
info. (the two logfiles generated don't contain anything in the way of
errors).
Thanks,
mjp
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