Hello,
Look in the directory logs and see what it says in the .o files, they should show you where individual processes got to. There are also .e files in case an error occurred.
Ivana
On 18 Apr 2012, at 20:30, Ilia M wrote:
> Hello all,
>
> I've set up POSSUM using the instructions at http://www.fmrib.ox.ac.uk/fsl/possum/run.html .
>
> POSSUM runs and the log file seems to state that it finishes:
>
> ________________________________________
> Making possum directory structure
> Processing stage
> Wed Apr 18 14:06:33 EDT 2012
> /usr/share/fsl/4.1/bin/fsl_sub -T 2 -l /net/synapse/nt/makedon1/physioBOLD/POSSUM/logs -N possum -t /net/synapse/nt/makedon1/physioBOLD/POSSUM/possum.com
> Post processing stage
> Wed Apr 18 14:06:33 EDT 2012
> /usr/share/fsl/4.1/bin/fsl_sub -T 10 -j 11711 -F -l /net/synapse/nt/makedon1/physioBOLD/POSSUM/logs /bin/possumX_postproc.sh /net/synapse/nt/makedon1/physioBOLD/POSSUM 1
> Done
> Wed Apr 18 14:06:33 EDT 2012
> ________________________________________
>
> Unfortunately, the output folder does not contain the output files.
>
> Here is a directory listing of the output folder:
>
> brain.nii.gz logs MRpar possum.com possum.log pulse.com pulse.posx pulse.posz slcprof T2timecourse
> diff_proc motion noise possum.fsf pulse pulse.info pulse.posy pulse.readme T2.nii.gz
>
> Note that image_abs.nii.gz, image_phase.nii.gz and signal are all missing.
>
> What went wrong?
>
> Thank you in advance.
>
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