Hi all ~
I have recently conducted a bunch of masked (i.e., ROI) analyses using
randomise (and randomise_parallel). I observed that the program got
*stuck* every now and then - without error output. On the cluster the
submitted job was reported "running", and when running locally the
program would get stuck at the second permutation (i.e., first attempt
to permute original input). All of my log files showed that all was
well... and yet, no new files were being produced.
Since this typically occurred when the mask (-m mask.nii.gz) was
anatomically small - I wondered whether the problem was that there
were no non-zero statistics in the map which was somehow confusing the
script. It turned out that this was true in all the cases in which I
checked.
So... I don't know if I've diagnosed correctly but there is definitely
something funky going on, and which can force randomise to a halt
without producing error messages.
The command I used is below - if you'd like to check out my inputs I'd
be happy to upload them...
# sge qsub randomise_parallel -i ${DATA_PATH} \
# -o ${CONTRAST}_${ROI_NAME[ROI]}_pos \
# -m ${MASK_PATH}/${ROI_NAME[ROI]}.nii.gz \
# -1 \
# -v 8 \
# -T \
# -V
Best ~
Agatha
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Agatha Lenartowicz, Ph.D.
Post Doctoral Scholar
Laboratory of R.A. Poldrack
www.poldracklab.org
UCLA Department of Psychology
1285 Franz Hall, Box 951563
Los Angeles, CA, 90095-1563
http://alenarto.bol.ucla.edu/
On Oct 28, 2008, at 7:04 PM, Koene Van Dijk wrote:
> For who is looking for the file "colourbar.nii.gz" that was
> mentioned in
> this thread. It is still attached to the post by Mark Jenkinson on
> this
> subject "fslview LUT color bar" (09-01-2008)
>
> This is the location of the attachment:
> http://www.jiscmail.ac.uk/cgi-bin/webadmin?A3=ind0801&L=FSL&E=base64&P=458288&B=--Apple-Mail-3-372292755&T=application%2Fx-gzip;%20name=%22colourbar.nii.gz%22&N=colourbar.nii.gz&attachment=q
>
> Thanks Mark, because I used it again today,
>
> Cheers,
> Koene
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