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.orgUCLA 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