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H, Sadly both the bedpostx and fsl_sub scripts are less than trivial examples of SGE usage (mea culpa). Send me your modified scripts and I'll see if I can work out what has gone wrong. On 13 Dec 2008, at 00:28, Tugan wrote: > Dear all, > > I hope someone might shed a light on the problem I am having to get > the > bedpostx running on a linux cluster using SGE. I have been > struggling to > find the source of the problem but not exactly there, yet. I > installed the > latest ver 4.1.2 on a CentOS 5 32 bit cluster and I am desperately > trying to > run the bedpostx. > > I made minor modifications to the bedpostx script to point to the > right > directory of SGE software on this machine and changed the email > address; but > nothing else. Did the same modifications in the fsl_sub, too. I had to > change the names of the queues, since they do not have them here. > > When I run the bedpostx script, it puts the preprocessing and > postprocessing > steps in the queue (I see bpx_prepro and bpx_postpr when I do > qstat). But > there is no bedpostx task in the queue. So, it quits after > preprocessing is > completed. Interestingly, if I execute the fsl_sub call from the > command > line by itself, it distributes the tasks in the commands.txt, and > runs fine > and I get the data processed in the cluster. Then I have to call the > post > processing separately to get the final results. This is, of course, > quite > tedious and I would like to do batch processing of large data. > > If anyone had experienced this problem and know how to solve it, I > would be > grateful if you can share your solution(s). > > kind regards, > > Tugan Muftuler > Cheers, Dave -- Dave Flitney, IT Manager Oxford Centre for Functional MRI of the Brain E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717 URL: http://www.fmrib.ox.ac.uk/~flitney