Thank you very much for your answer, I will try your suggestion!
About the HUGE amount of RAM, how much do I need approximately?
Thanks,
Live.
Sitat Stephen Smith <[log in to unmask]>:
> Hi - Matthew can comment on whether you might have an older, less
> efficient version of imglob. Apart from that question:
>
> 825 is a huge number to do a NxN registration on - are you sure you
> need to use this non-default option, rather than just registering
> direct to the FMRIB58 template? But if you do need the -n option
> then you could indeed take a random subset of the subjects in order
> to identify the most 'typical' one to use as a target.
>
> Presumably with 825 subjects, once you get to the later stages of
> TBSS, you will need a machine with HUGE amounts of RAM.
> Cheers.
>
>
> On 7 Dec 2010, at 12:34, Live Eikenes wrote:
>
> > Hi,
> >
> > I am running a large tbss analysis containing 825 individuals, and
> have some problems with tbss_2_reg -n. We are running the analysis on
> a linux cluster with a pbs (public batch system), and tbss_2_reg runs
> in parallell just fine when I have used it for 150 individuals.
> >
> > Our problem is that fsl uses a really long time only using one cpu
> (and not the 800 cpus that are avaliable for my analysis), and I
> think that it uses all this time working with imglob. And the process
> using imglob apparently is not running in parallell.
> >
> > The next thing is that fsl uses a long time making the
> pbsdispatch_commands file.
> >
> > So it seems that fsl is using a long time getting to the fsl_sub
> part where the process is running in parallell. Have I got this
> right, or am I missing something?
> >
> >
> > My questions are as follows:
> >
> > 1. Is it possible to also run the imglob in parallell?
> >
> > 2. Or is it possible to first run imglob on one cpu as an
> individual job, and then start the parallell jobs?
> >
> > 3. Or can we split the analysis in smaller parts, for example
> compare 100 images in one analysis and then do several analysis and
> finally bring them all together when continuing with tbss_3?
> >
> > Thank you in advance!
> >
> > Best regards,
> > Live Eikenes
> >
> > Post doctor
> > Trondheim fMRI group
> > Norwegian University of Science and Technology
> > Trondheim, Norway
> >
>
>
>
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> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>
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>
>
>
>
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