Hi,
By default FSL doesn't use SGE - so as long as you haven't somehow got
the SGE_ROOT environment variable set, it shouldn't be looking for it.
Hence - it should print out what you saw, and then start running all
the registrations. Are you sure it wasn't running? Try deleting FAi/
*.msf and try again? Once it's running, try typing "top" in a separate
terminal to check if anything is running.
Cheers.
On 1 Dec 2007, at 22:56, James Andrews wrote:
> Hi Steve,
>
> I would like to simply run "tbss_2_reg -T" on our single linux
> machine. How do I fix it
> so that the script does not try to run with SGE?
>
> Many thanks,
> James
>
>
> On Dec 1, 2007 2:16 AM, Steve Smith <[log in to unmask]> wrote:
> Hi,
>
> It looks like the script thinks that you are running SGE, and that it
> has submitted all the jobs to your cluster?
>
> Cheers.
>
>
>
> On 1 Dec 2007, at 00:47, James Andrews wrote:
>
> > Hi,
> >
> > I have run "tbss_1_preproc" without any problems, but when I run
> > "tbss_2_reg
> > -T" (which I thought should take several hours if I have 13
> > subjects) it
> > *instantaneously* gives me the message below. Also, for each
> > subject it
> > outputs one .msf file and another file (eg. "tbss_2_reg.e12436.1").
> > All
> > these files, though, contain 0 bytes. I would greatly appreciate
> > guidance
> > if anyone recognizes what is going wrong.
> >
> > Many thanks,
> > James Andrews
> > Stanford University
> >
> > CON_0659_dti_FA_FAi_to_target
> > CON_1906_dti_FA_FAi_to_target
> > CON_2552_dti_FA_FAi_to_target
> > CON_3204_dti_FA_FAi_to_target
> > CON_4606_dti_FA_FAi_to_target
> > PREM_0125_dti_FA_FAi_to_target
> > PREM_1355_dti_FA_FAi_to_target
> > PREM_3501_dti_FA_FAi_to_target
> > PREM_4208_dti_FA_FAi_to_target
> > PREM_4456_dti_FA_FAi_to_target
> > PREM_4751_dti_FA_FAi_to_target
> > PREM_5352_dti_FA_FAi_to_target
> > PREM_5901_dti_FA_FAi_to_target
> > 12436
>
>
> ---------------------------------------------------------------------------
> 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
> ---------------------------------------------------------------------------
>
---------------------------------------------------------------------------
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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