it means don't run BET. if you just run "melodic" from the command line
you can choose whether this will first run BET or not, called from within
the command-line binary program. however, if you are using the GUI, the
BET call, as with all the other pre-processing steps like mcflirt, are
made in their own right _before_ the melodic command-line program gets
called. thus melodic is always called with the --nobet option when using
the GUI.
any progress wrt the chequerboards?
thanks :)
On Thu, 20 Feb 2003, Jack Grinband wrote:
> So, what does "--nobet" mean? thanks,
>
> jack
>
> >This all looks correct. If you have BET turned on then "betfunc" will have
> >gotten called in the pre-stats processing, before running melodic.
> >
> >> When I run Melodic (GUI), I get the following outputs:
> >>
> >> with BET turned on:
> >>
> >> /export/apps/fsl/bin/melodic -i filtered_func_data -o
> >> /home/students/jgrinband/data/tst7/tst7r2.ica -v --nobet --bgthreshold=10
> >> --tr=3.0 -d 0 --mmthresh="0.5" --report --Ostats
> >>
> >> with BET turned off:
> >>
> >> /export/apps/fsl/bin/melodic -i filtered_func_data -o
> >> /home/students/public/cu52/cu52r1+.ica -v --nobet --bgthreshold=10 --tr=3.0
> >> -d 0 --mmthresh="0.5" --report --Ostats
> >>
> >> I'm just wondering if the BET button is doing what I think it's doing. Thanks,
>
Stephen M. Smith MA DPhil CEng MIEE
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe 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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