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Hi - Yes options at the end override options the precede them. Cheers Saad On 12 Oct 2012, at 20:32, Colin Reveley wrote: > Hi > > I notice that when I call bedpostx using xfibres switches, the defaults get passed to bedpostx_single_slice as well. like this > > /cm/shared/apps/sl6/fsl/interlagos/5.0/bin/bedpostx_single_slice.sh /mnt/lustre/scratch/inf/cmr25/PumHIGH_SNR_SCANS_MERGEDx3fibre_w1_b2000_rician 10 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=1 --cnonlinear --fudge=1 --rician --nfibres=3 --burnin=2000 > > where my options are at the end. > > I've messed a (very) little with a few scripts to make them work in my environment. I adapted the fsl 5 scripts based on my fasl 4.1.9 scripts. possibly I've messed some thing up. But possbibly this is the correct behavior. I've never really had a need to used the xibres syntax before (it's the rician I'm after). I think it did this with fsl 4.1.9 as well. > > So, is this normal behavior? will my options passed at the end override the defaults at the beginning? > > as instructed I'm passing only xfibres style arguments to the bedpostx script, like this: > > ~/bin_interlagosFSL5/bedpostx PumHIGH_SNR_SCANS_MERGEDx3fibre_w1_b2000_rician --fudge=1 --rician --nfibres=3 --burnin=2000 > > thanks, > > Colin -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.fmrib.ox.ac.uk/~saad