Hi Siew-Min,
I've just got a look at the script...
So instead of:
$FSLDIR/bin/fslswapdim all_${ALTIM}_symmetrised_skeletonised -x y z grotsym_all_${ALTIM}_symmetrised_flipped > /dev/null
$FSLDIR/bin/fslmaths all_${ALTIM}_symmetrised_skeletonised -sub grotsym_all_${ALTIM}_symmetrised_flipped -roi 91 91 0 218 0 182 0 `$FSLDIR/bin/fslval all_FA_skeletonised dim4` all_${ALTIM}_skeletonised_left_minus_right
in the tbss_sym script (where ${ALTIM} is FA here),
I think you could do:
$FSLDIR/bin/fslswapdim all_${ALTIM}_symmetrised_skeletonised -x y z grotsym_all_${ALTIM}_symmetrised_flipped
$FSLDIR/bin/fslmaths grotsym_all_${ALTIM}_symmetrised_flipped -sub all_${ALTIM}_symmetrised_skeletonised -roi 91 91 0 218 0 182 0 `$FSLDIR/bin/fslval all_FA_skeletonised dim4` all_${ALTIM}_skeletonised_right_minus_left
Cheers,
Gwenaelle
--- En date de : Mar 2.6.09, Siew-Min Gan <[log in to unmask]> a écrit :
> De: Siew-Min Gan <[log in to unmask]>
> Objet: Re: [FSL] Re : [FSL] randomise command after tbss_sym and sample size
> À: [log in to unmask]
> Date: Mardi 2 Juin 2009, 20h44
> is there a command line to invert the
> data or do these things instead of
> using the GUI, as Id be doing a lot of these analysis and
> it'd be nice to
> do these with the command lines instead of gui?
>
> thanks very much
>
> Siewmin
>
> Hi again,
> >
> > no, R-L flip the 4D image would only lead to the same
> result, only on the
> > other half part of the volume.
> >
> > Use the Glm gui, switch from timeseries design to
> higher-level analysis,
> > set the correct the number of subjects and then use
> the wizard with single
> > group average: that should create the design.mat and
> design.con
> > corresponding to the -1 option of randomise when you
> tested for L>R.
> > Then, you simply inverse the contrast in the .con to
> test for R>L.
> >
> > Cheers,
> > Gwenaelle
> >
> > --- En date de : Mar 2.6.09, Siew-Min Gan <[log in to unmask]>
> a
> > �crit :
> >
> >> De: Siew-Min Gan <[log in to unmask]>
> >> Objet: Re: [FSL] Re : [FSL] randomise command
> after tbss_sym and sample
> >> size
> >> �: [log in to unmask]
> >> Date: Mardi 2 Juin 2009, 20h04
> >> thanks very much it works. silly of
> >> me.
> >> on the website, it says : To test for R>L,
> either invert
> >> the data and
> >> re-run randomise, or create an appropriate design
> matrix
> >> and contrast
> >> file.
> >>
> >> Does inverting the data means fslswapdim input -x
> y z
> >> output? Which datas
> >> should I invert? alternatively, can you kindly
> give an
> >> example how to
> >> create an appropriate design matrix and contrast
> file.
> >>
> >> thanks
> >>
> >> Siewmin
> >>
> >> Hi Siew-Min,
> >> >
> >> >
> >> >> I then type the command
> >> >> randomise -i
> >> all_FA_skeletonised_left_minus_right.nii.gz
> >> >> -o
> >> >> mean_FA_symmetrised_skeleton_mask.nii.gz
> -1 -v 5
> >> -T
> >> >
> >> > your command is not exact: -o is the output
> of your
> >> stasticial test not
> >> > the mask for this test (your mask should be
> placed
> >> after -m) and you need
> >> > to specify the number of permutations (that's
> why
> >> nothing ran).
> >> >
> >> > Try with this instead:
> >> >
> >> > randomise -i
> >> all_FA_skeletonised_left_minus_right.nii.gz -m
> >> > mean_FA_symmetrised_skeleton_mask.nii.gz -o
> >> myresult_L-R -1 -v 5 -T -n
> >> > 1000
> >> >
> >> > Cheers,
> >> > Gwenaelle
> >> >
> >> >
> >> >
> >> >
> >> >
> >>
> >
> >
> >
> >
>
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