Hi Patricia,
The F-test is bi-directional so you don't need to include the negative contrasts. You need to include the f-contrasts file with -f as well as the t-contrasts file with -t.
Kind Regards
Matthew
> Hello Mark,
>
> thank you very much for your answer. I am not very sure what do you mean when you say "include one F-test that consisted of t-contrasts 1, 3 and 5." Does it mean that my contrast are allright but i have to include option F-test=1 and mark t contrast 1, 3 and 5? Why only these contrast?
>
> On the other way, should my randomise command be different than:
>
> randomise -i all_FA_skeletonised.nii -m mean_FA_skeleton_mask.nii -o resultados_TBSS -d matriz.mat -t matriz.con -n 5000 --T2 -V
>
> -t option in randomise should now be -f because of the F-test analysis?
>
> Thank you very much,
>
> Patricia.
>
>
> 2013/1/19 Mark Jenkinson <[log in to unmask]>
> Hi,
>
> If you want a single F-test that checks for any differences then it would be sufficient to use your existing t-contrasts and include one F-test that consisted of t-contrasts 1, 3 and 5.
>
> All the best,
> Mark
>
>
>
> On 17 Jan 2013, at 11:42, SUBSCRIBE FSL Patricia Pires <[log in to unmask]> wrote:
>
> > Dear fsl list,
> >
> > i have 4 different groups to analize FA index. I performed a Glm matrix:
> >
> > /Matrix
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> >
> > And their contrasts:
> >
> > /Matrix
> > 1.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00
> > -1.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
> > 1.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00
> > -1.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
> > 1.000000e+00 -1.000000e+00 0.000000e+00 0.000000e+00
> > -1.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
> > 0.000000e+00 0.000000e+00 1.000000e+00 -1.000000e+00
> > 0.000000e+00 0.000000e+00 -1.000000e+00 1.000000e+00
> > 0.000000e+00 -1.000000e+00 1.000000e+00 0.000000e+00
> > 0.000000e+00 1.000000e+00 -1.000000e+00 0.000000e+00
> > 0.000000e+00 -1.000000e+00 0.000000e+00 1.000000e+00
> > 0.000000e+00 1.000000e+00 0.000000e+00 -1.000000e+00
> >
> >
> > There are two contrast with significant results when i run randomise:
> >
> > randomise -i all_FA_skeletonised.nii -m mean_FA_skeleton_mask.nii -o resultados_TBSS -d matriz.mat -t matriz.con -n 5000 --T2 -V
> >
> > However this procedure has been criticized because there is not a previous overall of results and i am wondering if i first have to do a F-tests:
> >
> > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT/UserGuide#F-Tests
> >
> > I have to do a F-test first? In that case, what will indicate these results:
> >
> > - C1: Group A 1 0 0 0
> >
> > (if i found results here, e.g. cluster --in=resultados_FA_mean_FA_skeleton_mask_tfce_corrp_tstat1.nii.gz --thresh=0.95), would this indicating Group A differ from other groups and then i could finally do my first procedure? Or it is not necessary this first F-test analysis?
> >
> > Thanks in advance,
> >
> > Patricia.
>
