Hi Sergiu,
is this exactly the randomise command you typed? If so, the mask for the statistical analysis is missing (-m mean_FA_skeleton_mask) and, above all, the number of permutations (-n 5000). Without any permutation, you can not have a vox image (p-values uncorrected). Also, you might want to correct your possible results for multiple comparisons (with either -c or -T options). Please have a look at the randomise manual: http://www.fmrib.ox.ac.uk/fsl/randomise/index.html
Hope this helps,
Gwenaelle
--- En date de : Jeu 3.4.08, S. Groppa <[log in to unmask]> a écrit :
> De: S. Groppa <[log in to unmask]>
> Objet: Re: [FSL] Re : [FSL] empty vox_tstat after TBSS & randomise
> À: [log in to unmask]
> Date: Jeudi 3 Avril 2008, 18h53
> Dear Gwenaelle,
>
> thanks a lot,
>
> randomise -i all_FA(_skeletonise) -o xx -d *.mat -t *.con
> -g *.grp
>
> so actually nothing special(.
>
> my gratitude
> Sergiu
>
> .con:
> /ContrastName1 A
> /ContrastName2 B
> /ContrastName3 C
> /ContrastName4 PE-
> /ContrastName5 PE+
> /ContrastName6 P+E-
> /ContrastName7 P-E+
> /ContrastName8 P-E-
> /ContrastName9 D
> /NumWaves 3
> /NumContrasts 9
> /PPheights 1.000000e+00 1.000000e+00
> 1.000000e+00 1.000000e+00 1.000000e+00
> 1.000000e+00 1.000000e+00 1.000000e+00
> 1.000000e+00
> /RequiredEffect 1.518 1.294 0.915 1.995
> 1.773 1.995 1.585 1.773 1.585
>
> /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
> 1.000000e+00 -1.000000e+00 0.000000e+00
> 1.000000e+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
> -1.000000e+00 0.000000e+00 1.000000e+00
> 0.000000e+00 -1.000000e+00 1.000000e+00
>
>
> .mat:
> /NumWaves 3
> /NumPoints 41
> /PPheights 1.000000e+00 1.000000e+00
> 1.000000e+00
>
> /Matrix
> 1.000000e+00 0.000000e+00 0.000000e+00
> 0.000000e+00 1.000000e+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 1.000000e+00
> 0.000000e+00 1.000000e+00 0.000000e+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
> 0.000000e+00 0.000000e+00 1.000000e+00
> 0.000000e+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
> 0.000000e+00 1.000000e+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 1.000000e+00 0.000000e+00
> 0.000000e+00 1.000000e+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 1.000000e+00
> 0.000000e+00 0.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00 0.000000e+00
> 0.000000e+00 0.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00 0.000000e+00
> 0.000000e+00 0.000000e+00 1.000000e+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 1.000000e+00
> 0.000000e+00 0.000000e+00 1.000000e+00
> 0.000000e+00 0.000000e+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 0.000000e+00
> 0.000000e+00 0.000000e+00 1.000000e+00
> 0.000000e+00 0.000000e+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 0.000000e+00
> 0.000000e+00 0.000000e+00 1.000000e+00
> 0.000000e+00 0.000000e+00 1.000000e+00
>
> > Hi Sergiu,
>
> > could you please specify what randomise command you
> typed
> > *exactly* and also copy/paste your design.mat and
> design.con?
>
> > Thanks,
> > Gwenaelle
>
>
> > --- En date de : Jeu 3.4.08, S. Groppa
> <[log in to unmask]> a écrit :
>
> >> De: S. Groppa <[log in to unmask]>
> >> Objet: [FSL] empty vox_tstat after TBSS &
> randomise
> >> À: [log in to unmask]
> >> Date: Jeudi 3 Avril 2008, 18h37
> >> Dear list,
> >>
> >> I am trying to run randomise on a 4D all_FA or
> all_FA_sk.
> >> with 40 subj, 3 groups and getting empty vox_tstat
> for all
> >> contrasts...??
> >>
> >> how comes??
> >>
> >> sorry for the question, but I found no explanation
> in the
> >> list.
> >>
> >> thanks a lot and best wishes
> >> sergiu
>
>
> >
> >
> _____________________________________________________________________________
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> en contact. http://mail.yahoo.fr
>
>
>
> --
> Mit freundlichen Grüßen
> S. Groppa
> mailto:[log in to unmask]
_____________________________________________________________________________
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