Hi Philip,
by using the -m option in design_ttest2, you include individual group mean as the first two contrasts (tstat1 and tstat2) which are not really interesting...
What you're presumably interested in are in contrast 3 and 4 (contrasting your two groups), so anything with *tstat3/4.nii.gz.
Cheers,
Gwenaelle
--- En date de : Ven 13.3.09, Philip Koester <[log in to unmask]> a écrit :
> De: Philip Koester <[log in to unmask]>
> Objet: [FSL] Re : [FSL] Strange t-stats in vbm analysis
> À: [log in to unmask]
> Date: Vendredi 13 Mars 2009, 16h10
> Hi Gwenaëlle,
>
> thanks for your quick reply! I ran fslvbm with the standard
> scripts from the
> homepage (fslvbm_1_bet -b, fslvbm_2_template -a,
> fslvbm_3_proc and randomise
> -i GM_mod_merg_s2 -m GM_mask -o fslvbm -d design.mat -t
> design.con -T -n
> 5000 -V). My design.mat and design.con were created with
> design_ttest2
> design 20 20 -m, which represent the two groups i want to
> compare. I also
> tried the non-linear transformation in fslvbm_2_template
> which did not
> change the results. If i should upload files that could be
> more helpful, let
> me know.
>
> thanks a lot,
>
> Philip
