Hi Torsten,
Perhaps Jesper will correct me, but I think randomise does
right-tailed tests only. If you use design_ttest2 it produces two
contrasts, so that *tstat1* files are for grp1 > grp2 and tstat2 are
for grp1 < grp2 (where the latter is actually a right-tailed test of
the contrast grp2-grp1).
So if you are interested in the two-tailed alternative, then the
p-values are half what they should be (i.e. overly significant). I
think the two (1-p)-value images that get stored have zeros where the
other contrast is significant, so you could get a single two-tailed
(1-p)-value image by adding the p-images together, with a little
maths, something like (untested):
# for (ba)sh, where blah is something like image_max
fnm=blah_tstat
# for (tc)sh, where blah is something like image_max
set fnm=blah_tstat
# then:
avwmaths ${fnm}1 -mul -1 -add 1 -mul 2 ${fnm}1_p2
avwmaths ${fnm}2 -mul -1 -add 1 -mul 2 ${fnm}2_p2
avwmaths ${fnm}1_p2 -add ${fnm}2_p2 ${fnm}_p2
avwmaths ${fnm}_p2 -mul -1 -add 1 ${fnm}
where the final image is (1-p) for two-sided p-values.
Hope that helps,
Ged.
Torsten Ruest wrote:
> Dear Jesper,
>
> thanks again. I've run design_ttest2 design 6 6 to create my design files.
> In the description it reads "for the two-group unpaired t-test case". So I
> never used the glm gui. And these 2 groups are different, I mean they are
> genetically different, therefore I thought this setup should be right. But I
> am not sure if the output would be 2-tailed or not. I've assumed so, since
> the software cannot assume in which direction it would go, and because of
> the output (negative and positive values), I assumed that it's 2-tailed.
> So my only uncertainty is currently if the output of design_ttest2 design 6
> 6 would be 2-tailed or not.
>
> Thanks again for efforts.
>
> Cheers,
>
> Torsten
>
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