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Dear all,

I probably make things more complicated than they are. I am actually just
interested in the t-values (tstat images only). After having giving it a
thought, I guess it doesn't really matter if 1- or 2-tailed at this stage,
as I am taking the raw t-maps, and threshold later. 

So here is what I did:
I restriced the view to only show me values in the range of 2.23 to 6.21 in
the tstat_1, applied a LUT, and did the same for tstat_2. I then added those
views together, having red hot LUT for control>patient, and cyan hot for
control<patient t-values. 2.23 is the critical t-value for p=0.05 (2-tailed
ttest).
Is this a reasonable way of doing it, or do I miss something here. I.e. how
are the t-maps using design_ttest2 calculated, with n=n1+n2 (so 12 in my
case), or n=n (6 in my case)

Thanks in advance for your opinion.

Torsten


On Fri, 27 Apr 2007 14:08:29 +0100, Ged Ridgway <[log in to unmask]> wrote:

>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
>>