Hi,
Yes, your assumption is correct with regards to setting within subject
2nd to fixed effects.
To be precise, we are unsure what the problem is, other than not the
output not making sense. With our setup we get two contrasts out of
3rd level that are identical to each other when we examine the
opposite contrasts sent up from second level.
To explain in more detail: As shown in the attachments in the first
mail, the contrast c1 from 2nd level is condition 1 > condition 2, and
contrast c2 is condition 2 > condition 1. On third level we want to
examine the contrast C1 patient > control and C2 control > patient.
Since C1 c2 is identical (down to individual voxels) to C2 c1,
something is very wrong here - but we are unable to see what is wrong
here.
We have also conducted the same analysis, only difference was that we used a
unpaired, instead on paired, t-test between the two groups (normal vs
patients). The result was the same...
Do you think contrast masking could be an idea?
Thanks in advance
Cheers.
Hallvard
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