Hi,
Thresholding, masking and other post-stats are not carried up to the higher level.
You should apply a mask in your higher-level analysis if you want to restrict the analysis.
All the best,
Mark
On 6 May 2014, at 19:13, ramy kirollos <[log in to unmask]> wrote:
> Dear FSL users,
>
> I am using a Fixed Effects second level analysis to combine the 3 runs of a subject. In the first level analyses I used a prethresholded mask. In the second level analysis, I would like the mean activity across the 3 runs within this mask, but instead it is showing me whole-brain activity.
>
> Any advice on how to setup my analysis in 2nd level so that activity is restricted within the mask?
>
> Thank you,
>
> Ramy
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