Beate,

> I´m not sure whether subbrick #0 (Full_Fstat) is my baseline constant

Are you sure your sub-brick #0 is full-F? If so, the scaling in your method 2 was not done correctly because your sub-brick #0 is F-statistic, not real baseline.

Overlay in AFNI is usually a statistical value such as t or F for coloring activation pattern with thresholding, and the coloring is based on the values of your underlay (whatever you prefer to colorize).

> When I choose glt_Tstat as overlay both methods show similar results.

They should be because the thresholding remains the same.

> Does scaling before 3dDeconvolve change the information contained in the statistical subbricks
> (finally when scaling after 3dDeconvolve I only scale the coefficients)?

Scaling would not change your statistics if you only have one run of data. With multiple runs, things are a little complicated, and that is one of the reasons scaling is suggested as a pre-processing step.

See more here:

http://afni.nimh.nih.gov/sscc/gangc/TempNorm.html

Gang