Hi Gaurav,

This is a simple question which is a little difficult
to answer without just pointing to the regression class
handout. I hope that you have read through that again.

But as with any regressor in the model, it is fit to the
data along with every other regressor, where the baseline
terms are modeled with polynomials per run.

The answer whether 3dD uses the average of the time series
or just the average during rest periods for the baseline,
the answer is no, neither. The baseline is modeled as
polynomials, and counts the same as every other regressor
in the model.

For this I suggest you read the single subject analysis
tutorial, and focus on the section about the X-matrix.

The tutorial goes along with and is contained in AFNI_data6.
See AFNI_data6 FT_analysis tutorial .

- rick