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Thanks for the reply Bob. So, just so I'm clear on this, 3dDeconvolve can do the following:
1)Concatenate all my trials together.
2)Estimate the linear trend based for a user defined time window.
3)Estimate the baseline based on the ideal.1D file ( average value of the '0's in the ideal.1D file?).
4)Subtract (2) & (3) from the original data and save for display (-fitts)