Hello

I work with rodent fMRI and when using 3dDeconvolve, I use a custom-made stimulus file as a regressor/model. Also, I normalize each rodent's dataset to the baseline before inputting it into 3dDeconvolve. However, when I plot the -fitts output file, I notice that the fit'ed model doesn't start at 0. I am comparing multiple conditions and was wondering if this baseline shift of the fitt'ed model can cause miscalculations when doing a 2 sample t-test?

I have attached 2 images. The first is the raw data (blue) with the -fitt output.. showing good fit.. however you can see the fit time series baseline is above 0. The second image is comparing the 3 conditions' fit time series.. all start above baseline and it appears that the blue SHOULD have a significantly higher amplitude.. but due to the shift, it seems ANOVA isn't finding significance during 2 sample comparisons..

Is there a way to fix this? I thought perhaps normalizing the fit time series to baseline and inputting these again back into 3dDeconvolve.

Thanks for any assistance