For just looking at the data, the time shift stuff is unimportant.

It used to matter if the datasets were marked as "functional" or "anatomical", since AFNI would only let you display "anatomical" data as the grayscale underlay and "functional" data as the color overlay. This is no longer true.

However, AFNI (that is to say, I) consider EPI time series data to be anatomical and statistical maps to be functional. For what you are doing, the anatomical type is slightly more appropriate. But only slightly. It doesn't make much difference any more, as mentioned above.

If you want to look at timeseries graphs, you will set the 4D dataset you create with to3d to be the AFNI underlay dataset, then open an Image and Graph viewer.

bob cox