Kate,

I looked at the .1D files you sent me. I don't understand what the issue is. A negative shift does mean a shift backward in time. If I take the slice 17 before and after data you sent me and graph the 1st 100 points with the command
1dcat before_020_031_017.1D after_020_031_017.1D | 1dplot -stdin -one -use 100
then the before graph is in black and the after graph is in red. It is clear to me that the red graph is slightly shifted to be earlier in time, as it should be. A similar effort with the slice 02 1D files produces a plot where the red curve is shifted slightly to the right of the black curve - as it should be. This link [afni.nimh.nih.gov] should show you the slice 17 graph (grabbed from the 1dplot command above using xv).

Hope this helps - if not, please clarify -- bob cox