Hi Duong,

1,2) Those first 6 time points never even made it to the
results directory because of that initial 3dTcat command.
So after those 3dTcat commands, it is no longer necessary
to remove any time points, they do not exist anymore.

3) The single volume dataset called vr_base was extracted
at the end of the tshift block. Since it has only one
volume, no selection index is required.

4) Understand the script better before you think to change
anything. The effect of the script is indeed that volreg
happends first, as those transformations are concatenated
and then applied to the EPI data.

- rick