Not sure what you mean. 3dAutobox reduces the input file to the box that contains non-zero data, so you may want to apply 3dAutomask as a preceding step. Using the output of 3dAutobox, you can then apply the same box to the other data with 3dZeropad. Here's an example of how that might work:
3dAutomask -prefix test_am -dilate 2 epi_r1+orig'[0]'
3dAutobox -prefix test_am_abox test_am+orig.
3dZeropad -master test_am_abox+orig. -prefix epi_r1_abox epi_r1+orig
If the last step fails, you can script this to do this by sub-brick or by groups of sub-bricks, like a third of all at a time.
