The 3dZeropad program can also cut slices off a dataset; e.g.,
3dZeropad -I -3 -prefix mork mindy+orig
will cut off 3 slices at the Inferior edge of the mindy+orig dataset and put the new dataset into mork+orig.
You can use the 3dAutobox program to find the extent of nonzero slices in the dataset. For example, on a dataset I have lying around
3dAutobox hc_MASK+orig
++ Auto bbox: x=13..47 y=13..59 z=0..23
Perhaps the 3dZeropad program should have a "-autobox" option, but it doesn't.
If you have a bunch of datasets that need to be the same size after chopping up, the "-master" option to 3dZeropad could be useful.
bob cox