Do you have a dataset whose coordinates and orientations are marked incorrectly? Is that the problem? If so, then 3dLRflip is designed to flip the data left-right, leaving the header unchanged. An alternative would be to change the header to the correct orientation matching the data on disk. 3dLRflip was written for a specific case where a user here had acquired data on one subject backwardsly, analyzed it, and then realized that all that subject's stuff was wrong. We patched the problem with 3dLRflip.

However, if you have datasets that are oriented correctly (that is, the header and data match), and want to re-orient the two files (header and data) to a different ordering, then program 3daxialize or 3dresample is what you want.

3dLRflip is just for the case where the header and the data do not match! And when you want to flip the data rather than the header (which you would do with 3drefit). This should be an unusual circumstance. It has only been used once to my knowledge, in the conditions described above.