Sounds like you’re inadvertently touching on a topic that is still somewhat of a moving target in MRtrix3 development: how to represent and manipulate multiple spherical functions within a single image. This is a capability that will be increasingly utilised in the future, especially once @dchristiaens’s SHARD reconstruction makes its way into the software. But right now the capabilities for handling such are severely limited.
You can see in this Pull Request (the contents of which were included in the 3.0.0 release) that the
sh2amp commands are already compatible with such data, where the fifth image dimension is used to encode b-value shell. The fact that the
amp2sh command does not possess the corresponding capability should be considered a feature gap, and would be an entirely reasonable feature request if you wish to add it to the GitHub image list yourself (or we can add it for you).
The functionality would essentially be equivalent to running
amp2sh multiple times, manually specifying each b-value in succession using the
-shell option (as shown by @bjeurissen), ensuring that the
lmax is identical for all shells, and then running
mrcat to concatenate the results along the fifth image dimension. Note however that the only commands that would be capable of reading and interpreting such an image as intended would be
sh2amp; even loading that SH image in the
mrview ODF plot tool, there is not yet the capability to toggle the visualisation between shells within the interface. So while you can do it, you may not actually get any benefit from such currently.