Hello, in our lab we are experimenting with qsiprep. Unless we missed something, we did not find an option to register the T1 to the subject (as opposed to the default behoviour, register dwi to ACPC-aligned T1). Indeed, we acquire our datasets with canonical (pure axial) orientation, thus realigning to ACPC causes a lot of rotation, depending on head position.
I assume that this option would make things too complex to manage?
Alternatively, it would be useful a switch to force the output matrix size. For the same reason above, we end with preprocessed dwi image sizes that are wildly different bewtween subjects. Forcing to a common, user-defined matrix would make the data easier to manage afterwards.
BR, Federico