We distinguish between registration, the process of determining the transformation that aligns images, and transformation, the processes of transforming (and regridding if required or specified) one image into another space using a given fixed linear or nonlinear transformation.
Registration parameters and the algorithm sequence (initialisation) differ, hence you will end up with different transformations from the group-wise iterations in (
population_template) and direct pairwise registration of subject and template data (
mrregister). If you want to use images that were not used in the template creation, you’ll need to use the latter approach. Otherwise, you can use either warps but I do not know which one is better suited.
-noreorientation option currently has no effect if the number of volumes does not match that of a spherical harmonics image but that will change in the next version. In the FBA pipeline, we recommend to transform images without reorientation, fixelate, and then reorient the fixels to avoid FOD segmentation artefacts in the fixel calculation step. For template creation, you’d typically want the FODs to be reoriented when warping FODs to preserve directions and connectivity between adjacent voxels but this is not necessary for scalar quantities such as FA.