I thought about using mrregister to use midway space registration, only because that seems to be the common approach used in previous fixel longitudinal analysis / TBSS / VBM ect, and so I figured reviewers might take less issue with it as it is more commonplace.
So as you suggested I have used mrregister -type rigid -mask1 -mask2 image1 image2 -transformed_midaway image1_midway image_2midway for each pair to create 6 midway images. However after this, I notice that the midway file dimensions slightly change - e.g. all 3 images inputted are 169 x 169 x115 x45 with voxel size of 1.3 x 1.3 x 1.3 x 1. Where as resulting midway images are e.g. 170 x 173 x 120 x45 with voxel size of 1.36026 x 1.33205 x 1.33474 x 1 in one case and 171 x 172 x 121 x 45 and voxel sizes of 1.35452 ect ect for another resultant image.
So I’m unsure why this is, an how to average the 6 images with slightly differing voxel sizes/dimensions? Also wasn’t sure which command to use to perform this average - was that mraverageheader or another command?
Also when you mention about large deformations, as a ballpark, what parameters would you consider large?
Thanks very much for your ongoing help with this,