Fixel ids got flipped

[zhao-cy]

Sometimes we obverse that the fixel id got reverted. We suspect that this happens when loading into python and convert .mif -->nifti2. So far converting for 3D images is fine.

Goal is to figure out and make sure what happens here / what and where the bug is, so that we can predict when it happens.

updates on 2022.5.12:
Matt's suggestion: add a --flip flag. If output images look like ___ (provide an example, jumble image), then use --flip=TRUE