how not to assume orientation is encoded correctly

[raamana]

update mrivis docs to note that all my packages assume orientation is encoded correctly

find ways not to assume it.

[raamana]

related ref: https://www.frontiersin.org/articles/10.3389/fninf.2020.00018/full , which talks about EPI-to-Anatomical inconsistency in orientation (esp. L , R flip). They establish the presence of L-R flip by checking if the linear affine alignment cost between 1) EPI and T1w (originally supplied unflipped images) is higher than 2) EPI and intentionally flipped T1w in L-R. If the latter is smaller, one of the original images has a L/R flip.

a helpful visualization could the cross-modal edge overlay of EPI on T1w, and comparing it another based L/R flipped T1w