I (still) need to rotate some surfaces so that they enclose MR data that is sliced the same angle as data from the same brain was sliced on a microtome.

Transforming surfaces once made is a bit tricky.

Is there any reliance on the midline being on the y axis past the point of mri_fill/pretess?

(for: mris_fix_topology -mgz subject rh -orig orig -inflated inflated -sphere qsphere -ga -noaseg -noaparc 

mris_make_surfaces -noaseg -noaparc)

what I'd do is take the results from an ACPC aligned set, and apply a transform to T1,wm,filled,filled-pretess and so on.

then run the surface making script as normal.

the brain's midline is pretty rotated in Z the way I want it. It takes ages to run this so I'm wondering if there is any issue before I go ahead and try it.

best,

Colin