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