Folks:
I am (still!) trying to get traction on some aspects of the current FS coordinate system(s).
In the recon-all pipeline, am I right in assuming that from orig.mgz all the way through to aseg.mgz and then on to brain.mgz, wm.mgz and so on, that there's NO resampling to a new coordinate system (eg: the specific brain's data doesn't get resampled to rotate or talairach it)?
Ie: if you overlay, for example, wm.mgz's data onto orig.mgz, it'll align properly? (Ie: overlay the raw voxel data, unmolested by any clever viewer transforms...)
I *think* I'm right on this, but it's hard to be sure, because for example, mri_ca_normalize's docs say that it takes a gca transform file as input. But that *might* be so that mri_ca_normalize can resample some other standard file to match the specific brainmask.mgz file.
<scratching of head>
Graham