Hi Graham,
yes, they are all in the same coordinate system. mri_ca_register takes a transform to initialize the nonlinear atlas alignment, but everything is in the same voxel space at the end of the day.
cheers, Bruce On Tue, 12 Sep 2006, Graham Wideman wrote:
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
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