Let us know if you need help with this. It's pretty much what Cody suspected -- SureFit vs Caret differences. SureFit surfaces were generated in voxel space, with the origin set to the lower left corner of the cropped bounding box, and the [XYZ]min parameters (in the params file) specifying how to translate the cropped bounding box to full brain grid.

When you segment using Caret, the underlying segmentation algorithm is unchanged, but the volume loading/visualization is in coordinate space rather than voxel space, and the volume and surface are both centered on the volume's origin (causing problems during eyefat/hindbrain removal and ventricle filling if the origin is too far from the AC, or the alignment too far off AC-PC).

So the params file now really just stores the white matter and gray matter peaks.

Donna Dierker
Van Essen Lab