Hi Nick,

Ziad wrote this script years ago, when SureFit was a stand-alone program that used the lower left corner of the bounding box as the origin. Since then, SureFit functions (including segmentation) have been merged into Caret, which looks at things from a more coordinate system point of view than the old SureFit, which was more slice-based.

The params file's AC[xyz] and whole volume counterparts aren't set, because John Harwell didn't code Caret to store everything SureFit used to.

But the fact that the origin has moved from the lower left corner of the bounding box to the +tlrc origin is the biggest source of your error.

The exact steps needed to get around this problem aren't crystal clear to me at this point, but I am reminded of a visit to NIH in February 2006, when Ziad made a small change to Vecwarp for me, which he annotated in the usage like so:

N.B.-1: For those using SureFit surfaces created after
the SureFit/Caret merger (post. 2005), you need
to use the flag -new_surefit. Talk to Donna about
this!

I think we need the -new_surefit equivalent in @SUMA_Make_Spec_Caret.

If you email me off-list, I can send you my upload link, so I can look at your dataset.

Donna
Van Essen Lab