Hello Donna,

thanks for your help!

Donna Dierker wrote:

> 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.

Does that mean that Surefit is not used in combination with SUMA anymore?

> 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.

Yes, that makes sense. However I'm not sure if it explains why difference vectors based on pairs of nodes in the coord file are different from the difference vectors based on the coordinates that SUMA reports...

>
> 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.

Ok, that sounds like a good idea. That would mean adding some scripting code to this @SUMA script? Please let me know how I can help.

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

Thanks, I just did that.

best,
Nick