Hi @Lexus_H and @bpaniagua
Sorry i was bit busy.
I did use the models Erin send for registration with CMF Regis - surface registration
With max iterations and max landmarks.
Please see the video
The registration is not good. This is similar to problem i encountered with my previous work.
I solve my problem with cloud compare but i wanted to stick to one software for my work and i got good results with CMR- ROI registration.
In this case i did not do the ROI registration because i again encountered the bug that i reported on this some time back.
I use these models in cloud compare even with default setting i got good results.
please check the color maps with both registration methods
Erin i think you can try CMF ROI method. I think it should work pretty well.
Also since you have DICOM data why don’t you do the Image registration (General Registration -BRAINS) and then do the segmentation. Then your segments will be created properly registered. It would be great if @bpaniagua or Prof @lassoan can tell further about this.
Is registration on DICOM will be more accurate than registering the Surface models/Segments ?
Despite the answer to me previously by Prof Lasso on registration i am still baffled by the accuracy of cloud compare registration over CMF Surface registration. 
In any case the problem that we set out to see seems like you are not measuring the model to model distance properly. Please see the video.