These are the results I get with the cloud compare fine registration with RMS. As you can see when i look at the model to model distance and view it in shape population viewer with the same setting… our land marks show almost exact matches ( Green ) in the viewer.
I get almost same resutls with the cloud compare iteration method also. Again very good match on the landmarks we put in surgically.
However when i used the CMF surface registration results are like this, with not very good registration.
I managed to get good results with IGT fiducial registration wizard but it was after lot of playing around with fiducial markers and changing ti manually until i could get very good alignment. This took lot of time to chaging the location of fiducials until it gave this result.
**So my major Problem is ** why is cloud compare fine alignment gives better results in comparison to CMF surface registration ? Because as i read on both the module they use the ICP algorithms and why should it then give different results ?
Today i installed nightly version because i wanted to try it with CMFreg ROI method since i did not knew how to do only to select the region of interest as you suggested in a stl file and as for some reason in the stable version in my computer ROI registration was not marking the regions of interest for some reason. So i tried with nightly version and it worked and gave excellent results with ease compared to IGT registration. But still cloud compares registration is fully automated as i do not need to select any points.
So i am out of interest and also because almost all the research that we have planned or are currently been conducted involves registration i am very much interested in learning about this and for publication purposes i think it is much convenient to stick to one software (3D slicer) to do the registration and the model to model distance and colour mapping.