With the files selected it's possible to visualize it in Axial, Coronal or Sagittal views (The 'Axi/Cor/Sag' option is currently not available).

The first image shown is the 'Fixed Volume', the second is the 'Moving Volume' and the third is are both, one above another. To see how much far are the two images, move the 'Cross Fade' slide option.

To start the registration click in 'Add Landmark' it will created a landmark in the image. The landmark might appears far from the image. Move the landmark to where the image should be and change the views (between axial, coronal and sagittal) to see the exactly landmark's localization. To adjust it better click in the '+ Zoom' it will zoom all the images.

Move the landmark to your region of interest and when the fixed volume's landmark and the moving volume's landmark be in the same location of each image, add another landmark and move it the another region of interest. It's a rigid registration, so, 3 landmarks should do the work of registering.

This is a image after three landmarks placed at the skul-base. Looking at the third image (fixed image and moving image on top of each other) it shows that mandible and the maxilla had a noticeable change after the treatment.

Note that this is just for visualization, it means that the files are note modified yet. In order to apply the matrix generated (Target Linear Transform) go to 'Apply Matrix' module. Instructions here.

Observation: Slicer do not save files automatically. To have the files saved on the computer click in 'File' on the upper left corner and then in 'Save'. A new window will appear allowing the user to modify the file name, format and directory.

For more information about ITK-snap.

For more information about 3D Slicer

For more information about the CMFreg documentation.

For access the CMFreg source code.