landmark registration

Landmark Registration Tutorial

Landmark Registration module is used to approximate two time points images by placing landmarks in equivalent positions into the images. At the end the module creates an Registration Matrix file (.txt, .tfm, .mat) which needs to be applied to the 'moving Volume'.

PS: The landmarkRegistration doesn't accept zipped files (.gz, .zip, .tar) or any file that have a dot "." in the name, besides the dot of the extension (.gipl, .nrrd, .img).

To start the registration, load the files time 1 and time 2 into Slicer and select it as 'Fixed' and 'Moving' Volumes, make sure to center both files (To see how to center the files click here). Don't select anything for 'Transformed Volume'. Check the 'Linear Registration Type' option at the bottom and check the 'Registration Active' option. It will created a 'Target Linear Transform' and a 'Transformed Volume'.

With the files selected it's possible to visualize it in Axial, Coronal or Sagittal views separately and all the same time.

The first image shown is the 'Fixed Volume', the second is the 'Moving Volume' and the third are both, one above another. Move the 'Cross Fade' slide option to see just one of the two images.

To start the registration click in 'Add Landmark' it will created a landmark in the image. To adjust it better click in the '+ Zoom' it will zoom all the images.

Move the landmark to your region of interest until the fixed volume's landmark and the moving volume's landmark are at the same location of each image, add another landmark and move it again to the 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 skull-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.