5. 3D Alignment of 3D Images

At this point of the process, all sections of brains are aligned. In this step we want to align brains in the same space coordinates to be able to compare them statistically.

The first step is to align them in term of rotation and translation (rigid registration). Then a non rigid registration (B-spline) is used to deforme locally organs to align them.

There are two ways to align brains: image per image or pipeline. A pipeline can be used to process several brains at the same time.

First, if you click on , the following options appear :

You have three choices : Rigid Registration, Bspline Registration or Pipeline.

Image per Image

If you click on Rigid Registration or Bspline registration,

For Rigid Registration, load the fixed image wich might be called: Recale.mhd. Do the same thing for the moving image wich might be also called Recale.mhd. Once both are loaded, click on the compute button :

For the B-spline registration, you have to load images called RigidPipeline.mhd for the moving image. For the fixed image always load the Recale.mhd. In the case of B-spline regsitration, you have to load the mask of images. They should be called MaskRigid.mhd. Those images (mask) are created during the Rigid Registration step.

Once the step is done, save images using the save button.

Pipeline

If you want to process several images at the same time, use the pipeline button: , the following options appear :

First load the fixed image, , then load images in the browser using the add image button, , then choose the type of registration: rigid, B-spline or all Registration and press the compute button, .

All images are saved in their own directory with the name RigidPipeline.mhd and MaskRigid.mhd if you have used  the rigid registration process and with the name BsplinePipeline.mhd if you have used the B-spline registration process.

Issues during the B-spline registration step

Once all the registration process is done, images are aligned in the same space coordinates. But, sometimes, due to the sectionning procedure, some parts of the sections are missing:

This create huge artefacts in the B-spline registration step as shown in the following figure:

To correct this artefact, the missing part has to be manually defined. To do that return to the main menu and click on .