PET Center University of Debrecen 2005

1. Positron Emission Tomography- training -IBRO CEERC Summer School 2005MiklósEmri , IvánValastyán, Gábor Opposits PET Center University of Debrecen 2005

2. Exercise5: Image registration based on the manually adjusted affine transformation

3. Adjustable transformations Translation Rotation Scaling Shearing

4. Load two unregistered volumes • Clear all volumes and VOIs • Select VOI toolbox and choose the Delete all VOIs button • Select File/Close all volumes menu • Select Dual Visualization mode on the toolbar. • Click on the reference (left) volume viewer: the border of this viewer will turn red. • Load practice/p5/t1.mnc data file (T1-weighted MRI), select gray scale and adjust the low and high level of the colour palette. • Click on the reslice (right) volume viewer: the border of this viewer will turn red. • Load practice/p5/fdg.mnc data file (FDG study) and adjust the colour palette. • Select the Fusion visualization mode. • Try the Blending-value ruler near the volume selector boxes.

5. Manually adjusted affine transformation based registration • Choose the Register visualisation mode from the toolbar. • Switch on the Sync cursor button • The cursor will be positioned to the same point in all the three volume viewers. • Choose the Transform toolbox • Click on the reslice (middle) volume and it becomes the source volume of the transformation. • Translate or rotate the source volume using the mouse or the sliders. • Try the fused visualisation mode and the transformation manipulation buttons • Watch on the fused volume viewer and stop when the transformation is OK press the Apply button.

6. Exercise6: Landmark Based Registration

7. Landmark Based Registration • Choose the register visualisation mode from the taskbar. • Click on the first (reference) volume viewer and load the reference volume of the registration (practice/p5/t1.mnc). • Click on the middle (reslice) volume viewer and load a volume from the same patient. (practice/p5/fdg.mnc). This volume will be transformed into the coordinate system of the reference volume. • Select the 6-parameter transformation type (3 translations and 3 rotations) from the XFM-type list box. • Switch on the edit mode button:. • Switch off the sync cursor mode button on the toolbar. • Move the cursors of the reference and reslice volume viewer into the anatomical equivalentanatomical position and put down landmarks: • by the right mouse button, or • by the spacebar on the keypad. • If a point is not in the proper place drag it with the left mouse button and move it into the best place.

8. Landmark Based Registration • Put additional 4 landmarks. In the case of the first 4 landmarks only the translation parameters will be calculated while if there are more than 4 landmarks the parameters of the rotation will be estimated too. • When you have exactly as many landmarks as you need, select the target ‘lattice’ of the transformed volume. • Select the interpolation method. (Possible values: ‘nearest neighbour’, ‘linear’ ) • If you want to save the landmarks or the transformation matrix into a file save them before using the apply button, because after the transformation of the reslice volume all landmarks will be deleted and the transformation matrix will be set as identical matrix. • Click on the Apply button to transform the reslice volume into the coordinate space of reference volume. Important note: This procedure erases all landmarks and sets the current transformation matrix to identity.

9. Landmark Based Registration

10. Check your result • Select the dual visualization mode (clear all landmarks!) • Load into the left volume visualisation area the practice/p5/t1-fdg.mnc • Choose the bottom volume selector box your registered fdg volume (t_fdg.mnc) • Choose the fusion visulization mode and check the difference of the volumes. • Repeat the registration if it is necessary! • Try to solve the butanol-T1 and metionine-T1 registration. Use the practice/p5/but.mnc and practice/p5/met.mnc files!

11. Task 1: Create VOIs on fused images