Positron Emission Tomography- training -

IBRO CEERC Summer School 2005

Miklós Emri , Iván Valastyán, Gábor Opposits

PET CenterUniversity of Debrecen

2005

Exercise 5: Image registration based on the manually adjusted affine

transformation

Adjustable transformationsTranslation

Rotation

Shearing

Scaling

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.

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.

Exercise 6: Landmark Based

Registration

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 equivalent anatomical 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.

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.

Landmark Based Registration

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!

Task 1: Create VOIs on fused images