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Slicer3 Tutorial ManualRegistration

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Slicer3 Tutorial ManualRegistration

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Cheery Guo

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NA-MIC

National Alliance for Medical Image Computing

http://na-mic.org

Slicer3 Tutorial

Manual Registration

Dominik Meier, Ron Kikinis

January 2010
Overview
takes how long to do?
1. Introduction
2. Prerequisites
3. Loading Example Dataset 10 sec

4. Creating New Transform 10 sec

5. Associate Transform with Image 5 sec

6. Move Image 2 min

7. Apply & Save 15 sec

Note: contains animated GIFs, view in Presentation Mode

National Alliance for Medical Image Computing

http://na-mic.org
Introduction / Background
What is “Image Registration” or “Data Fusion” ? Before Registration
• the two terms are often used synonymously.
At a basic level they are the same thing.
• The goal is to bring two or more images into alignment such that
corresponding content (anatomy, structure) appears in the same location
an orientation when viewed together.
• In this tutorial example we have 2 MRI scans of the same subject, acquired
with different head positions, so that when they are viewed simultaneously,
they do not show matching anatomy. In other words they are “shifted” and
“rotated” relative to eachother.
• Because the image is a digital representation, registration involves a
reformatting of the stored image data. The common practice is to leave one
image as is and reformat the other in the orientation of the first.
• You could think of it as a second re-scan of the subject, along the same
orientation as the reference image.
• When you manually adjust the “display” of one image such that both
images roughly show the same location, you are performing a type of
registration.
• Because images are 3-dimensional, there are complex ways in which the
two images can differ in orientation. For the brain example shown here we
have relative shifts in any of 3 directions and 3 possible rotations (yaw,
pitch & roll). This means as many as 6 parameters must be adjusted to
register the two images.
After Registration
• 3D Slicer offers both manual and automated ways to do this task. This
tutorial explains the manual procedure. animated GIFs: view in Presentation Mode
National Alliance for Medical Image Computing
http://na-mic.org
Prerequisites

• Slicer version 3.4 or later

• Example Dataset: download and extract the dataset for this
tutorial: Slicer_ManualRegExample.zip. It should contain:
– ManualRegTutorial.ppt Power Point File with this tutorial
– ManualRegTutorial.pdf PDF with this tutorial
– ManualRegTutorial_video1.mov Quicktime Movie with Narrated
Video Tutorial
– ManualRegistrationExample_SlicerScene.mrml Slicer Scene File to load
– ManualRegistrationExample_fixed.nrrd file of first MRI image
– ManualRegistrationExample_moving.nrrd file of second MRI image to be aligned with first

• Tutorials to complete first (helpful but not required):

– Slicer3Minute Tutorial
– Loading and Viewing Data
– http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training

National Alliance for Medical Image Computing

http://na-mic.org
1. Loading Example Dataset
To get the Example Dataset loaded into Slicer:
1. Menu: File: Load Scene…
– Select the Slicer Scene file that comes with the dowloaded example dataset,
called: ManualRegistrationExample_SlicerScene.mrml
– This will load all the associated images

1. Select Layout: From the icon bar, click on the

Layout menu and select “Four-up Layout”.

1. Link Views: Click on the Ring Icon in any of the

slice views to link all the views together. This
will save you the work of making selections for
each slice window separately.

1. Choose Foreground: moving

2. Choose Backgroung: fixed.

National Alliance for Medical Image Computing

http://na-mic.org
Adjust Slice Views
• To interactively align images, we need
to see them both at the same time:

• Set Visibility Slider to halfway between

foreground and background. This
allows you to see both images.

• Note how the display changes as you

move the slider.

Note: For your own dataset, you

may need to adjust the level as
well as each image’s Window &
Level settings to comfortably see
both images.

National Alliance for Medical Image Computing

http://na-mic.org
Create New (blank) Transform
1. You can create a new Transform in the
Data module directly:

2. Right-click on the “Scene” node in the

MRML tree. From the pulldown menu
select: “Insert Transform Node”

3. We change the name of the new transform:

1. Click on the little triangle to expand the

“MRML Node Inspector” tab at the bottom
of the panel

2. select the new node (“vtkMRMLLinearTransformNode”)

3. type the new name, e.g. “ManualInit”

4. hit “ENTER”

National Alliance for Medical Image Computing

http://na-mic.org
Link Image to New Transform
1. You see the newly created transform
listed along with the two image volumes.
We now associate the moving image with
the transform:

1. In the MRML tree window, select the

node for the “MRI_moving” image and
drag it on top of the “Manual Init”
transform. You should now see the
diagram updated with the volume listed
within the transform

animated GIF: view in Presentation Mode

National Alliance for Medical Image Computing

http://na-mic.org
Move Image
1. Return To the Transforms module
2. Move the sliders to align the two images:
1. Move the translation sliders labeled “IS” to the left
until it reads about “-21”. Watch the display update
as you move the slider
2. Move the “PA” translation slider to the left while
watching the display until the two brain roughly
align. The “PA” slider should read around “-24”
3. Move the “IS” rotation slider to rotate the volume
clockwise until the axial planes have roughly the
same orientation. (ca. 14 degrees).
4. Move the “LR” translation slider to the right to
animated GIF: view in Presentation Mode
compensate for the shift that occurred from the
rotation. Reading now is ca.”+26”.
5. If you get stuck you can easily start over by clicking
the “Identity” button at the bottom, which will reset
the transform.
6. You can tune the sensitivity of the translation
sliders by setting the min and max. Setting smaller
range allows more precise changes.
7. You can also move by entering the numbers in the
text fields and the hit the “TAB” or “Return” key.

National Alliance for Medical Image Computing

http://na-mic.org
Apply Transform
• You can now use this transform as input to an automated
registration: In most automated registration modules you will
find a menu called “Load Transform” or “Initial Transform”.
To use simply select from the pulldown menu.

• You can save the transform to apply elsewhere. This is done

via the “File/Save” menu.

• You can apply the transform to other volumes. You can drag
any other volume inside the transform to apply it and then
select “Harden Transform” (see next page) to finalize, or you
can use the “Resample Volume” module for more options.

National Alliance for Medical Image Computing

http://na-mic.org
Apply & Save
We apply the transform to the moving image and
save the result volume:

1. Go back to the “Data” module

2. Right-click on the “MRI_moving” image.

From the pulldown menu, select “Harden
Transform”. This finalizes the transform and
resamples the volume in the new orientation.
You will see the “MRI_moving” node moved
back out into the main hierarchy level.

National Alliance for Medical Image Computing

http://na-mic.org
Save
1. Select “Save” from the File Menu. In the Dialog uncheck
all lines except for “MRI_moving”. In the “FileName” field,
double click and select a new filename, e.g.
“ManualResult.nrrd”
2. To also save the transform, check the box next to
“Manual Init”. The transorm will be saved as a small text
file containing all the necessary parameters.
3. click “Save”.

National Alliance for Medical Image Computing

http://na-mic.org
What Next
• Try the automated Registration Tutorial or one of the tutorials from
the Registration Case Library.

– http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:UseCaseInventory

– http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration#Registration_in_3D_Slicer