NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Registering Image Volumes in Slicer
Steve Pieper
National Alliance for Medical Image Computing http://na-mic.org
Requirements
• The tools described here are part of Slicer 2.5
http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.5_Getting_Started
National Alliance for Medical Image Computing http://na-mic.org
Data to Use
• Get the two datasets:http://www.na-mic.org/Wiki/images/a/aa/Reg-sample.zip
http://www.na-mic.org/Wiki/images/5/5c/Mrt-images.zip
• These are the same subject, taken on two different scanners– 1.5 Tesla diagnostic MR scanner (low
resolution for better interactivity)– 0.5 Tesla intraoperative MR scanner
National Alliance for Medical Image Computing http://na-mic.org
Load First Data Volume
1: Click Add Volume
2: Pick Nrrd
3: Browse to reg.nhdr
4: Click Apply
National Alliance for Medical Image Computing http://na-mic.org
Load the Second Volume
1: Click Add Volume
4: Click Apply
3: Browse to I.001 in mrt images dir
2: Use Basic Reader
National Alliance for Medical Image Computing http://na-mic.org
View Initial (Mis)Registration
Put One Volume inBackground with Bg andOne in Foreground with Fg
Use Fade Slider andToggle to Compare
National Alliance for Medical Image Computing http://na-mic.org
Add a Transformation
1: Select Volume
2: Click Add Transform
Transform and Matrix areCreated Around Selected Volume
3: Double-Click MatrixTo Enter AlignmentsModule
National Alliance for Medical Image Computing http://na-mic.org
Transformation Notes
• Slicer Transforms are 4x4 matrices– Support Linear Affine Transformations
• Transformations can be Nested in a Hierarchy– But Automated Registration Requires Only One Level
(like current example)
• Transformations are RAS <-> RAS– RAS = Right, Anterior, Superior– Meaning they are in Patient Space (mm)– Scan Order (Axial, Coronal, etc) Already Taken into
Account Before Transformations are Applied
• Transformations are Stored in MRML Scene File
National Alliance for Medical Image Computing http://na-mic.org
Manual Transform
Local: Moves Relative to VolumeGlobal: Moves Relative to World
Use the Sliders, Buttons andMouse Actions and WatchHow the Volume Moves
Use Left Mouse Button in SliceViews to Edit Transform
Reset to Identity
National Alliance for Medical Image Computing http://na-mic.org
See/Edit the Actual Matrix
Matrix is Shown in theProps Tab
You Can Edit the Elements(If you know what you are doing!)
The Last Column is the Translation
National Alliance for Medical Image Computing http://na-mic.org
ITK-Based Automated Registration
Go to the Auto Tab
Volume to Move is the One Inside the Transformation
Reference is the One Outside the Transformation
Use Intensity Registration, withMutual Information Method,Normal Interface. Optimized forMR-MR, but Works Well forOther Tasks Too.
National Alliance for Medical Image Computing http://na-mic.org
Registration Modes
Scroll to See the Start Button if needed
Pre-Programmed Modes:-Coarse: large steps, animated-Fine: small steps, animated-Good and Slow: run tocompletion, usually gets goodresult-Very Good and Very Slow:run to completion; if this doesn’twork, use manual to get closer
Runs the Registration
National Alliance for Medical Image Computing http://na-mic.org
Registration Result
• After Running Very Good and Very Slow (actually takes less than a minute on a laptop for this data)
National Alliance for Medical Image Computing http://na-mic.org
Resampling Volumes
• Use the TransformVolume Module– New in Slicer 2.5
• Makes a New Slicer Volume with Dimensions, Spacing, and Orientation to Match Registration Target
National Alliance for Medical Image Computing http://na-mic.org
TransformVolume
Select Transform Node from Data Tree (NB: May Contain MultipleVolumes to Transform)
Deformation Not Yet Supported
Select ReferenceVolumeResample Mode and the Volumethe Result Should be Like (In Termsof Orientation, Dimensions, Spacing)
Generally Cubic for Image Volumes,Nearest Neighbor for Labels
Creates New Volumes with Given Prefix
National Alliance for Medical Image Computing http://na-mic.org
Nonrigid Registration• Uses the AG Module
– Developed by Alexandre Guimond, PhD while working at the BWH Center for Neurological Imaging (Charles Guttmann, M.D., Director); Slicer Integration by Lifeng Liu, PhD.
– Based on Original Work Done at Inria, France– A. Guimond, A. Roche, N. Ayache, and J. Meunier.
Multimodal brain warping using the demons algorithm and adaptative intensity corrections. Technical Report 3796, Institut National de Recherche en Informatique et en Automatique, Sophia Antipolis, France, November 1999.
– ftp://ftp.inria.fr/INRIA/publication/publi-pdf/RR/RR-3796.pdf
• Implemented Using Custom VTK Classes (not ITK)
• Nonlinear Registration Not Supported in MRML Tree, so Resampled Volumes are Created
National Alliance for Medical Image Computing http://na-mic.org
AG Basics
Select Reference Volume and Volume to Move
Create New Resampled Output
Optional Label Map (e.g. ICC)
Optional Second Channel
Run Registration
National Alliance for Medical Image Computing http://na-mic.org
AG Methods
Methods:-Initial (Optional) Uses SlicerMatrix as Starting Point; Select Matrixin Transform Tab-Linear Run Linear Alignment as Selected in Expert Tab-Non-linear Run Warp TransformRegistration as Selected in Expert Tab
NB: Registration is Multi-Step: First Linear (Translation, Rigid, Affine) Then Non-Linear Warp
National Alliance for Medical Image Computing http://na-mic.org
AG to Transform Volumes
Co-Registration:-Resamples Volumesusing Currently CalculatedTransformation (Linear andNon-linear-Run Volumes One-at-a-Time-Useful for Atlas Registration
Scroll Down
National Alliance for Medical Image Computing http://na-mic.org
AG Transform Tab
Select Matrix and Toggle On/OffButton to Use Initial Transform
Load and Use Existing Non-LinearWarp File (One Displacement Vectorper Voxel)
Export Current Linear Transformto Slicer Matrix
Save Non-Linear Warp to a File (.vtk format)
National Alliance for Medical Image Computing http://na-mic.org
Some AG Expert Settings
Where to Stop the Linear Step
Type of Non-Linear
Intensity Compensation Function
Registration Metric (GCR is GeneralizedCorrelation Ratio;Robust for Multi-Modality)
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