Image Registra,on with 3D Slicer

Sonia Pujol, Ph.D.

Director of Training & Educa,on, 3D Slicer
Assistant Professor of Radiology
Brigham and Women’s Hospital
Harvard Medical School

 Objec,ve
•  Guiding you step-by-step through the process
of automa,cally registering two structural MR
datasets acquired on two different subjects
using rigid and non-rigid registra,on

•  This tutorial is built upon the Registra,on Case

Libray 31 tutorial available at
hSp://www.na-mic.org/Wiki/index.php/
Projects:Registra,onLibrary:RegLib_C19

© Sonia Pujol, Ph.D. All Rights Reserved 2
 Mo,va,on

Registra,on algorithms bring

different image datasets into
Image 1 spa,al alignment, in order to
achieve anatomical agreement.

Image 2

3
 Before Image Registra,on

Image Space 1 Image Space 2

V1 V2

4
 Image Registra,on
Image Space 1 Image Space 2

I! 2 = T (I 2 )
V1 V2

By applying the registra,on transform T to the ini,al volume I2, we generate a new
volume spa,ally aligned with the volume I1.
Image registra+on enables the extrac+on of complementary informa+on from the two
volumes.
5
 A\er Image Registra,on
Image Space1

I! 2 = T (I 2 )
I1

~
I1

6
 Tutorial Dataset
•  Clinical study: Mul,-contrast group analysis

•  The case includes T1-weighted and T2-

weighted MRI scans of two subjects A and B.

•  This dataset is Registra,on Case #19 of the NA-
MIC registra,on case library (P.I. Dr. Dominik
Meier, Ph.D.)
© Sonia Pujol, Ph.D. All Rights Reserved 7
 Registra,on pipeline

Step 1:
Subject A, T2 to T1 registra,on

Subject A: T1 Subject A: T2 Step 2:
Subject B, T2 to T1 registra,on

Step 3:
Subject B, T1 to Subject A, T1 registra,on

Image courtesy
of Dominik
Meier, Ph.D.
© Sonia Pujol, Ph.D. All Rights Reserved 8
Subject B: T1 Subject B: T2
 Subject A: Data loading
Drag and Drop the
folder SubjectA into
Slicer

© Sonia Pujol, Ph.D. All Rights Reserved

 Subject A: Data loading
Click on
Drag andOK
Drop
to load
the the data
folder SubjectA into
Slicer

© Sonia Pujol, Ph.D. All Rights Reserved

Subject A: Data loading

© Sonia Pujol, Ph.D. All Rights Reserved

Subject A: Data loading

Subject A: Initial mis-registration

© Sonia Pujol, Ph.D. All Rights Reserved 13

 Registra,on pipeline
Step 1:
Subject A, T2 to T1 registra,on

Subject A: T1 Subject A: T2

© Sonia Pujol, Ph.D. All Rights Reserved 14

Subject B: T1 Subject B: T2
Subject A: Data registration

Set Initialization mode to

UseCenterOfHeadAlign

Set Registration Phases to Rigid and

Affine

Click on Apply

© Sonia Pujol, Ph.D. All Rights Reserved 15

Subject A: Data registration

© Sonia Pujol, Ph.D. All Rights Reserved 16

Subject A: Data registration

Switch to the module Data

Select the tab Transform Hierarchy

© Sonia Pujol, Ph.D. All Rights Reserved 17

Subject B: Data Loading

© Sonia Pujol, Ph.D. All Rights Reserved 18

Subject B: Initial mis-registration

© Sonia Pujol, Ph.D. All Rights Reserved 19

 Registra,on pipeline

Subject A: T1 Subject A: T2

Step 2:
Subject b, T2 to T1 registra,on

© Sonia Pujol, Ph.D. All Rights Reserved 20

Subject B: T1 Subject B: T2
Registration Module

© Sonia Pujol, Ph.D. All Rights Reserved 21

Subject B: Data Registration

Set Initialization mode to

UseCenterOfHeadAlign

Set Registration Phases to Rigid and

Affine

Click on Apply

© Sonia Pujol, Ph.D. All Rights Reserved 22

Subject B: Data Registration

Switch to the module Data

Select the tab Transform Hierarchy

© Sonia Pujol, Ph.D. All Rights Reserved 23

 Registra,on pipeline

Subject A: T1 Subject A: T2 Step 3:

Subject B, T1 to Subject A, T1 registra,on

© Sonia Pujol, Ph.D. All Rights Reserved 24

Subject B: T1 Subject B: T2
Registration of Subject B to Subject A

Set the Percentage of Samples to 0.02

Set the B-Spline Grid size to 3,3,3

Set the Bspline Transform to

Xf2_SubjectB_T1_to_SubjectA_T1

Set Output Image Volume to

SubjectB_T1_Xf2_transformed

© Sonia Pujol, Ph.D. All Rights Reserved 25

Registration of Subject B to Subject A

Set Initialization mode Off

Set Registration Phases to Bspline

Click on Apply

© Sonia Pujol, Ph.D. All Rights Reserved 26

Co-registration of Subject B to Subject A

© Sonia Pujol, Ph.D. All Rights Reserved 27

Harden Transform

Right Click on SubjectA_T2

Select Harden Transform

© Sonia Pujol, Ph.D. All Rights Reserved 28

Harden Transform

Right Click on SubjectA_T2

Select Rename

Rename the volume

SubjectA_T2_Xf0_transformed

© Sonia Pujol, Ph.D. All Rights Reserved 29

Harden Transform

Right Click on SubjectB_T2

Select Harden Transform

© Sonia Pujol, Ph.D. All Rights Reserved 30

Harden Transform

Right Click on SubjectB_T2

Rename the volume

SubjectB_T2_Xf1_transformed

© Sonia Pujol, Ph.D. All Rights Reserved 31

Final set of registered volumes

© Sonia Pujol, Ph.D. All Rights Reserved 32

Visualizing the transform
Select the module
Transforms

Select the transform

Xf2_SubjectB_T1_to_SubjectA_T1

Click on the Display and

Visualization tab.

Select Visible in 3D view

© Sonia Pujol, Ph.D. All Rights Reserved 33

Visualizing the transform

Select the region

SubjectB_T1_Xf2_tran
sformed

Select the Visualization

3D Grid

© Sonia Pujol, Ph.D. All Rights Reserved 34

 Visualizing the transform

Slicer shows a 3D
view of the
deformation field

© Sonia Pujol, Ph.D. All Rights Reserved 35

 Acknowledgments
•  Na,onal Alliance for Medical Image Compu,ng
(NA-MIC)
NIH U54EB005149

•  Neuroimage Analysis Center (NAC)
NIH P41EB015902

© Sonia Pujol, Ph.D. All Rights Reserved NaLonal Alliance for

3D Data Loading and VisualizaLon
Medical Image CompuLng
ARR 2012-2016