NA-MIC

National Alliance for Medical Image Computing

http://na-mic.org

DTI atlas building for

population analysis:
Application to PNL SZ study
Casey Goodlett, Tom Fletcher, Sarang
Joshi, Guido Gerig
UNC Chapel Hill, Univ. of Utah
 Building of Population Averages
Motivation:
Map population into
common coordinate
space
Learn about normal
variability
Describe difference
from normal
Use as normative atlas
for segmentation
Sarang Joshi, Brad Davis, Matthieu Jomier, Guido Gerig, Unbiased Diffeomorphic Atlas
Construction for Computational Anatomy, vol. 23, NeuroImage 2004
B. Avants and J.C. Gee, Geodesic estimation for large deformation anatomical shape averaging and
interpolation, Neuroimage, vol. 23, pp. 139150, 2004.

National Alliance for Medical Image Computing

http://na-mic.org Slide 2
Population-Based DTI Analysis

Casey Goodlett,
MICCAI06

National Alliance for Medical Image Computing

http://na-mic.org Slide 3
 Registration
Atlas
Structural
Scalar Images (Affine,
Operator
DTI Images From Manifold Fluid) Structural
(1:N) Detector on FA Average

H-fields H-1-fields
(1:N) (1:N)

National Alliance for Medical Image Computing

http://na-mic.org Slide 5
Atlas formation

Rotate Tensors
based on JH-1
DTI Images

Tensor DTI Atlas

Averaging

H-fields
Riemannian
(1:N)
Symmetric
Space

National Alliance for Medical Image Computing

http://na-mic.org Slide 6
 Structural Image
Want images aligned by geometry of fiber
tracts
FA occurs in thin manifolds
sheets
tubes
FA'' highlights fiber geometry (maximum
eigenvalue)
FA'' does not directly optimize
correspondence of tensor derived property

National Alliance for Medical Image Computing

http://na-mic.org Slide 7
FA image and Curvature Image

National Alliance for Medical Image Computing

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 Mathematics of Spatial Transformation

h(x) is a mapping from R3 to R3. h(x) can be locally

approximated as a linear function.
h x = x Fx
F is the local Jacobian of the transformation and can be processed the same

as for a global transformation. SVD can be used to extract the rotation

component of F.

F= UR
T
D' = RDR
National Alliance for Medical Image Computing
http://na-mic.org Slide 11
 Processing of DTI
Diffusion tensors are symmetric positive-
definite matrices
Riemannian symmetric spaces (Fletcher,
Pennec)
Log-Euclidean Framework

National Alliance for Medical Image Computing

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National Alliance for Medical Image Computing
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Atlas: Average + Set of
transformed tensor fields

ROIs and
tracts in atlas
space
transferred to
every image.

National Alliance for Medical Image Computing

http://na-mic.org Slide 15
Atlas-Based Tractography

Image A Image B

National Alliance for Medical Image Computing Atlas Slide 16

http://na-mic.org
 PNL Data: Colored FA and MD

Average of
Control Group
(N=13)

FA MD

Average of SZ
Group
(N=12)
FA MD

National Alliance for Medical Image Computing

http://na-mic.org Slide 17
 Full Brain Tractography on Atlas

MedINRIA Tool (Pierre Fillard, INRIA)

NEW: NAMIC compatible: Reads NRRD format and writes
NAMIC fiber format output, is promoted together with NAMIC
FiberViewer tool.
National Alliance for Medical Image Computing
http://na-mic.org Slide 18
 Tractography in PNL Atlas

Cingulum full

Corpus Callosum middle part

Cingulum spine
National Alliance for Medical Image Computing
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 more tracts

Uncinate Fasciculus UF colored with FA

ant post
National Alliance for Medical Image Computing
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FA distributions in cross-sections

National Alliance for Medical Image Computing

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Tractography per Group

Cingulum Control Group Cingulum SZ Group

Tractography applied to tensor fields of the set of controls mapped

to the atlas (left) ad the set of SZ mapped to the atlas (right).

National Alliance for Medical Image Computing

http://na-mic.org Slide 22
 Very, very preliminary tests

FA along cingulum per group

0.6

0.5
SZ seems to have
lower FA in middle 0.4
FA-NC
portion of cingulum. FA-SZ
FA

0.3
Poly. (FA-SZ)
What does it mean Poly. (FA-NC)
0.2
w.r.t. diffusion
properties? 0.1

0
-80 -60 -40 -20 0 20 40
National Alliance for Medical Image Computing arclength (mm)
http://na-mic.org Slide 23
 ctd.
L1 along cingulum per group L23 along cingulum per group

14 10

9
12
8
10 7
L1-NC 6 L23-NC
8
L1-SZ L23-SZ

L23
L1

5
Poly. (L1-SZ) Poly. (L23-SZ)
6
Poly. (L1-NC) 4 Poly. (L23-NC)
4 3
2
2
1

0 0
-80 -60 -40 -20 0 20 40 -80 -60 -40 -20 0 20 40
arclength (mm) arclength (mm)

SZ group seems to have lower lambda1 and slightly higher radial

diffusion (average lambda2 + lambda3) in middle region.

National Alliance for Medical Image Computing

http://na-mic.org Slide 24
 ctd.
MD along cingulum per group GA along cingulum per group

12 1
0.9
10
0.8
0.7
8
MD-NC 0.6 GA-NC
MD-SZ GA-SZ
MD

GA
6 0.5
Poly. (MD-SZ) Poly. (GA-SZ)
Poly. (MD-NC) 0.4 Poly. (GA-NC)
4
0.3
0.2
2
0.1

0 0
-80 -60 -40 -20 0 20 40 -80 -60 -40 -20 0 20 40
arclength (mm) arclength (mm)

MD seems very similar for both GA shows same pattern as FA but

groups. much higher values.

National Alliance for Medical Image Computing

http://na-mic.org Slide 25
same game with cc

Middle cc in central region

shows decrease of FA and
increase of MD for SZ group
National Alliance for Medical Image Computing
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 and with uncinate fasciculus

Maybe no group difference.

National Alliance for Medical Image Computing

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Voxel-based Analysis: FA

axial low

axial high

Control Atlas SZ Atlas Difference

Can we trust these difference maps? Do we see
residuum of deformation or FA difference?
National Alliance for Medical Image Computing
http://na-mic.org Slide 28
Voxel-based Analysis: MD

axial low

axial high

Controls SZ Difference
Mismatch of two atlases illustrates a problem of our
atlas building: Edges of structures not well-aligned.
National Alliance for Medical Image Computing
http://na-mic.org Slide 29
Problem: What is a good
image match feature?

Features from
tensor field
driving nonlinear
registration?

National Alliance for Medical Image Computing

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Image match should consider
boundaries and tract locations

Maxev FA MD

Maxev FA MD

National Alliance for Medical Image Computing

http://na-mic.org Slide 31
 Towards improved image
match features
MD does not show
underlying wm structure
FA shows strong wm
features but not anatomical
boundaries
FA (Hessian) emphasizes
center lines Thick and thin structures
show similar center features
Would like measure
derived from full tensor field
National Alliance for Medical Image Computing
http://na-mic.org Slide 32
 Hessian of tensor field?

M xx Each element is
M xy M xz
matrix
M yx M yy M yz Choice of Norm?
M zx M zy M zz

National Alliance for Medical Image Computing

http://na-mic.org Slide 33
 Hessian of Tensor Field
max_ev: maximum
eigenvalue of each
element i j ev

norm: norm of each

element i j

tensor_ev: SIAM*
H
iill ijll kknn
*Lathauwer, SIAM J. MATRIX ANAL.
APPL. Vol. 21, No. 4, pp. 12531278 3x3x(3x3) = 3*27elements

National Alliance for Medical Image Computing

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Hessian of Tensor Field

National Alliance for Medical Image Computing

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 Current Work: Towards better
image match features

Collaboration
with
Fillard/Pennec,
tensor_ev max_ev norm INRIA

Second
derivative of
tensor field (1st
tensor_ev max_ev norm ev of Hessian)

National Alliance for Medical Image Computing

http://na-mic.org Slide 36
 Conclusions
Core methods: Nonlinear deformation (diffeomorphic)
and good feature maps
Atlas-building will require Slicer-3 pipeline (currently
Linux script)
After automatic construction of atlas with set of
deformed tensor fields:
Efficient, user-guided analysis (15 per tract or region)
Full set of measurements (FA, GA, MD, lambda1..3, radial
diffusion etc.)
Current research: Image match features
Set of tracts with associated tensors from aligned
images: Ready for tensor statistics (Fletcher, e.g.)
National Alliance for Medical Image Computing
http://na-mic.org Slide 37
Conclusion PNL DTI study
Low hanging fruits were not as low as
expected
What was promised for Christmas is
available now
Encouraging results on multiple key
structures (cc, UF, cingulum, fornix etc.)
Plan for programmers week: To teach
about tools and generate clinically
relevant results (Goodlett, Kubicki, Bouix).
National Alliance for Medical Image Computing
http://na-mic.org Slide 38