Transcript SeeBrain: A System for Comparative Visualization of Brain Nerve Fiber Tracts Joshua New Dr. Jian Huang Dr.

SeeBrain:
A System for Comparative
Visualization of
Brain Nerve Fiber Tracts
Joshua New
Dr. Jian Huang
Dr. Zhaohua Ding
www.cs.utk.edu/~seelab
JN 11/6/2015
Outline
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Background – MRI, DT-MRI
Data Pre-Processing
Design Decisions
Demos
Future Work
www.cs.utk.edu/~seelab
JN 11/6/2015
Background
http://science.howstuffworks.com/mri1.htm
• Atom’s nucleus precesses
around an axis like a top
• Main magnetic field aligns atoms’
axes (toward patient’s head or feet)
• Opposing directions cancel each
other out except for a few out of
every million
• Radio waves change precession
of atoms
www.cs.utk.edu/~seelab
JN 11/6/2015
Background
http://science.howstuffworks.com/mri1.htm
• Magnetic – 0.5-2 tesla (10K Gauss) machines on
humans, up to 60 tesla used in research (resistive,
permanent, and superconducting magnets with -452oF liquid
He)
• Resonance – a local radio frequency pulse
precesses atoms in direction and frequency based
upon magnetic field and type of tissue
• Image – coils measure energy radiated in a “slice”
as atoms drift back to their normal precession and
convert through Fourier to an image
www.cs.utk.edu/~seelab
JN 11/6/2015
Background
http://science.howstuffworks.com/mri1.htm
• Disadvantages:
– Patients with pacemakers, claustrophobia, weight
– Noise of continuous rapid hammering from current
in wires being opposed by the main magnetic field
– Must hold still for 20-90 minutes during scan
– Artifacts from implants altering the magnetic field
– Very expensive to own and operate
– Typical voxel resolution is 2.5mm whereas human
nerves have diameter 1-12μm: A-b 5-12μm (60m/s);
A-d 2-5μm (5-25m/s); C 1μm (1m/s)
www.cs.utk.edu/~seelab
JN 11/6/2015
Background
http://science.howstuffworks.com/mri1.htm
• Advantages:
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Imaging of density is similar to X-rays
Slice direction: axial, sagittal, and coronal
Resolution for voxels 0.2-5mm per side (~2.5)
Non-invasive inspection of: multiple sclerosis,
tumors, infections, torn ligaments, shoulder
injuries, tendonitis, cysts, herniated disks, and
stroke
• Future of MRI
– Wearable MRI devices
– Modeling the brain
www.cs.utk.edu/~seelab
JN 11/6/2015
Background
www.cs.utk.edu/~seelab
JN 11/6/2015
Background
• Diffusion Tensor MRI
– Diffusion – the process or condition of being
spread about or scattered; disseminated
– Tensor – mathematical generalization of a vector
• DT-MRI shows direction and magnitude of
fluid flow in the brain (brain is ~78% water)
Barycentric Space
0 0 0 
0 1  1 Extract Major

 Eigenvectors
0  1 1 
www.cs.utk.edu/~seelab
JN 11/6/2015
System Diagram
fMRI
MRI
DT
0
0 0

0 1  0.0376 . . .

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0 0 0.0024 
...
Volume
Normalization
Volume
Fiber Tracts
Normalized
Tracts
Visualization
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Tensor Data
MRI Density
Tensor at each
voxel location
0
0 0

0 1  0.0376


0 0 0.0024 
www.cs.utk.edu/~seelab
JN 11/6/2015
Normalization
• Mat2img – data normalization (SPM2)
www.cs.utk.edu/~seelab
JN 11/6/2015
Fiber Tractography
DT-MRI
Seed Point
JN 11/6/2015
www.cs.utk.edu/~seelab
Extract Features
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Vertex Features
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Turtle Geometry (Wh,Wl,Wu) – first derivatives
capturing local geometry
Geometry (Curv,Kappa,Torsion) – 2nd and 3rd
derivates for bending and twisting
Tensor (Planar,Spherical,Fractional Anisotropy) –
maturity of nerve fibers
Fiber Statistics
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Mean, median, variance, feature distance,
length, centroid
www.cs.utk.edu/~seelab
JN 11/6/2015
Design Decisions
• Medical research needs an analytical tool for
cohorts of DT-MRI brain data
• Provide interactive, multi-patient, querybased visualization support for brain nerve
fiber tracts
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Comparative feature analysis
Query specification interfaces
Optimized data structures
Graphical Processing Unit (GPU) acceleration
www.cs.utk.edu/~seelab
JN 11/6/2015
Design Decisions
• Comparative feature analysis
– Parameter space plots in Cartesian plane of each
vertex color-coded by dataset
– Mouse: click-and-drag brushing to select vertices,
shift-click/drag to deselect vertices
• Allows qualitative analysis
www.cs.utk.edu/~seelab
JN 11/6/2015
Design Decisions
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Query specification interface (3 levels):
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Vertex-level [9 features – (TurtleGeometry)Wh,Wl,Wu,
(Geometry)Curv,Kappa,Torsion,
(Tensor)Planar,Spherical,Fractional Anisotropy]
Fiber-level (fiber mean for each feature)
Cluster-level (fiber length)
Allows quantitative analysis
www.cs.utk.edu/~seelab
JN 11/6/2015
Design Decisions
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Optimized data structure:
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Stores DB-like records with Fiber IDs as the key
B-tree based range-query per feature
Faster than Oracle
2,4,…
www.cs.utk.edu/~seelab
JN 11/6/2015
Design Decisions
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GPU acceleration:
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Old QuadroFX1000 ($240 new,$99 ebay) only
300/650Mhz (CPUs are 2-4Ghz) but have 8/24
independent fragment processors… 8x300=2.4Ghz
SLI for 2-4 video cards (www.tomshardware.com)
OpenGL 2.0 (10/04) with GLSL (Cg or DirectX’s HLSL)
exposed hardware to programmability
www.cs.utk.edu/~seelab
JN 11/6/2015
Design Decisions
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Programming GPU:
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Store data as texture (similar to 2D array)
RoT: data structures, kernels, matrices, reduce
communication, reduce conditionals
Triangle
~3,042 pixels
Each pixel
processed by
fragment processor
each frame
www.cs.utk.edu/~seelab
JN 11/6/2015
Design Decisions
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GPU uses:
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Example Shader
Games often use for
custom lighting, dynamic
contrast, etc.
Shader programs: 3-100
lines of code (10 avg.)
General uses:
illumination, signal
processing, image
compression, computer
vision, sorting/searching
(www.gpgpu.org)
www.cs.utk.edu/~seelab
JN 11/6/2015
Demos
www.cs.utk.edu/~seelab
JN 11/6/2015
Thanks
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Questions?
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If you try to fail, and succeed, which have you done?
If mothers feed their babies with tiny little spoons and forks, what do
Chinese mothers use? Toothpicks?
If it's true that we are here to help others, then what exactly are the
others here for?
Is there another word for synonym?
If a parsley farmer is sued, can they garnish his wages?
If one synchronized swimmer drowns, do the rest drown too?
What was the best thing before sliced bread?
Do people who spend $2.00 apiece on those little bottles of Evian water
know that spelling it backwards is Naive?
www.cs.utk.edu/~seelab
JN 11/6/2015
SeeBrain v4.4 Reference
Function Keys
F1 – Full-Screen Mode
F4 – activeCluster Mode
F5 – Cluster query: floor down
F6 – Cluster query: floor up
F7 – Cluster query: ceiling down
F8 – Cluster query: ceiling up
F9 – Toggle Vertex/Fiber Query Keys
F12 – Show/hide parametric space
Keyboard
Esc – Exit
Parametric Interaction:
Insert – deselect all parametric points
Shift – deselect parametric points
Home/End – X-axis up/down
PageUp/Dn – Y-axis up/down
Query keys:
Q* – Increase floorA* for feature 0
Z* – Decrease floorA* for feature 0
A* – Toggle floor/ceiling for feature0
* Move to the right for each
consecutive feature
Pre-Processing
• Data
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Matlab tensor data (Vanderbilt – Dr. Ding)
Mat2img/SPM2 normalize data
Mat2dat Matlab script
Dat2binf executable
– IntVisWS1.2f – extracts fibers (Nathan Fout)
– FeatureExtractor1.4 – extracts features from DT
and fiber geometry
– FiberRenderer – allows querying of data
www.cs.utk.edu/~seelab
JN 11/6/2015