SeeBrain: A System for Comparative Visualization of Brain Nerve Fiber Tracts

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www.cs.utk.edu/~seelab

SeeBrain:A System for Comparative

Visualization ofBrain Nerve Fiber Tracts

Joshua NewDr. Jian Huang

Dr. Zhaohua Ding

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Outline

• Background – MRI, DT-MRI

• Data Pre-Processing

• Design Decisions

• Demos

• Future Work

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• 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

Backgroundhttp://science.howstuffworks.com/mri1.htm

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• 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


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• 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)


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• Advantages:– 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


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Background

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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)

110

110

000Extract Major Eigenvectors

Barycentric Space

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System Diagram

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MRI

fMRI Volume VolumeNormalization

DTFiber Tracts

Normalized Tracts

Visualization

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Tensor Data

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Tensor at eachvoxel location

MRI Density

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Normalization

• Mat2img – data normalization (SPM2)

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Fiber Tractography

DT-MRI

Seed Point

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Extract Features

• Vertex Features– 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– Mean, median, variance, feature distance,

length, centroid

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Design Decisions

• Medical research needs an analytical tool for cohorts of DT-MRI brain data

• Provide interactive, multi-patient, query-based visualization support for brain nerve fiber tracts– Comparative feature analysis– Query specification interfaces – Optimized data structures– Graphical Processing Unit (GPU) acceleration

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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

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Design Decisions

• Query specification interface (3 levels):– 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

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Design Decisions

• Optimized data structure:– Stores DB-like records with Fiber IDs as the key– B-tree based range-query per feature– Faster than Oracle

2,4,…

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Design Decisions

• GPU acceleration:– 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

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Design Decisions

• Programming GPU:– Store data as texture (similar to 2D array)– RoT: data structures, kernels, matrices, reduce

communication, reduce conditionals

Triangle~3,042 pixels

Each pixelprocessed by

fragment processoreach frame

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Design Decisions

• GPU uses:– 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)

Example Shader

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Demos

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Thanks

• Questions?– 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?

SeeBrain v4.4 Reference

F1 – Full-Screen ModeF4 – activeCluster ModeF5 – Cluster query: floor downF6 – Cluster query: floor upF7 – Cluster query: ceiling downF8 – Cluster query: ceiling upF9 – Toggle Vertex/Fiber Query KeysF12 – Show/hide parametric space

Function Keys

Esc – ExitParametric Interaction:Insert – deselect all parametric points Shift – deselect parametric pointsHome/End – X-axis up/downPageUp/Dn – Y-axis up/downQuery keys:Q* – Increase floorA* for feature 0Z* – Decrease floorA* for feature 0A* – Toggle floor/ceiling for feature0* Move to the right for each consecutive feature

Keyboard

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Pre-Processing

• Data– 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

SeeBrain: A System for Comparative Visualization of Brain Nerve Fiber Tracts

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