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

1. SeeBrain:A System for Comparative Visualization ofBrain Nerve Fiber Tracts Joshua New Dr. Jian Huang Dr. Zhaohua Ding

2. Outline • Background – MRI, DT-MRI • Data Pre-Processing • Design Decisions • Demos • Future Work

3. Backgroundhttp://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

4. Backgroundhttp://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

5. Backgroundhttp://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)

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

7. Background

8. Barycentric Space Extract Major Eigenvectors 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)

9. System Diagram VolumeNormalization Volume fMRI MRI Fiber Tracts DT Normalized Tracts Visualization

10. MRI Density Tensor at eachvoxel location Tensor Data

11. Normalization • Mat2img – data normalization (SPM2)

12. Fiber Tractography DT-MRI Seed Point

13. 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

14. 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

15. 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

16. 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

17. 2,4,… 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

18. 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

19. Design Decisions • Programming GPU: • Store data as texture (similar to 2D array) • RoT: data structures, kernels, matrices, reduce communication, reduce conditionals Triangle~3,042 pixelsEach pixelprocessed by fragment processor each frame

20. Example Shader 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)

21. Demos

22. 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? Thanks

23. Function Keys Keyboard 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 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 SeeBrain v4.4 Reference

24. 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