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IPAM Graduate Summer School Mathematics in Brain Mapping UCLA July 17, 2004 Cortical Surface Correction and Conformal Flat Mapping: TopoCV and CirclePack.

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Presentation on theme: "IPAM Graduate Summer School Mathematics in Brain Mapping UCLA July 17, 2004 Cortical Surface Correction and Conformal Flat Mapping: TopoCV and CirclePack."— Presentation transcript:

1 IPAM Graduate Summer School Mathematics in Brain Mapping UCLA July 17, 2004 Cortical Surface Correction and Conformal Flat Mapping: TopoCV and CirclePack Monica K. Hurdal Department of Mathematics, Florida State University, Tallahassee

2 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 2 Mapping the Brain Functional processing mainly on cortical surface Surface-based (2D) analysis methods desired rather than volume-based (3D) methods => Cortical Flat Maps Impossible to flatten a surface with intrinsic curvature (such as the brain) without introducing metric or areal distortions: “Map Maker’s Problem” Metric-based approaches (i.e. area or length preserving maps) will always have distortion

3 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 3 Flattening Surfaces with Intrinsic Curvature What about preserving angles? –a conformal map preserves angles and angle direction Mathematical theory (Riemann Mapping Theorem, 1850’s) says there exists a unique conformal mapping from a simply-connected surface to the plane, hyperbolic plane (unit disk) or sphere Conformal maps offer a number of useful properties including: –mathematically unique –different geometries available –canonical coordinate system

4 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 4 Conformal Mapping Conformal maps preserve angles and angle sense (angle direction) where an angle between 2 curves is defined to be the angle between the tangent lines of the 2 intersecting curves.  In the discrete setting, mapping a surface embedded in R 3 conformally to the plane corresponds to preserving angle proportion: the angle at a vertex in original surface maps so that it is the Euclidean measure rescaled so the total angle sum measure is 2 

5 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 5 Cortical Surface “Flattening” Extract region of interest from MRI volume Cortical regions defined by various lobes and fissures color coded for identification purposes Create triangulated surface of neural tissue from MRI volume ALL flattening methods required a surface topologically equivalent to a sphere or disc: surface topology corrected

6 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 6 Cortical Surfaces Few algorithms (but more emerging) are available for creating topologically correct cortical surfaces; widely used algorithms, such as the marching cubes/tetraheda algorithms, generate surfaces with topological errors Cortical surface topologically corrected –a topological sphere has no boundary components –a topological disc has a single closed boundary component formed by the boundary edges Cortical flattening: a single closed boundary cut may be introduced into a topological sphere to act as a map boundary under flattening

7 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 7 TopoCV: Software for Correcting Cortical Surface Topology Topological problems are detected and repaired using topological invariants and examining the connectivity of the surface If S is a surface then: –the Euler characteristic of S is defined to be where v, e, f are the numbers of vertices, edges and faces of S respectively –the genus of S is defined to be where m(S) is the number of boundary components of S

8 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 8 Topological Invariants If a surface is topologically correct, then it is a topological sphere if and only if  (S) = 2 and it is a topological disc if and only if  (S) = 1 NOTE: a surface with  (S) = 2 is NOT necessarily topologically correct The number of handles in S = g(S) Typical topological problems include multiple- connected components, non-manifold edges, holes and handles

9 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 9 Types of Topological Problems Unused vertices –vertices which do not belong to any triangle face –checked/corrected by examining the connectivity of the surface Duplicate triangles –triangle faces which are listed twice: f m = f n –checked/corrected by examining the vertex components of f k Non-manifold edges –each edge of S is required to be an interior edge or a boundary edge –edges which occur 3 or more times are non-manifold edges i.e. walls, ridges, bubbles –checked/corrected using a region growing algorithm

10 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 10 Multiple-connected components –every triangle belongs to the main part of the surface –checked/corrected using a region growing algorithm Triangle orientation –all triangles are required to be oriented in the same direction; by convention, orientation assumed to be counter clockwise –checked/corrected by examining each interior edge Surface Problems Continued Triangle gives edges 1-2, 2-3, 3-1 Triangle gives edges 2-4, 4-3, 3-2

11 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 11 Vertex problems: singularity (pinched surface) –the surface touches itself at a single point –checked/corrected using vertex neighbors which form a vertex flower: –each vertex should be the center of at most 1 flower –if vertex v i belongs to flower of v j, then vertex v j must belong to the flower of v i v1v1 v2v2 v3v3 v4v4 v5v5 v6v6 v7v7 v8v8 vjvj vivi Surface Problems Continued v i : v 1, v 2, v 3, v j, v 7, v 8 v j : v 3, v 4, v 5, v 6, v 7, v i v v1v1 v2v2 v3v3 vnvn closed flower v: v 1, v 2, …, v n, v 1 v vnvn v1v1 v2v2 v3v3 v n-1 open flower v: v 1, v 2, …, v n

12 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 12 Holes –a surface should contain at most one closed boundary component; additional boundary components are holes –checked/corrected by examining the boundary components and “filling” in missing regions with additional triangles Handles (or Tunnels) –each handle contributes -2 to the Euler characteristic –the number of handles can only be determined after all other topological problems have been corrected –a handle can be corrected in 2 possible ways: cut handle and then “cap” off ends or fill in handle “tunnel” –unless a priori information about handles are known or assumed, then handle correction should be guided by volumetric data used to create the surface

13 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University

14 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 14 Fixing Handles

15 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 15 CirclePack: Software for Discrete Conformal Flat Mapping A circle packing is a configuration of circles with a specified pattern of tangencies Discrete Uniformization Theorem, Circle Packing Theorem and Ring Lemma guarantee that this circle packing is unique and quasi-conformal –If triangulated surface consists of equilateral triangles, then the discrete packing converges to the conformal map in the limit. Given a simply-connected triangulated surface: –represent each vertex by a circle such that each vertex is located at the center of its circle –if two vertices form an edge in the triangulation, then their corresponding circles must be tangent –assign a positive number to each boundary vertex

16 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 16 A Circle Packing Example

17 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 17 The Algorithm Iterative algorithm has been proven to converge Surface curvature is concentrated at the vertices A set of circles can be “flattened” in the plane if the angle sum around a vertex is 2  To “flatten” a surface at the interior vertices: Positive curvature or cone point (angle sum < 2  Zero curvature (angle sum = 2  Negative curvature or saddle point (angle sum > 2 

18 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 18 v rvrv rvrv w rwrw rwrw u ruru ruru For all faces containing vertex v:

19 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 19 The Algorithm (Continued) This collection of tangent circles is a circle packing and gives us a new surface in R 2 which is our quasi- conformal flat mapping. Easy to compute the location of the circle centers in R 2 once the first 2 tangent circles are laid out. Each circle in the flat map corresponds to a vertex in the original 3D surface. Similar algorithm exists for hyperbolic geometry. No known spherical algorithm: use stereographic projection to generate spherical map. NOTE: A packing only exists once all the radii have been computed!

20 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 20 The Cerebellum

21 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 21 Euclidean & Spherical Maps

22 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 22 Hyperbolic Maps

23 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 23 Flat Maps of Different Subjects

24 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 24 Left Hemisphere and Occipital Lobe Maps

25 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 25 Occipital Lobe Temporal Lobe Parietal Lobe Frontal Lobe Limbic Lobe Boundary Parcellated data courtesy of David Van Essen, Washington U. School of Medicine, St. Louis The Visible Man Cerebrum

26 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 26 Animation

27 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 27 Twin Study As with non-twin brains, identical twin brains have individual variability i.e. brains are NOT identical in the location, size and extent of folds Aim: determine if twin brains more similar than non- twin brains –if so, this can be used to help identify where a disease manifests itself if one twin has a disease/condition that the other does not Flat maps can help identify similarities and differences in the curvature and folding patterns Examining medial prefrontal cortex Collaboration with Center for Imaging Science (Biomed. Eng.), Johns Hopkins U. & Psychiatry and Radiology Departments, Washington U. School of Medicine

28 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 28

29 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 29 VMPFC Coordinate System Mean Curvature

30 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 30 An advantage of conformal mapping via circle packing is the flexibility to map a region to a desired shape. Boundary angles, rather than boundary radii are preserved. For a rectangle: 4 boundary vertices are nominated to act as the corners of the rectangle. Aspect ratio (width/height) is a conformal invariant of the surface (relative to the 4 corners) and is called the extremal length. Conformal modulus represents one measure of shape. Two surfaces are conformally equivalent if and only if their conformal modulus is the same. Circle Packing Flexibility: Rectangular Discrete Conformal Maps

31 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University Euclidean Maps: Specify Boundary Radius or Angle Left Right Left Twin A Twin B Extremal Length 3D Surface Euclidean Map: Boundary Radius Euclidean Map: Boundary Angle

32 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 32 Cortical Region Containing VMPFC CG = cingulate gyrus CS = cingulate sulcus GR = gyrus rectus IRS = inferior rostral sulcus LOS = lateral orbital sulcus MOG = medial orbital gyrus OFC = orbital frontal cortex OFS = olfactory sulcus ORS = orbital sulci PS = pericallosal sulcus SRS = superior rostral sulcus

33 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 33 Future Mathematical Issues comparing maps between subjects: metrics alignment of different regions –align one volume or surface in 3-space to another and then quasi-conformally flat map –quasi-conformally flat map 2 different surfaces and then align/morph one to the other (in 2D) analysis of similarities, differences between different map regions projecting functional data onto cortical surface

34 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 34 Summary A neuroscientific research goal: understand functional processing of human brain & make conclusions regarding individual differences in functional organization -- may lead to better diagnostic tools Functional processing mainly on brain surface 2D analysis methods rather than volumetric analysis methods needed -- brain flat maps Conformal flat maps are mathematically unique with a variety of features and may lead to localization of functional regions in normal & diseased subjects Conformal extremal length measures need to be investigated 150 year-old mathematics being used in medical research

35 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 35 Software The software TopoCV (Topology Checker and Viewer) is available for download from and runs on Linux. SGI, SUN and AIX platforms.www.math.fsu.edu/~mhurdal Links to the conformal flattening software CirclePack Software (written by Ken Stephenson) can also be found there. The TopoCV software will also reformat surfaces into the format required by CirclePack. TopoCV can read in and output surfaces in a variety of file formats (including byu, obj, off, vtk, CARET, CirclePack and FreeSurfer).

36 IPAM - Mathematics in Brain Imaging, July17, 2004 © 2004 Monica K. Hurdal URL: Department of Mathematics, Florida State University 36 Acknowledgements De Witt Sumners, Phil Bowers (Math, FSU) Ken Stephenson, Chuck Collins (Math, UTK) Kelly Rehm, Kirt Schaper, Josh Stern, David Rottenberg (Radiology, Neurology, UMinnesota) Michael Miller, Center for Imaging Science (Biomed, JHU) & Kelly Botteron (Radiology, Psychiatry, WashU), Agatha Lee NIH Human Brain Project Grant EB02013 NSF Focused Research Group Grant DMS More information on Brain Mapping: URL:


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