(c) Moo K. Chung mkchung@wisc.edu

Department of Biostastics and Medical Infomatics

Waisman Laboratory for Brain Imaging and Behavior

University of Wisconsin-Madison

Description

December 17, 2011

The
following MATLAB code will
load the both outer and inner cortical surface mesh format
into MatLab. It is tested on MATLAB 2009 (version 7.9,
64-bit Mac intel). The complete data set is used in
studies [1] [2] [4]. If you want to use the data set for publication,
please contact Moo K. Chung.

load
autism.mesh.coord.mat

The data
set contains the both inner and outer cortical surfaces of 16
autistic and 11 control subjects. In the mat
file, the variable autism_inner is 3 dimensional array of size
16 x 3 x 40962. Each dimension indexces subject number,
(x,y,z) coordinates and coordinate values. To visualize
the inner surface of the 1st autistic subject, need to
reformat the data structure.

surf.vertices=squeeze(autism_inner(1,:,:))';

surf.faces=tri;

figure;
figure_wire(surf, 'yellow',
'white');

The outer
surface is visualized as follows:

surf.vertices=squeeze(autism_outer(1,:,:))';

surf.faces=tri;

figure;
figure_wire(surf, 'yellow', 'white');

To
visualize the y-coordinate values on the outer surface

figure;
figure_trimesh(surf,surf.vertices(:,2))

The
cortical thickness for the first autism subject is computed as

thickness=squeeze(L2norm(autism_outer(1,:,:)
- autism_inner(1,:,:)));

figure;
figure_trimesh(surf,thickness)

The
cortical thickness values are highly noise so we need to perform heat kernel
smoothing. See [1] and [2] for the detailed
implemenation of heat kernel smoothing. We can also extract
cortical thickness values at vertex 10 for all subjects

thickness1=L2norm(autism_outer(:,:,10) - autism_inner(:,:,10))

thickness2=L2norm(control_outer(:,:,10)
- control_inner(:,:,10))

figure;

plot(thickness1,'or');

hold
on;

plot(thickness2,'ob');

MNI surface mesh format

May 9
2006.

The following MATLAB
code will
load MNI cortical mesh format into MatLab. It only read
ASCII-based MNI
format. MNI surface mesh format always ends with *obj
extension. This is based on MATLAB
6.1. implementation. The MNI
cortical mesh datat set has
been used in the studies [1-4].

- mni_getmesh.m loading triangle MNI mesh format into MATLAB.
- Outsurface.obj sample cortical surface mesh.
- sphere.obj cortical surface flattened onto a sphere.

- [tri,coord,nbr,normal]=mni_getmesh('outersurface.obj');
- load thickness.data;
- output=hk_smooth(thickness',tri,coord,nbr,1,200);
- trisurf(tri, coord(1,:),coord(2,:),coord(3,:),output);

- coord (3x40962) gives Cartesian coordinates of 40962 nodes.
- nbr
(40962x6) gives neighboring node indices. Each node has up
to 6
neighboring nodes. First 12 nodes have only 5 neighbors
while the
remaining 40962-5 nodes have 6 neighbors.

- normal (3x40962) gives the normal vectors of the cortex.
- tri (81920x3) gives node indices that forms each of 81920 triangles.

References

December 17,
2011

- Chung, M.K., Robbins, S., Evans, A.C. 2005. Unified statistical approach to cortical thickness analysis. Information Processing in Medical Imaging (IPMI). Lecture Notes in Computer Science (LNCS) 3565:627-638. Springer-Verlag.
- Chung, M.K., Robbins,S., Dalton, K.M., Davidson, Alexander, A.L., R.J., Evans, A.C. 2005. Cortical thickness analysis in autism via heat kernel smoothing. NeuroImage 25:1256-1265.
- Shen, L., Chung, M.K. 2006. Large-scale modeling of parametric surfaces using spherical harmonics. Third International Symposium on 3D Data Processing, Visualization and Transmission (3DPVT).
- Chung, M.K., Bubenik, P., Kim, P.T. 2009. Persistence
diagrams of cortical surface data. Information
Processing in Medica Imaging (IPMI). Lecture Notes in
Computer Science (LNCS). 5636:386-397.