Question

I am trying to plot a 3d view of a very large CT dataset. My data is in a 3d matrix of 2000x2000x1000 dimension. The object is surrounded by air, which is set to NaN in my matrix.

I would like to be able to see the greyscale value of the surface of the object (no isosurface) but I cannot quite work out how to do that in Matlab. Can anyone help me please?

Given that I a dealing with a huge matrix and I am only interested in the surface of the object, does anyone know a good trick how to reduce the size of my dataset?

Answer 1

I managed to get it working:

function [X,Y,Z,C] = extract_surface(file_name,slice_number,voxel_size)
LT          = imread(file_name);%..READ THE 2D MAP
BW          = im2bw(LT,1);%..THRESHOLD TO BINARY
B           = bwboundaries(BW,8,'noholes');%..FIND THE OUTLINE OF THE IMAGE
X           = B{1}(:,1);%..EXTRACT X AND Y COORDINATES
Y           = B{1}(:,2);
indices     = sub2ind(size(LT),X,Y);%..FIND THE CORRESPONDING LINEAR INDICES
C           = LT(indices);%..NOW READ THE VALUES AT THE OUTLINE POSITION
Z           = ones(size(X))*slice_number;

I can then plot this with

figure
scatter3(X,Y,Z,2,C)

Now the only thing I could improve is to have all these points in the scatter plot connected with a surface. @upperBound you suggested delaunay3 for this purpose – I cannot quite figure out how to do this. Do you have a tip?