subvolume

Extract subset of volume data set

Syntax

[Nx,Ny,Nz,Nv] = subvolume(X,Y,Z,V,limits)
[Nx,Ny,Nz,Nv] = subvolume(V,limits)
Nv = subvolume(...)

Description

[Nx,Ny,Nz,Nv] = subvolume(X,Y,Z,V,limits) extracts a subset of the volume data set V using the specified axis-aligned limits. limits = [xmin,xmax,ymin, ymax,zmin,zmax] (Any NaNs in the limits indicate that the volume should not be cropped along that axis.)

The arrays X, Y, and Z define the coordinates for the volume V. The subvolume is returned in NV and the coordinates of the subvolume are given in NX, NY, and NZ.

[Nx,Ny,Nz,Nv] = subvolume(V,limits) assumes the arrays X, Y, and Z are defined as

[X,Y,Z] = meshgrid(1:N,1:M,1:P) 

where [M,N,P] = size(V).

Nv = subvolume(...) returns only the subvolume.

Examples

This example uses a data set that is a collection of MRI slices of a human skull. The data is processed in a variety of ways:

  • The 4-D array is squeezed (squeeze) into three dimensions and then a subset of the data is extracted (subvolume).

  • The outline of the skull is an isosurface generated as a patch (p1) whose vertex normals are recalculated to improve the appearance when lighting is applied (patch, isosurface, isonormals).

  • A second patch (p2) with interpolated face color draws the end caps (FaceColor, isocaps).

  • The view of the object is set (view, axis, daspect).

  • A 100-element grayscale colormap provides coloring for the end caps (colormap).

  • Adding lights to the right and left of the camera illuminates the object (camlight, lighting).

    load mri
    D = squeeze(D);
    [x,y,z,D] = subvolume(D,[60,80,nan,80,nan,nan]);
    p1 = patch(isosurface(x,y,z,D, 5),...
         'FaceColor','red','EdgeColor','none');
    isonormals(x,y,z,D,p1);
    p2 = patch(isocaps(x,y,z,D, 5),...
         'FaceColor','interp','EdgeColor','none');
    view(3); axis tight; daspect([1,1,.4])
    colormap(gray(100))
    camlight right; camlight left; lighting gouraud
    

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