Create a cylindrical mask in a 3D matrix

Hi, I would like to create a mask in a 3D matrix in the shape of a cylinder. The reason why I want to do this is to analyse the properties of the MRI data within the mask only.

The following parameters are given:

• Coordinates of the center of the two faces of the cylinder.
• The radius of the cylinder.
• The size of the matrix.

Answer 1

[Matt J]

• Coordinates of the center of the two faces of the cylinder. Call this c1,c2
• The radius of the cylinder. Call this r
• The size of the matrix. Call this [sx,sy,sz]

o=(c1+c2)/2; %origin
h=norm(c1(:)-c2(:)); %cylinder height

n=normalize(c1(:)-c2(:),'n')';
R=[n; null(n)']';  %rotation matrix

[I,J,K]=ndgrid((1:sx)-o(1),(1:sy)-o(2),(1:sz)-o(3));
C=[I(:),J(:),K(:)]*R;  %rotated coordinates

mask=reshape( vecnorm(C,2,2)<=r & abs(C(:,1))<=h/2   ,sx,sy,sz);