Getting specimen dimensions of a non-uniform 3D-body

I have a matrix M of dimensions ( I x J x K ) which is a numerical representation of the body. Within this matrix, each organ is represented by a number N. I am interested in manipulating the properties of organ-i. Specifically, I want to add small droplets inside organ-i, such that new organ-i consists of two tissue types: i and i-tilde

I have obtained the points which corresponds to organ-i. The x,y,z coordinates of each of the points of organ-i is

% coordinates of points 
X = myimage_3d.organPoints(:,1);
Y = myimage_3d.organPoints(:,2);
Z = myimage_3d.organPoints(:,3);

Basically, I want to replace the the values M(x,y,z) = i into M(x,y,z) = i-tilde.

I would like to use Ayad's existing aggregate packer: https://nl.mathworks.com/matlabcentral/fileexchange/73188-aggregate-packing-generator to generate the points within the body which should be masked. The function requires the the x-, y- and z-dimensions of the 3D body as inputs.

Is it possible to generate the x,y and z dimensions of my body given the known X,Y,Z points?