Read Image Coordinates

Hi all ,

I need a way to read the (x,y,z,colors) of a 3D image .

Thanks

[Walter Roberson]

What format is your 3D image in? For example is a volumetric slice that you are using DICOM for? Or do you mean that you have a 2D image that represents a 3D scene and you wish to calculate the 3D position of each object? Or do you have a stereo pair?

[Yassmin Abdallah]

it's a slices of DICOM i use the CAT function to convert them to 3D .

[Image Analyst]

So then it's a monochrome, volumetric image? Not a color volumetric image? So why can't you just do

intensity = image3D(row, column, slice)?

[Yassmin Abdallah]

yes it's monochrome , i need a away to read the X of the image in a variable similarly Y , Z ,colors

[Walter Roberson]

We do not understand? Monochrome images are not usually spoken of as having "colors" ?

The X, Y, Z that you want: do you want pixel indices, or do you want them translated into space coordinates by examining the DICOM headers for the spacing information?

[Yassmin Abdallah]

function [F,V,col] = MarchingCubes(x,y,z,c,iso,colors)

im = dicomread('IM-0001-0001.dcm');

im2 = dicomread('IM-0001-0012.dcm');

im3= dicomread('IM-0001-0079.dcm');

im = im2double(im); % this line to convert from uint16 to double

im2 = im2double(im2);

im3 = im2double(im3);

im = mat2gray(im); % this line to put the data in range [0,1]

im2 = mat2gray(im2);

im3 = mat2gray(im3);

);

c = cat(3,im,im2,im3 );

x

y

z

colors

this is the code i try to run ,sorry if i presented the question the wrong way :(

[Image Analyst]

All that code does is to stack your slices into a volumetric gray scale image, and type out your inputs to the command window. It doesn't do anything like marching cubes.

Answer 1

[Walter Roberson]

x, y, z, and colors are inputs to the MarchingCubes routine.

You should be reading the data before you call MarchingCubes.

If your x, y, and z are equally spaced then

[x, y, z] = ndgrid( 1:size(c,1), 1:size(c,2), 1:size(c,3) );

[Yassmin Abdallah]

thanks so much for your help .