How to plot a 3D DICOM image in millimetre (mm) knowing the voxel size?

How can I change the axis to physical units when I plot a 3D dicom image? for example, the DICOM image has dimensions of 200x200x100 where 100 is the number of 2D slices size 200x200. I already know that the voxel size is 3.6458mm x 3.6458mm x 3.27mm.

I am using the following code to plot e.g. a segmented part of the DICOM image, but the axis are 200x200x100. How should I change the axis to mm having the voxel size?

   figure;
   w = smooth3(Segmented_area,'gaussian', [11 11 11]);
   isosurface(w,.1);
   view(3)
   axis equal

"Segmented_area" is a 3D binary matrix. I would like to plot both DICOM image and segmented area in mm.

Answer 1

[Walter Roberson]

You can pass X, Y, and Z coordinates to isosurface() . You would probably construct those as

[X, Y, Z] = meshgrid( (0 : size(Segmented_area,1)-1) * 3.6458, (0 : size(Segmented_area,2)-1) * 3.6458, (0 : size(Segmented_area,3)-1) * 3.27 );

[ML]

Thanks, but after running the above line for a matrix 200x200x100, I get X, Y, and Z matrices with dimensions of 197x197x97. What should I do next?

[Walter Roberson]

I tested the code; if you are getting 197 x 197 x 97 out for X, Y, and Z, then your Segmented_area matrix must currently be 197 x 197 x 97, not 200 x 200 x 100. Perhaps you made a mistake in transcribing the code?

Once you have the X, Y, Z matrix the same size as your Segmented_area matrix, then use

isosurface(X, Y, Z, w, .1);

and the coordinates should now be labeled in values that correspond to mm.

[ML]

Thanks, that worked for binary seg files. How about ploting the actual DICOM image (not segmented binary)in mm? How can I do that?

[Walter Roberson]

See http://www.mathworks.com/help/matlab/ref/slice.html#zmw57dd0e762044 if you want to plot over several images at the same time.

For any particular image,

ImageNumber = 7;

y = (0 : size(YourImages,1)-1) * 3.6458;
x = (0 : size(YourImages,2)-1) * 3.6458;
image(x, y, YourImages(:,:,ImageNumber) );

However, you might find that x and y axes are switched around. It depends on which coordinate system you use. MATLAB use the first dimension as Y (distance up or down) and the second dimension as X (distance left or right), and that might not agree with how your data is stored. You might want to transpose when you plot.

[ML]

Hi, how can I do the same thing with patch function while I only have the faces and vertices?

I am getting error by

patch(X, Y, Z, 'Faces', FV.faces, 'Vertices', FV.vertices);

[Walter Roberson]

If I recall correctly, if you provide the full Faces and Vertices information then patch will build the XData, YData, and ZData internally and you do not need to provide them.

[Basilia Quispe Huillcara]

Excuse me, I'm working on a research project where I need to build a 3D image voxelization using TC DICOM. I've already seen how to getting information, read, show DICOM images. Also check how to build 3D image. Can you help me with some recommendations about off material to review.

[Walter Roberson]

If you have already seen that information, then I am not sure what else you are looking for?

[Basilia Quispe Huillcara]

I do not know how to divide the 3D image into voxels and I need the output of MCNP input format. can you support me Thank you!.

[Walter Roberson]

I do not appear to be eligible to get the MCNP source code, and the user manual itself is considered to be Export Controlled.

When you read in a 3D array from DICOM, the result is already voxels.

Perhaps you are trying to segment a transcranial DICOM image? Transcranial would tend to be MRI modality, but your reference to MCNP suggests to me that you might be working with either CT or with radiation therapy ?

[Basilia Quispe Huillcara]

Thank! for your answer, if I'm working with CT.

Answer 2

[abdey munaf]

thanks in advance to all of you. can you tell me how you come to know ''the voxel size is 3.6458mm x 3.6458mm x 3.27mm .'' ?

[Walter Roberson]

https://www.mathworks.com/matlabcentral/answers/215612-how-can-i-convert-pixels-to-mm-for-a-specific-dicom-image#answer_178301