How to change the orientation of a medical Volume object ?

I'm using the new Medical Imaging Toolbox.

I want to know how to change the orientation of a medical Volume object, for example how to resample voxels from "transverse" to "sagittal" or "coronal" ? Is there a simple way to do it with medicalref3d object ?

Thank you very much.

[Lipi Vora]

Hello David,

Is there a reason or use case or workflow down the line that requires you to change the orientation as you describe?

Thanks,

Lipi Vora

[David Hassanein BERRO]

Hello Lipi,

Yes of course, most of the time, medical doctors need to see the images in the 3 planes of view. Usually images are acquired in one orientation, and we need to resample them in the orther 2 orientations.

Regards

Answer 1

[Shaik mohammed ghouse basha]

Hi @David Hassanein BERRO,

I understand that you want to resample voxels from "transverse" to "sagitta" or "coronal".

You can do this by using resample function. In resample function you pass old medical volume object and and new resample options via medicalref3d object.

Refer to https://in.mathworks.com/help/medical-imaging/ref/medicalvolume.resample.html for more information and example.

[David Hassanein BERRO]

Hi @Shaik mohammed ghouse basha

Thank you for your answer.

Yes that what I wanted to do, resample voxels from "transverse" to "sagittal" or "coronal".

I already read the resample function page. There is a good example on how to change the voxel size in the same orientation, but I'm stuck on how to change the orientation. Can you just give me some clues ?

Thank you

[Shaik mohammed ghouse basha]

Hi @David Hassanein BERRO,

I understand your query. Transverse to saggital can be changed by rotating along Y - axis by 90 degrees. In the given documentation link it was an example of changing ratio right. With the sample example I modified it to change orientaiton to saggital.

Here is the code of it:

zipFile = matlab.internal.examples.downloadSupportFile("medical","MedicalVolumeDICOMData.zip");
filepath = fileparts(zipFile);
unzip(zipFile,filepath)

dataFolder = fullfile(filepath,"MedicalVolumeDICOMData","LungCT01");

medVol = medicalVolume(dataFolder);
O = medVol.VolumeGeometry;

A = [0 0 1 0; 0 1 0 0; -1 0 0 0; 0 0 0 1]; % rotate along Y - axis

t = affinetform3d(A);

R = medicalref3d(size(medVol.Voxels), t);
R = orient(R, O.PatientCoordinateSystem);
N = resample(medVol, R); % N is the new medical volume object with orientation as saggital. 

To change orientation you need to rotate along X - axis.

For this you just need to change the vector A, [1 0 0 0; 0 0 -1 0; 0 1 0 0] by using this matrix you get orientaiton of N as coronal.

[David Hassanein BERRO]

Hi @Shaik mohammed ghouse basha

Thank you very much.

You gave me the good point to start with and to improve (such as the size of the volume). Now I understand.

Best Regards