How to go from a coordinate in a 3D slicer software to a coordinate on the new STL

I was wanting to take a 3D image and use a 3D slicer tool (ITKSNAP, 3D Object Slicer, or any other reccomended software) to obtain a new mesh file.

How could I design a pipeline to go from a coordinate of a specific pixel in a 3D image to identifying the coordinates of the same pixel on a mesh generated from the original 3D image?

Thanks

Answer 1

[Anurag]

Hi Andrew,

I understand that you want to generate and identify the coordinates of 3D of pixels on a mesh generated from the original 3D image.

Refer to the pipeline below for doing the same:

• Acquire your 3D image and use segmentation tools to segment the region of interest containing the structure you are interested in.
• Generate mesh. In MATLAB you can use “generateMesh” for that.
• Use the transformation matrix to transform the pixel coordinates from the image space to the mesh space.

Example in MATLAB using NIfTL Header information:

% Load NIfTI image
image = load_nii('path/to/your/image.nii');

% Voxel coordinates
voxel_coords = [i, j, k];

% Apply transformation to get physical world coordinates
world_coords = image.hdr.hist.qform * [voxel_coords, 1]';

In this example, image.hdr.hist.qform is the transformation matrix stored in the NIfTI header.

"World_coords" now represent the physical world coordinates.

Hope this helps!

Regards,

Anurag

Please refer to the below documentation to know more about the “generateMesh” and further readings:

• https://in.mathworks.com/help/pde/ug/generate-mesh.html
• https://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image