How can I change voxel size in a volume?

Hi everyone,

I have a 3D matrix with size 100x100x41, (obtained by uploading a DICOM file, but that's not the point). From the header, I know that voxels have size 0.723x0.723x1 mm; I'd like to get them 0.08x0.04x0.027 mm, how can I do? I was thinking about imresize and imresize3, using for each the respective scaling factor, but it does not convince me at all, since in no way Matlab has a pixel/voxel size reference, it reads them only as elements of a matrix. Moreover, memory "explodes" using imresize3, because it increases the number of slices a lot.

DCM=rand(100,100,41); % here I create a similar volume, but it can be any
DCM_resize=imresize(DCM,'Scale',[9.0375 18.0832],'method','bicubic');

Last think, I'd like the image not to be stretched, keeping its aspect ratio. Thanks for your help.

[Bjorn Gustavsson]

What do you intend to reveal with this rather large up-sampling? Almost a factor of 40 in the third dimension?

Answer 1

[Walter Roberson]

In order to keep the aspect ratio, all dimensions must be interpolated by the same factor, which would be max() of the requested factors.

You want your Z to be about 39 times finer (1/0.027) so that is the factor you would have to use for each dimension to avoid changing the aspect ratio.

This refers to keeping the aspect ratio within the matrix. If you are just concerned with keeping the aspect ratio for display purposes, rather than for computation, then there may be additional options.

[Simone Cotta Ramusino]

For display purposes, I found I can fix everything just setting

daspect auto

what I am not sure about, is that imresize just "add" pixels along the directions, and don't effectively resample the volume: indeed, if I visualize and zoom it after the resizing, I can see that pixels are still squares and not rectangles, as they should be. I had the same results with other functions of resampling such as interp3, so I'm starting to think that it is impossible to do what I want on Matlab.

[Bjorn Gustavsson]

@Simone Cotta Ramusino, that takes you back to my question: What do you want to achieve with this interpolation operation?

[Simone Cotta Ramusino]

Sorry, I thought I replied you. This is for a 3D printing job, and the printer ideally accepts voxels with the indicated size. The resampling in the third dimension is the less important, anyway.

[Walter Roberson]

do not daspect auto

daspect(0.08, 0.04, 0.027)

[Simone Cotta Ramusino]

Thanks, that seems fine.

For the 'size thing', I am more and more convinced that it is impossible to achieve it in Matlab. Or, at least, thath imresize is the best approximation possible.

[Walter Roberson]

Could you give an example of the problem you are encountering with imresize() ?

M = zeros(100,100);
M([20:30, 45:55, 80:90], 20:90) = 1;
M(31:79, 20:35) = 1;
M = max(M, eye(size(M)));
figure; imshow(M); title('original')

existingR = [0.723, 0.723, 1];
desiredR =  [0.08, 0.04, 0.027];

newrows = round(existingR(1)/desiredR(1) .* size(M,1));
newcols = round(existingR(2)/desiredR(2) .* size(M,2));
Mr = imresize(M, [newrows, newcols]);

figure(); imshow(Mr); title('resized, default aspect');

figure(); imshow(Mr); daspect(desiredR); title('resized, aspect');

size(M)

ans = 1×2

100 100

size(Mr)

ans = 1×2

904 1808

[Simone Cotta Ramusino]

No problems with imresize (unless too much memory required for imresize3), I was just not sure it does its duty in actually changing voxel size. But if you think it's a good choice and that there aren't any other similar functions to try, I will accept this answer.

Thanks

[Walter Roberson]

Remember that MATLAB does not know the relative dimensions of each pixel, except if you have used daspect() or except if you used imshow() and passed in a georeference object.

When you image() MATLAB just assumes that it should fit the image in the available axes Position using whatever aspect ratio works to show all of the data... unless you use daspect or "axis image".

When you imshow() MATLAB is more deliberate about using square pixels. Which is a problem when the actual aspect ratio is 1:2.

Pixel size information is not stored along with arrays. MATLAB does not have an "image data" class that stores metadata: it just has numeric arrays that have no information about the relationship with physical sizes.

[Simone Cotta Ramusino]

That's what i thought. So the image I obtained from imresize could be both a 0.723x0.723 and a 0.08x0.04..it is just a matter of visualization, right?

Thanks for the clear explanation.

[Simone Cotta Ramusino]

Last thing: you spoke about a georeference object using imshow(), how does it work?

I'd like to use imshow3D() from File Exchange, it can work in a similar way?

[Walter Roberson]

https://www.mathworks.com/help/images/ref/imref2d.html

[Walter Roberson]

imshow3d does not know anything about reference objects.

See also volumeviewer()

[Simone Cotta Ramusino]

Thanks sir, you cleared my mind.