How can I control the voxel size using 'imwrite'?

Hello All,

I have an input tiff file image that has 342 slices, and I would like to extract each slice individually and save as a separate file.

% x = imread("inputTiffFile.tif", 100);
% imwrite(x, "slice_100.tif");

% x = imread("inputTiffFile.tif", 163);
% imwrite(x, "slice_163.tif");

However, I have one problem: The voxel spacing in the input image is [1, 1, 1], but the voxel spacing after using 'imwrite' is changed to [0.352778, 0.352778, 1]. I require the voxel spacing to be same as input.

Any inputs on how to avoid this change in voxel size would be very helpful.

Thanks,

Answer 1

[Shreshth]

Hi Harsha,

To avoid the change in voxel size when using the "imwrite" function in MATLAB, you can specify the resolution of the output image using the 'Resolution' name-value pair argument. Here's an example:

imwrite(x, "slice_100.tif", 'Resolution', [1, 1, 1]);
% Note - [1, 1, 1] specifies that the voxel spacing should be the same as the input image.

Please refer to the following MathWorks documentation for more information on the “imwrite” function and 'Resolution' name-value pair argument:

https://www.mathworks.com/help/matlab/ref/imwrite.html#:~:text=Resolution%20%E2%80%94%20X%2D%20and%20Y%2Dresolution

Hope this helps!

[Walter Roberson]

Note that the Resolution option of imwrite() is valid only for TIFF output files.

If you happen to want to output as PNG, then you would use XResolution and YResolution and ResolutionUnit

imwrite() does not support writing resolution for any file types other than TIFF or PNG. If you happen to want to write JPEG files then you need to resort to using external functions to write EXIF information to the image, as imwrite() does not support writing EXIF (writing EXIF would be a very useful enhancement to imwrite())