How can Nifti files be restructured so that they can be fitted in a CNN?

Question

Most of my Nifti files have different x y Z dimensions. How can I arrange them so that they have the same dimensionality and then be able to train them in a CNN?

Answer 1

You can resample the images to have the same voxel size and then crop them to cover the same physical size. This is important because if you just re-size the images then each pixel (or voxel in 3D) will be a different physical size, and your CNN will be learning features at different scales.

If you are interested in performing this in Python, then I strongly suggest SimpleITK . Another package built on top of this is platipy - which has tools for isotropic resampling and cropping which could be useful.