image-processingbioinformaticsmedical-imaging

How to understand the dimensionality of 3D MRI or Nifti images?

I see that 3D images in the shape of XYZ, where X is the height of the image, Y the breadth, and Z the depth. Depth indicates the number of 2D images that make this single 3D MRI images. Right?

Is my understanding correct or is there something that I need to more?

Solution

  • You are correct with the general idea about image shapes.

    One important consideration is that different software packages index images different. For example in Python, images stored as numpy.ndarray objects are indexed as [z,y,x] but in SimpleITK.Image format they are indexed as [x,y,z].

    There are also higher-dimensional images, for example 4D-CT scans (with time being the fourth dimension), and vector images like diffusion MRI.