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pythonmedical-imagingsimpleitk

read nifti files 3d slicer vs other methods

I have some nii.gz files which, when I open using imajeJ , or any python library such as SimpleITK or Monai I get a stack of MRI images, as if taken from top to bottom. That being said, when I open the same file with slicer, I also get a stack of images, taken from the side and from the front, the G and Y channels. My question is, do the images from the different angles exist inside the file, or is 3D slicer inferring how these channels would look like based on the R channel. I am asking this because the other methods don’t seem to be able to find the other views. Thank you.

3D slicer enter image description here

ImageJ

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Monai. SimpleITK in google colab enter image description here

Solution

  • Viewers like Slicer, ITK-Snap, etc. also display the view from the different anatomical planes. Depending on the orientation of the patient inside the volume, the contained volumetric information can be displayed along the three planes and their corresponding axis. Each picture in that view is just a 2D representation of a slice along one of the axes.

    So yes, this information is just inferred and is usually not contained in a DICOM (or NIFTI) file and is purely inferred for viewing purposes.