I’m working with Nifti files and I’m having problems figuring out how to get them in the right orientation. I converted these files from DICOM using dcm2niix. I’d like to understand how to plot a slice of the Nifti array in a certain orientation, specifically axial. I thought that the conversion from DICOM to Nifti would take care of the orientation, such that plotting data_array[:,:,slice_nr] would give a slice in the axial plane. This works for most images, but not all. Some of them get plotted with right and left sides flipped, or simply in another plane.
Opening the images with a Nifti viewer (ITKsnap) works fine, so I assume my naive approach is simply wrong.
I’ve uploaded two Nifti images here as an example. Plotting either the flair or the T2 image using data_array[:,:,slice_nr] gives an axial plane, while doing the same with the T1 image gives the sagittal plane.
Any pointers would be much appreciated!