I am wondering what is the differences between Slicer and ITKSNAP when loading images and segmentation. Here are the snapshot of dicom images and auto-segmentation based on the nifti image (using dcm2nii conversion) in Slicer (left image) and ITKSNAP (right image). There is a misalignment when I load images in ITKSNAP, I am wondering how Slicer read it correctly, so that I can avoid this misalignment issue when coding my own project. Thanks!
ITKSNAP (right image)
To add to @pieper comment, based on the image you shared, the segmentation loaded in ITKSNAP does not align with the underlying structure visible on the loaded dicom image.
Slicer (left image)
whereas the segmentation loaded in Slicer is properly aligned.
I would just add that definition of image orientation in NIFTI files can be ambiguous. Therefore sometimes the same files show up differently in different software. I would recommend to use NRRD file format instead of NIFTI to avoid such issues.