1. I am going to assume you have a uncompressed NIfTI image (e.g. img.nii), if you have a compressed image ("img.nii.gz") uncompress it first.
2. Open the image with MRIcroGL
3. From the "Layers" panel, choose the Options->ShowHeader button
4. Select the "Statistics" tab, set the "Intention" pull down menu to be "Labels"
5. Choose the File/SaveHeader menu item and overwrite the header of your image.
6. Reopen your image, it is now recognized as a atlas with discrete regions, not a scalar image.