While NIFTI datasets are a completely different file format from the AFNI format, they can carry an extra field in the dataset that effectively copies the AFNI format header into the NIFTI dataset. The NIFTI format is a somewhat sparse format preserving mostly the most minimal information, but the AFNI "extension" can help carry information that AFNI can use. The AFNI extension does not usually interfere with the interpretation of the data, but this duplication of information can occasionally produce confusing behavior in how AFNI programs handle the dataset. See the messageboard for some examples. The NIFTI format files are typically stored with file extensions of .nii, .nii.gz or .hdr/.img pairs. AFNI format datasets are usually stored as .HEAD/.BRIK or .HEAD/.BRIK.gz files.
