afni.nimh.nih.gov

If your current version doesn't read NIFTI, you can probably still do all this with a generic binary format. Amira can read in the BRIK file as a binary image. Write out the binary data (even the .img file from the Analyze file should work) and convert it back to AFNI format with to3d -geomparent, using the original dataset as the geometry parent dataset. Other options are to use AFNI's Draw Dataset to draw the ROIs or another program that works with NIFTI format, like MIPAV.