Did some searching about IDL and found out that IDL have a Java bridge (http://www.ittvis.com/idl/pdfs/IDL63_EBAM_WP.pdf). Hence, if you are willing to use the bridge any Java-based NifTI library will help.
On top of my head for Java-based NifTI library:
(1)niftijlib from niftilib.sourceforge.net : Simple/straight forward.
(2)LONI has made its Java Image I/O routine open sourced (http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=17) : Good candidate if you do a lot of visualization-related stuff.
(3)I am currently writing one which concentrates on manipulating header information. It fit a programming framework better. It has those nicety for programmers such as INiftiDataValidators and I separated I/O handling from Nifti dataset itself. Compared to (1) it is not for the faint-hearted. I am at present working away the unsigned datatype type problem and will add a SWT toolkit for header info manipulation later. Future development direction includes Eclipse Integration. I have authority from the university to release it under GPL. Probably put it on SourceForge as part of brainfx.sourceforge.net in the near future. Email me if you want to have a look
