NIS (NeuroImaging Software) package version 3.5     August 1, 2001


Code written by Jonathan D. Cohen, Todd S. Braver, Robert J. Orr,
Steven D. Forman, and Leigh E. Nystrom, 1995-1999.  STAT code written
by Gary Perlman.  Maintenance/updates by Victor Ortega (vor+@pitt.edu)
and Kate Fissell (fissell+@pitt.edu).  Please send any questions,
comments or suggestions about this distribution to Victor Ortega.  See
also the NIS web page at http://ccn.wpic.pitt.edu/nis/


Description of package structure

All source code resides in the src directory.  Inside that directory,
there are three directories: utils, which holds the source code for a
library that performs basic NIS routines; stats, which contains some
statistical routines (taken unchanged from the STAT package) used by
the NIS package; and misc, which contains source code for defunct NIS
programs and programs which require licensed software such as
Numerical Recipes in C.  The bin directory is where the binaries will
go after installation.  The "binary install directory" (BININSTDIR in
Makefile.defs) will only hold symbolic links to the binaries in the
bin directory.  Similarly for the man directory.  The include
directory holds all the header files for the NIS programs.  The
scripts directory contains a set of shell script templates used to
invoke the NIS programs and some scripts used by the java programs.
The java directory contains java NIS applications and documentation
(requires FisWidgets package).  The demo directory shows how some of
the NIS programs can be used to analyze data.  A sample dataset with
output can be downloaded from the NIS web page.  See the README file
in the demo directory for more information.  The doc directory
contains programmer-level documentation of NIS library functions.


Installation instructions

Most of the programs in this package require AIR or imgio, so you
should install those two first.  See the NIS web page for pointers.
Make sure that AIR and imgio are installed such that the images they
produce have the same number of bits per voxel; this usually means
changing OUTBITS to 16 in AIR.h and recompiling AIR.

First, go into the include directory and modify commands.h to show the
full paths for some basic commands (compress, cat, grep, etc.) for
your site.  Then, go into the src directory and modify Makefile.defs
to the needs of your site.  Finally, simply type 'make' to create the
binaries, and if everything goes well, then type 'make install' to
install binaries and scripts in the bin directory inside the NIS
package.  You can then also type 'make links' if you want to make
links in some other directory in your system to point to the binaries
in the NIS bin directory.  Type 'make installman' to install the man
pages.  Type 'make clean' to remove the binaries and object files from
the src directory, and type 'make squeaky' to also remove the
libraries and object files from the utils and stats directories under
src.  Be sure to read the README in the scripts directory before
installing those scripts.


This package has been installed and tested on the following platforms
and operating systems: SGI IRIX 6.5, Sun Solaris 7, Intel Linux 2.2.14