------------------------------
                              EMMA 1.0.0

                            5 February 2010
                    ------------------------------

This version fixes a segmentation fault that commonly occurs on
64-bit architectures. It is a mystery why 32 bits work, but this
could be related to the Matlab mex compiler in 32 vs 64 bits. The
new code seems to work in both 32 and 64 bits with recent versions
of Matlab and the surfstats package.

The maintainer of this release is Claude Lepage, claude@bic.mni.mcgill.ca

                    ------------------------------
                              EMMA 0.9.9

                            10 January 2008
                    ------------------------------

This version can now be built with minc2 (which has become the default
for compilation). The following steps are suggested to build it:
1 - build minc2, HDF5, netcdf
2 - make MINCLIBPATH=... MINCINCPATH=... CC=gcc MATLAB_INSTALL_DIR=...
    BIN_INSTALL_DIR=... DOC_INSTALL_DIR=... 
    make MINCLIBPATH=... MINCINCPATH=... CC=gcc MATLAB_INSTALL_DIR=...
    BIN_INSTALL_DIR=... DOC_INSTALL_DIR=... install
    where you have to fill in the blanks for the paths in the above.
    The Makefile will try to autodetect your architecture (if Linux,
    IRIX, SunOS or Darwin). For minc1, add the option MINC_BASE=1.
    MINCLIBPATH has the form MINCLIBPATH=-L/usr/local/mni/bin (this
    string is passed to the linker so you must add -L in front).
    MINCINCPATH has the form MINCINCPATH=-I/usr/local/mni/include
    (this string is passed to the preprocessor to you must add -I 
    in front). 

The maintainer of this release is Claude Lepage, claude@bic.mni.mcgill.ca

                    ------------------------------
                              EMMA 0.9.6

                            11 March 2004
                    ------------------------------

This version is a maintenance release which deals with some of the
issues arising from changes in Matlab's programming interface for MEX
files.  There should be no user-visible changes in EMMA 0.9.6 relative
to EMMA 0.9.5

The maintainer of this release is Bert Vincent, bert@bic.mni.mcgill.ca

                    ------------------------------
                              EMMA 0.9.4

                           20 October, 1997
                    ------------------------------


Welcome to EMMA!
================

EMMA is a MATLAB package developed at the McConnell Brain Imaging Centre
(BIC) of the Montreal Neurological Institute, created to allow MATLAB
programmers to develop medical image analysis applications quickly and
interactively.  Previously this development was done at the BIC with
FORTRAN on a VAX.  In spite of the inherent loss of speed due to using
an interpreted language, the reduced time and complexity of development
offer a significant advantage.  (In fact, MATLAB code written to
carefully take advantage of MATLAB's vectorized nature can compete with
code written in compiled languages.  Of course, it doesn't hurt that
today's Unix workstations are a heck of a lot faster than yesterday's
VAXen.)

Release 0.9.4 is mostly a bug-fix release; see the CHANGES file for
details.  Several of those bugs only revealed themselves when we tested
EMMA under MATLAB 5, though, so this release has the distinction of
being the first to compile and run under both MATLAB 4 and 5.

The acronym EMMA stands for whatever you want it to stand for.
Current favourites include:
   EMMA Makes MATLAB Acceptable
   EMMA: MATLAB and MINC Arguing
   Elbowing MATLAB and MINC into Agreement
   Everyone's Memory Munching Alternative
   Effortlessly Making MINC Accessible

In a nutshell: it makes quantitative analysis of medical image data in
MINC files readily accessible to MATLAB programmers.


Components
----------

EMMA consists of:

     1) MATLAB scripts.  These do not need to be compiled.
     2) CMEX programs.  These are dynamically loaded by MATLAB when
        they are called, and must be compiled.  You will need the cmex
	script supplied with MATLAB, as well as the MINC and NetCDF
	libraries.  You should have obtained these libraries along with
	EMMA; if not, they are available by anonymous ftp from
	ftp.bic.mni.mcgill.ca, in /pub/minc.
     3) Stand-alone C programs.  These require both the MINC and
        netCDF libraries.
     4) LaTeX documentation.  Figures are included using the widely
        available psfig package.  PostScript versions of the
        documentation are included in case you don't have LaTeX.


Building
--------

To build EMMA (after unpacking the archive):

     1) Edit Makefile.site for various site-dependent parameters.
	These include the architecture type, the directories where
	MATLAB, MINC, and NetCDF are installed, and the directories
	to which EMMA will be installed.  Be sure to read the comments	
	in Makefile.site carefully.
     2) Take a look in the Makefile for your architecture (one of
        Makefile.irix4, Makefile.irix5, Makefile.sun4, and
        Makefile.linux), and ensure that the compiler and compiler flags
        are reasonable.  (The C compiler used must be ANSI compliant,
        hence the default for SunOS is 'gcc'.  You might prefer to use
        'acc' if you have it.)
     3) Type "make".

If your architecture is not supported by EMMA, don't despair -- all you
have to do is create a Makefile fragment named after your architecture,
using one of the existing machine-specific Makefiles as a model.  If you
have to do create a new machine-specific Makefile fragment, please let
us know -- we want EMMA to be readily usable on as many Unix-like
platforms as possible, and including your new Makefile in future EMMA
distributions will help.


Installation
------------

     1) Type "make install".  (Note that you must have already edited
	Makefile.site to set the destination directories.)  All MATLAB
	files (.m and CMEX) will be copied to a specified directory
	(MATLAB_INSTALL_DIR), the standalone binaries will be copied to
	a different directory (BIN_INSTALL_DIR), and the documentation
	(in PostScript form) to a third directory (DOC_INSTALL_DIR).

Assuming that MATLAB is installed under /usr/local/matlab (this can be
changed in Makefile.site), then EMMA will by default be installed to
/usr/local/matlab/toolbox/emma.  You will have to modify the MATLAB
path to search this directory; this can be done for an individual user
by setting the MATLABPATH environment variable, i.e. add

     setenv MATLABPATH /usr/local/matlab/toolbox/emma

to your .cshrc file (or equivalent to your .profile, if you're a
sh/zsh/bash/ksh type of person).  To make a system-wide modification,
add the line

     path (path, '/usr/local/matlab/toolbox/emma');

to the system matlabrc.m file.  (This file lives in toolbox/local
under the root MATLAB directory.)  (Of course, you could also set
MATLABPATH for all users, or you could put a 'path' statement in your
personal startup.m file.  Take your pick.)

The binary executables should be somewhere in your default search
path.  Therefore, the default is to put them in /usr/local/bin; you
could give them their own directory, but you'd have to ensure that
they are on the system search path ($PATH, not MATLAB's search path)
whenever EMMA is used.

The documentation files can go wherever you normally put documentation
files.  We provide the original LaTeX source files, DVI files, and
PostScript(tm) output files.  Between all these options, you should
have some way of printing out the final documentation.  We are
currently working on an interactive HTML (Hyper Text Markup Language)
version of the documentation suitable for browsing with a World Wide
Web (WWW) client; you should be able to find this documentation at the
BIC's web site:

   http://www.bic.mni.mcgill.ca/



Bug Reports
-----------

EMMA is fairly mature at this point (even though it's still not at
release 1.0), but we make no guarantees that it's free of bugs.  If
you think you have found a bug, we very much want to hear about it.
(Even if you haven't found a bug, it may be that the documentation
isn't clear or is erroneous; this is considered a documentation bug,
and will be dealt with accordingly.)

The current maintainer of EMMA is Greg Ward; he can be reached at:

E-mail:      greg@bic.mni.mcgill.ca

Snail-mail:  McConnell Brain Imaging Centre
             McGill University
             3801 University Street
             Montreal, Quebec        H3A 2B4
             Canada


Authors & Acknowledgements
--------------------------
The authors of EMMA are:
             Mark Wolforth
             Greg Ward

    EMMA started as a summer project back in 1993, when both of us
    were undergraduates (Mark in electrical engineering, Greg in
    physics).  It has undergone continued maintenance throughout our
    years of graduate school (biomedical engineering and computer
    science, respectively), and has been in constant use at the BIC
    for the last four years.

    We would like to thank Sean Marrett for being the driving force
    behind this project.  He provided invaluable guidance when all
    seemed lost.

    We would also like to thank Brad Beattie from Memorial
    Sloan-Ketering Cancer Center, who was the first to suffer the
    installation process, and gave many important pointers to where we
    had gone wrong.


Copyright Notice and Disclaimer
-------------------------------

    Copyright (c) 1993-97 Mark Wolforth and Greg Ward, McConnell Brain
    Imaging Centre, Montreal Neurological Institute, McGill
    University.

    Permission to use, copy, modify, and distribute this software and
    its documentation for any purpose and without fee is hereby
    granted, provided that the above copyright notice appear in all
    copies.  The authors and McGill University make no representations
    about the suitability of this software for any purpose.  It is
    provided "as is" without express or implied warranty.