--- a/AUTHORS
+++ b/AUTHORS
@@ -1,5 +1,10 @@
-Peter Neelin designed, coded, and maintained MINC (1993-2002).
-David MacDonald designed, coded, and maintained VolumeIO (1993-1998).
+Peter Neelin designed, coded, and maintained MINC (1992-2002).
+David MacDonald designed, coded, and maintained VolumeIO (1991-1998).
+
+
+Current maintenance is done on the minc-development mailing list.
+  http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
+
 
 MINC Contributors
 

--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,12 @@
+2003-01-17  Steve M. Robbins  <steve@nyongwa.montreal.qc.ca>
+
+	* INSTALL.minc: new.
+
+	* AUTHORS:
+	* GETTING_STARTED:
+	* INSTALL:
+	* README: Tune up for release.
+
 2003-01-10  Steve M. Robbins  <steve@nyongwa.montreal.qc.ca>
 
 	* testdir/Makefile.am (INCLUDES): 

--- a/GETTING_STARTED
+++ b/GETTING_STARTED
@@ -14,31 +14,28 @@
 some enhancements to NetCDF (automatic type conversion, for example),
 as well as image conversion routines for dealing with image pixel
 value issues as well as image size and orientation. Documentation
-consists of a programmer's guide and reference (minc_user.tex (.dvi)
-and minc_reference.tex (.dvi) in the minc/doc directory). An example
-C program exists in minc/progs/mincexample.
+consists of a programmer's guide and reference (minc_user.tex and
+minc_reference.tex in the doc directory).  Example C programs exist
+in progs/mincexample.
 
 3) A high-level C library called volume_io provides a Volume data
 type, with functions like input_volume to give simple access to data
 while handling issues of pixel range conversion and voxel-to-world
-coordinate conversion. There is no documentation for this, but the
-source lives in minc/volume_io. An example program exists in 
-minc/volume_io/example called convert_volume_to_byte.c
+coordinate conversion. Documentation consists of a programmer's
+reference volume_io/Documentation/volume_io.tex.  Example programs
+exist in volume_io/Testing.
 
-4) Generic MINC applications. Check minc/bin/*minc*. All
-applications should take the -help option for a listing of options.
-Man pages exist for mincresample, rawtominc, mincheader and mincinfo (these
-are found in minc/man).
+4) Generic MINC applications. These will be in the top-level build
+directory.  All applications should take the -help option for a
+listing of options.  All have man pages.
 
-5) Specific MINC applications like register (for displaying one or two
-minc volumes and doing point tagging) and postf (display minc images).
-A man page exists for register and postf has -help option (for
-options) and a -describe option for some details. These are available from
-the Montreal Neurological Institute on request (contact 
-Peter Neelin <neelin@pet.mni.mcgill.ca>).
+5) Specific MINC applications like Display and register (for visualization)
+and mni_autoreg -- a.k.a. ANIMAL (for registration) are available from
+the BIC web page, www.bic.mni.mcgill.ca.
 
-The include file for minc is in ../include (just include <minc.h>,
-netcdf.h will automatically be included).  Volume_io includes are in
-../include/volume_io (just include <volume_io.h>). Library
-files are in ../lib.
+Applications that use MINC alone need to #include <minc.h> and
+link with "-lminc -lnetcdf -lm".
 
+Applications built with VolumeIO need to #include <volume_io.h>
+and link with "-lvolume_io -lminc -lnetcdf -lm".
+

--- a/INSTALL
+++ b/INSTALL
@@ -1,3 +1,9 @@
+Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002 Free Software
+Foundation, Inc.
+
+   This file is free documentation; the Free Software Foundation gives
+unlimited permission to copy, distribute and modify it.
+
 Basic Installation
 ==================
 
@@ -8,20 +14,27 @@
 those values to create a `Makefile' in each directory of the package.
 It may also create one or more `.h' files containing system-dependent
 definitions.  Finally, it creates a shell script `config.status' that
-you can run in the future to recreate the current configuration, a file
-`config.cache' that saves the results of its tests to speed up
-reconfiguring, and a file `config.log' containing compiler output
-(useful mainly for debugging `configure').
+you can run in the future to recreate the current configuration, and a
+file `config.log' containing compiler output (useful mainly for
+debugging `configure').
+
+   It can also use an optional file (typically called `config.cache'
+and enabled with `--cache-file=config.cache' or simply `-C') that saves
+the results of its tests to speed up reconfiguring.  (Caching is
+disabled by default to prevent problems with accidental use of stale
+cache files.)
 
    If you need to do unusual things to compile the package, please try
 to figure out how `configure' could check whether to do them, and mail
 diffs or instructions to the address given in the `README' so they can
-be considered for the next release.  If at some point `config.cache'
-contains results you don't want to keep, you may remove or edit it.
+be considered for the next release.  If you are using the cache, and at
+some point `config.cache' contains results you don't want to keep, you
+may remove or edit it.
 
-   The file `configure.in' is used to create `configure' by a program
-called `autoconf'.  You only need `configure.in' if you want to change
-it or regenerate `configure' using a newer version of `autoconf'.
+   The file `configure.ac' (or `configure.in') is used to create
+`configure' by a program called `autoconf'.  You only need
+`configure.ac' if you want to change it or regenerate `configure' using
+a newer version of `autoconf'.
 
 The simplest way to compile this package is:
 
@@ -55,14 +68,16 @@
 =====================
 
    Some systems require unusual options for compilation or linking that
-the `configure' script does not know about.  You can give `configure'
-initial values for variables by setting them in the environment.  Using
-a Bourne-compatible shell, you can do that on the command line like
-this:
-     CC=c89 CFLAGS=-O2 LIBS=-lposix ./configure
+the `configure' script does not know about.  Run `./configure --help'
+for details on some of the pertinent environment variables.
 
-Or on systems that have the `env' program, you can do it like this:
-     env CPPFLAGS=-I/usr/local/include LDFLAGS=-s ./configure
+   You can give `configure' initial values for configuration parameters
+by setting variables in the command line or in the environment.  Here
+is an example:
+
+     ./configure CC=c89 CFLAGS=-O2 LIBS=-lposix
+
+   *Note Defining Variables::, for more details.
 
 Compiling For Multiple Architectures
 ====================================
@@ -75,11 +90,11 @@
 the `configure' script.  `configure' automatically checks for the
 source code in the directory that `configure' is in and in `..'.
 
-   If you have to use a `make' that does not supports the `VPATH'
-variable, you have to compile the package for one architecture at a time
-in the source code directory.  After you have installed the package for
-one architecture, use `make distclean' before reconfiguring for another
-architecture.
+   If you have to use a `make' that does not support the `VPATH'
+variable, you have to compile the package for one architecture at a
+time in the source code directory.  After you have installed the
+package for one architecture, use `make distclean' before reconfiguring
+for another architecture.
 
 Installation Names
 ==================
@@ -95,6 +110,11 @@
 PATH as the prefix for installing programs and libraries.
 Documentation and other data files will still use the regular prefix.
 
+   In addition, if you use an unusual directory layout you can give
+options like `--bindir=PATH' to specify different values for particular
+kinds of files.  Run `configure --help' for a list of the directories
+you can set and what kinds of files go in them.
+
    If the package supports it, you can cause programs to be installed
 with an extra prefix or suffix on their names by giving `configure' the
 option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
@@ -117,22 +137,32 @@
 Specifying the System Type
 ==========================
 
-   There may be some features `configure' can not figure out
-automatically, but needs to determine by the type of host the package
-will run on.  Usually `configure' can figure that out, but if it prints
-a message saying it can not guess the host type, give it the
-`--host=TYPE' option.  TYPE can either be a short name for the system
-type, such as `sun4', or a canonical name with three fields:
+   There may be some features `configure' cannot figure out
+automatically, but needs to determine by the type of machine the package
+will run on.  Usually, assuming the package is built to be run on the
+_same_ architectures, `configure' can figure that out, but if it prints
+a message saying it cannot guess the machine type, give it the
+`--build=TYPE' option.  TYPE can either be a short name for the system
+type, such as `sun4', or a canonical name which has the form:
+
      CPU-COMPANY-SYSTEM
 
-See the file `config.sub' for the possible values of each field.  If
+where SYSTEM can have one of these forms:
+
+     OS KERNEL-OS
+
+   See the file `config.sub' for the possible values of each field.  If
 `config.sub' isn't included in this package, then this package doesn't
-need to know the host type.
+need to know the machine type.
 
-   If you are building compiler tools for cross-compiling, you can also
+   If you are _building_ compiler tools for cross-compiling, you should
 use the `--target=TYPE' option to select the type of system they will
-produce code for and the `--build=TYPE' option to select the type of
-system on which you are compiling the package.
+produce code for.
+
+   If you want to _use_ a cross compiler, that generates code for a
+platform different from the build platform, you should specify the
+"host" platform (i.e., that on which the generated programs will
+eventually be run) with `--host=TYPE'.
 
 Sharing Defaults
 ================
@@ -145,32 +175,55 @@
 `CONFIG_SITE' environment variable to the location of the site script.
 A warning: not all `configure' scripts look for a site script.
 
-Operation Controls
+Defining Variables
 ==================
 
+   Variables not defined in a site shell script can be set in the
+environment passed to `configure'.  However, some packages may run
+configure again during the build, and the customized values of these
+variables may be lost.  In order to avoid this problem, you should set
+them in the `configure' command line, using `VAR=value'.  For example:
+
+     ./configure CC=/usr/local2/bin/gcc
+
+will cause the specified gcc to be used as the C compiler (unless it is
+overridden in the site shell script).
+
+`configure' Invocation
+======================
+
    `configure' recognizes the following options to control how it
 operates.
 
+`--help'
+`-h'
+     Print a summary of the options to `configure', and exit.
+
+`--version'
+`-V'
+     Print the version of Autoconf used to generate the `configure'
+     script, and exit.
+
 `--cache-file=FILE'
-     Use and save the results of the tests in FILE instead of
-     `./config.cache'.  Set FILE to `/dev/null' to disable caching, for
-     debugging `configure'.
+     Enable the cache: use and save the results of the tests in FILE,
+     traditionally `config.cache'.  FILE defaults to `/dev/null' to
+     disable caching.
 
-`--help'
-     Print a summary of the options to `configure', and exit.
+`--config-cache'
+`-C'
+     Alias for `--cache-file=config.cache'.
 
 `--quiet'
 `--silent'
 `-q'
-     Do not print messages saying which checks are being made.
+     Do not print messages saying which checks are being made.  To
+     suppress all normal output, redirect it to `/dev/null' (any error
+     messages will still be shown).
 
 `--srcdir=DIR'
      Look for the package's source code in directory DIR.  Usually
      `configure' can determine that directory automatically.
 
-`--version'
-     Print the version of Autoconf used to generate the `configure'
-     script, and exit.
+`configure' also accepts some other, not widely useful, options.  Run
+`configure --help' for more details.
 
-`configure' also accepts some other, not widely useful, options.
-

new file mode 100644
--- /dev/null
+++ b/INSTALL.minc
@@ -0,0 +1,48 @@
+See INSTALL for generic installation instructions.
+
+		Shared or Static libraries?
+		---------------------------
+
+By default, only a static version (i.e. libminc.a) will be produced.
+A shared version of the library may be enabled using the configure
+flag "--enabled-shared".  See also "--disable-static".
+
+
+		Finding NetCDF
+		--------------
+
+The NetCDF library 
+
+    http://www.unidata.ucar.edu/packages/netcdf/
+
+must be built and installed before you can build MINC.
+
+1. This library may already be installed in a location where the
+compiler can find it.  If so, you have nothing to do.
+
+2. Third-party libraries are commonly installed such that the headers
+live in /usr/local/include and the library file lives in
+/usr/local/include.  The prefix may be something else; "/opt" is
+common, too.  If this is the case, you should pass the argument
+"--build-path=/usr/local" (substitute appropriate prefix) to
+configure.
+
+3. Otherwise, you need to pass appropriate -I and -L flags to
+configure using something like 
+
+    ./configure CPPFLAGS="-I/a/b/c" LDFLAGS="-L/d/e/f"
+
+
+
+		FORTRAN Interface
+		-----------------
+
+The fortran interface is no longer built.
+
+The FORTRAN interface is no longer maintained.  Should you need it,
+all the sources and the old Makefiles are located in the fortran
+directory.  Please let us know of your success should you get it
+to build.
+
+The minc fortran interface is only supported under irix.
+

--- a/README
+++ b/README
@@ -38,7 +38,9 @@
 that allows the user to roam simultaneously through two data volumes
 plus the combined volume that overlays the data of the other two. Emma
 is a minc interface to matlab (from The MathWorks) with functions to
-facilitate image processing and display.
+facilitate image processing and display.  Mni_autoreg provides automated
+registration, both linear and nonlinear.
+
 
 GETTING MINC
 ------------
@@ -52,36 +54,6 @@
 Minc requires that the NetCDF package be built and installed first. It
 is available through anonymous ftp from the Unidata Program centre at
 the University Corporation for Atmospheric Research (unidata.ucar.edu). 
-You should also be able to get it from the same site that provided
-this package. Automatic registration software may also be available on
-request. 
 
-For building and installation instructions, refer to the general
-autoconf INSTALL file provided in this directory. Please note a few
-changes and additions: 
-
-   1. The default installation directory has changed to /usr/local.
-      This is different from the NetCDF default.
-
-   2. Only a few of the many configure options are used: prefix,
-      exec_prefix, and CC, to name a few. Additionally, you can set
-      NETCDF_PREFIX to tell it where to look for the netcdf stuff (if
-      it is not in .. or /usr/local).
-
-   3. The documentation in the doc subdirectory is only built if you
-      use the command "make docs". Manual pages for programs are 
-      converted by default.
-
-   4. You can selectively "make libs" or "make programs" if you wish 
-      to build the package in separate pieces (for creating shared 
-      libraries, for example).
-
-   5. The fortran interface is no longer built by default. Because of
-      changes to the NetCDF fortran code, the minc fortran interface
-      is now only supported under irix and the C wrappers are no longer 
-      generated for different platforms. In order to force a build of
-      the interface, set the environment variable BUILD_FORTRAN to "yes"
-      before running configure.
-
-   6. The package has not been set up for cross-compiling.
-
+For building and installation instructions, refer to the files
+INSTALL.minc and INSTALL.