INSTALL.quick

If you are using a version of mni_autoreg from CVS, please
read README.CVS before continuing.

This is the short form of the installation instructions for MNI
AutoReg.  See the files INSTALL, README, and TESTING for more details
--- especially if anything goes wrong.


** Prerequisites for a successful installation:

    * ANSI-compliant C compiler
    * the NetCDF library
    * the MINC library
    * Perl 5 version 5.002 or later
    * the Getopt::Tabular perl module

** Installation procedure:

    1. ./configure, or ./configure --prefix=/your/favourite/place
    2. make
    3. make check
    4. make install

If `configure' complains about not being able to find certain things,
though, you may have to give it some hints.  In particular, this may be
necessary if you have installed NetCDF, MINC, Volume_IO, or Perl 5 in
weird places.  

If configure cannot find Perl 5, set the environment variable `PERL' prior
to running configure.  In a Bourne-compatible shell, this is accomplished
for example using

	PERL=/usr/strange/bin/perl ./configure ...

If configure does not find the required libraries, give optional flags
on the configure command line.  This is relatively easy to do if
everything has been installed into a common hierarchy.  Here at the
MNI, we put all the libs into /usr/local/mni/lib, and their associated
include files into /usr/local/mni/include.  In this case, mni_autoreg can
be configured using

        ./configure --prefix=/usr/local/mni --with-build-path=/usr/local/mni

If the required libraries are in several different hierarchies, no problem:
the argument to build path is a colon-separated list of locations to check.
For example, if you need to look in /usr/local/lib as well as 
/usr/local/mni/lib, then

        ./configure --with-build-path=/usr/local/mni:/usr/local

will do the trick.

If you have a more complicated setup, and, e.g. need to choose among
multiple installed versions of some library (it happens!), you can
specify the location of the libraries and their headers using
configure's --with-* options, such as

	--with-netcdf-library=/usr/strange/lib
  	--with-netcdf-includes=/usr/strange/include

There are similarly-named options for MINC and Volume_IO; see
`./configure --help' for the complete list.  (Note carefully the
spelling of the options.  Spelling errors are silently ignored!)

As described in the file INSTALL, you can affect the installation
directories using options --prefix, --bindir, and the like.  Besides
executables, scripts, and their man pages, MNI_Autoreg installs

	configuration files	in $sysconfdir/mni_autoreg,

and will look for 

	model files		in $datadir/mni-models

These directories can all be set at configure time.

Note that if you feel like setting ALL of these (e.g., to install
MNI_AutoReg to /tmp or your home directory), you're generally better
off using `--prefix'.  If you want to impose a more centralized
structure (eg. with all MNI_AutoReg-related files under
/usr/local/lib/mni_autoreg), you'll have to override most of the
defaults with configure arguments.

*** Important: MNI_AutoReg doesn't actually install anything to
MODELDIR; that is done by another package, the MNI Average Brain
Stereotaxic Registration Model However, MNI_AutoReg produces a custom
version of the mritotal program (the main driver for stereotaxic
registration) with MODELDIR hard-coded into it.  Be sure to use the
same MODELDIR when configuring and installing the two packages, or you
will always need to use mritotal's `-modeldir' option to override the
(incorrect) built-in default.


** Using MNI AutoReg:

You will have to build and install the stereotaxic model before you
can do actual fitting of MRI data to Talairach space.  This is
available as a separate package from packages.bic.mni.mcgill.ca; see the
README file for more information.

Finally, you should test the package on real data -- one example is
the file mni_autoreg_small_example_mri.mnc, available from
ftp.mni.mcgill.ca:/pub/mni_autoreg.  See the TESTING file for details.