Installation

In order to make the MNI_AutoReg package:

0a)

You will need an ANSI-compliant C compiler; if your system is lacking in one (Sun workstations commonly are), we recommend the GNU C Compiler (gcc), available from

ftp://prep.ai.mit.edu/pub/gnu/

or any GNU mirror site.

1)

You may have to build and install the netCDF library.

2)

You may have to build and install the MINC library (check that you have version 0.6 or later).

3)

You may have to build and install Perl 5. (check using perl -V that it is version 5.003 or later)

4)

You may have to install the Getopt::Tabular module for Perl.

5)

We have used the GNU autoconf program to create a `configure' script that will automatically determine various system- dependent values and generate Makefiles needed to build the package.

In the directory where you unpacked the MNI_AutoReg tar file, type

./configure

`configure' works by poking around your system to determine all the system-specific values needed to build and install MNI_AutoReg. Once it has done that, it creates Makefile.include, which is the granddaddy Makefile used by all the programs in the package. If `configure' runs successfully, skip to step 7 below.

If `configure' complains about not being able to find certain things, though, you may have to give it some hints. In particular, this be necessary if you have installed netCDF, MINC, Volume_IO, or Perl 5 in weird places. The easiest way to do that is with the --prefix option; for instance, at the MNI, we keep home-grown software under /usr/local/mni, so here we run `configure' like this:

./configure --prefix=/usr/local/mni

and the MINC and Volume_IO files will be found in various directories under /usr/local/mni. (netCDF is not home-grown, so we keep it under /usr/local. Luckily, `configure' is smart enough to look there if all else fails.) If you simply can't get `configure' to find some files, you can set various environment variables, e.g. NETCDF_INCLUDE to specify the directory where netcdf.h lives. For instance, if you installed netCDF to /tmp, its include file would be in /tmp/include, and you could say:

env NETCDF_INCLUDE=/tmp/include ./configure

Here are all the environment variables you might want to set to help configure find things:

NETCDF_INCLUDE	where to find netCDF header (netcdf.h)
NETCDF_LIB	where to find netCDF library (libnetcdf.a on most Unix-like systems)
MINC_INCLUDE	where to find MINC header (minc.h)
MINC_LIB	where to find MINC library (libminc.a)
VOLUMEIO_INCLUDE	where to find Volume_io headers (volume_io.h, volumes.h, etc.)
VOLUMEIO_LIB	where to find Volume_io library (libvolume_io.a)
PERL	where to find Perl binary (must be Perl 5.003)

Note that these are all inputs required to build MNI_AutoReg. There are also a number of output directories that determine where various files are installed to; these are explained below. If you have built shared-library versions of netCDF, MINC, or Volume_io, configure should be able to find these. It looks for libraries first with a ".a" extension, then with ".so"; this appears to be a quite common convention under various Unices, and is known to work under IRIX and Linux. If your system has a different scheme for naming shared libraries, you might need to set the LIBEXT variable; e.g. to only look for ".so" files,

env LIBEXT=".so" ./configure

(LIBEXT is just a space-separated list of extensions, including the dot on each one.)

6)

You might also want to set various site-specific installation directories when running `configure'. MNI_AutoReg installs many files in various directories, and expects to find other files in certain directories, so it's important to know where you want stuff to go. By default, it all gets put under /usr/local, unless you specify a different base directory with `--prefix'). In particular:

binary executables:	/usr/local/bin
scripts:	/usr/local/bin
Perl libraries:	(see "Important point #2", below)
configuration files:	/usr/local/etc/mni_autoreg
man pages:	/usr/local/man/man1
stereotaxic brain model:	/usr/local/lib/model

(Binaries and scripts are distinguished in case you have a multi-platform environment and want to share scripts between machines, e.g. using /usr/local/share.) All of these directories can be customized, either by setting an environment variable before running `configure' or by editing Makefile.include after `configure' has run. If you wish to use environment variables, set them as follows:

BINDIR	directory for binary executables
SCRIPTDIR	directory for scripts (machine-independent executables)
PERLLIBDIR	Perl library files
CONFIGDIR	configuration files
MAN1DIR	man pages
MODELDIR	stereotaxic brain model files

Note that if you feel like setting ALL of these (e.g., to install MNI_AutoReg to /tmp or your home directory), you're probably better off to use `--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 environment variables.

If you prefer to edit Makefile.include, just read the instructions there - but be warned that any changes you make will be lost if you re-reun `configure'! Important point #1: MNI_AutoReg doesn't actually install anything to MODELDIR; that is done by another package, the MNI Average Brain Stereotaxic Registration Model (which you should have downloaded as mni_autoreg_model-1.0.tar.gz). 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.

Important point #2: the directory where Perl library files are installed is determined, logically enough, by asking Perl. (In particular, the "installsitelib" configuration variable is checked.) For Perl 5.002 and later, this is enough; if Perl was installed using all the default directories, the Perl library files will end up in /usr/local/lib/perl5/site_perl. However, if you're still running Perl 5.001, "installsitelib" is not set. In this case, `configure' will use a default directory of lib/perl5/site_perl under your prefix directory, which (if prefix is /usr/local), will be the same as you would have got using Perl 5.002's default installation directories. In this case, though, the directory is most likely not on Perl's default search path. You will be warned if this is the case when you do "make install"; if you get this warning, you should set the PERLLIB variable with

setenv PERLLIB /usr/local/mni/lib/perl5

(assuming you use a csh-variant) in your ~/.cshrc or the global /etc/cshrc file. (Or, if you're a Bourne-shell, ksh, zsh, or bash type of person, put

PERLLIB=/usr/local/mni/lib/perl5/site_perl ; export PERLLIB

in ~/.profile or /etc/profile.) Just remember: when you upgrade to Perl 5.002 or later, this setting of PERLLIBDIR might be redundant, so you'll probably want to remove it at that time.

7)

In the directory where you have unpacked both the MNI_AutoReg package and the test data, type:

make build

make test

make install

make installman

and you're ready to build the model files needed to perform full-blown MRI->Talairach fitting with perl script mritotal. Note that you may need to set the environment variable TMPDIR to some more appropriate place than /usr/tmp on systems where /usr/tmp has little available space.

8)

Unpack mni_autoreg_model-1.0.tar.gz somewhere, and follow the instructions in the README there. When editing the Makefile, be sure to set MODELDIR to the directory used for MODELDIR above! When you have done "make build" and "make install", then the model will be ready to go; and, as long as you set MODELDIR correctly in both packages, mritotal will be ready to run with that model.

9)

Now, you're ready to test mritotal on real data. Please see the file TESTING, included with this distribution, for more information.