Table of Contents
./configure make make install
To install software in a directory other than the default:
The default directory is /usr/local/
One more worthwhile tidbit: if you do install packages in a
non-default directory, you'll have to tell the configuration of
subsequent packages about where to find those libraries and
headers. This is done by setting the LDFLAGS and CPPFLAGS environment,
setenv LDFLAGS "-L/usr/local/mni/lib" setenv CPPFALGS "-I/usr/local/mni/include" ./configure
replace the above invocation with
if you are using a bash rather than csh variant shell.
This is, of course, just the bare bones outline of how to use autoconf and automake packages. For more details, go to the autoconf homepage or the automake homepage. Without any further ado, here are the packages currently available from this site - go to packages.bic.mni.mcgill.ca to download source packages and/or binaries.
NetCDFWhat minc is based on - should be the first package to be compiled and installed. NetCDF was not developed at the BIC, check the NetCDF homepage for more information.
MINCThe core to BIC software - both libraries (libminc and volume_io) as well as multiple tools.
Getopt::TabularNot imaging software, though it was developed at the BIC by Greg Ward (check CPAN for more info). This is a Perl library for command line option handling that is widely used by perl-scripts distributed with some of the following packages. Uses the perl package mechanism for installation.
MNI PerllibMultiple Perl libraries that are extensively used by our Perl scripts. Uses the Perl package mechanism for installation.
BICPLAn extensive collection of algorithms and data-types packaged in a library, written by David MacDonald.
N3Non-uniformity correction software written by John Sled.
ConglomerateA very wide variety of tools; most of which are based on the bicpl library. Mostly written by David MacDonald.
EBTKS (INSECT)EBTKS - stands for Everything But The Kitchen Sink - is Alex Zijdenbos library of numerical types and algorithms, and is needed by classify and inormalize. It is, unfortunately, awkward to build due to its use of C++ templates; as far as we know it requires g++ version 3 or greater. This is part of INSECT
Inormalize (INSECT)Tool for intensity normalisation between or within volumes. Written by Alex Zijdenbos. Also part of INSECT.
Classify (INSECT)Tissue classification, written by Alex Zijdenbos. Part of INSECT as well.
MNI-autoreg (ANIMAL)Registration and segmenation package, written by Louis Collins.
MNI-autoreg Models (ANIMAL)The MNI Average 305 Model to be used by MNI-autoreg.
RegisterVisualization and manual registration tool written by David MacDonald.
ray_traceCommand line generation of images, written by David MacDonald.
DisplayVisualization and brain painting tool written by David MacDonald.
JIVA Java based volume viewer written by Chris Cocosco. Has both bytecode as well as the source.