Table of Contents
IRIX 6.5 binariesIRIX binaries are provided for 6.5 and later systems. All tardists intall their software under /usr/local/mni. As it stands right now, they are all compiled as n32 binaries, and the libraries themselves are installed under /usr/local/mni/lib32. We are working on 64 bit binaries as well; feel free to try them, but expect bugs for now. In other words, unless you need to access files over 2GB, I'd stick with n32.Intel Linux binariesWe are working on two package formats for linux: RPM and dpkg (debian). The code was built using gcc 3.2 on a linux box running the 2.4 kernel series. And yes, the compiler actually does matter, since any C++ library can only link against other C++ code if built with the same minor version number of gcc (though supposedly versions greater than 3.2 ought to be compatible with 3.2). The software installs under /usr/local/mni.MacIntosh OS X binariesBinaries for MacIntosh's OS X operating system are also available, at this point distributed in a monolithic distribution. There is a special page for dealing with MINC tools under OSX here; please check it out for all known issues and tentative ideas/schedules about how to fix them.
Compilation InstructionsWe also provide the sources for all of the software that is distributed here. The build process is, unfortunately, not always trivial. Most of the packages below use the autoconf and automake mechanism for compilation. The basic steps are thus:./configure make make install To install software in a directory other than the default: ./configure --prefix=/some/other/directory 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,
e.g.: setenv LDFLAGS "-L/usr/local/mni/lib" setenv CPPFALGS "-I/usr/local/mni/include" ./configure replace the above invocation with export LDFLAGS="-L/usr/local/mni/lib" 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.Prerequisites:
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.Prerequisites:
N3Non-uniformity correction software written by John Sled.
Prerequisites:
ConglomerateA very wide variety of tools; most of which are based on the bicpl library. Mostly written by David MacDonald.Prerequisites:
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 INSECTPrerequisites:
Inormalize (INSECT)Tool for intensity normalisation between or within volumes. Written by Alex Zijdenbos. Also part of INSECT.
Prerequisites:
Classify (INSECT)Tissue classification, written by Alex Zijdenbos. Part of INSECT as well.
Prerequisites:
MNI-autoreg (ANIMAL)Registration and segmenation package, written by Louis Collins.Prerequisites:
MNI-autoreg Models (ANIMAL)The MNI Average 305 Model to be used by MNI-autoreg.
RegisterVisualization and manual registration tool written by David MacDonald.Prerequisites:
ray_traceCommand line generation of images, written by David MacDonald.Prerequisites:
DisplayVisualization and brain painting tool written by David MacDonald.Prerequisites:
JIVA Java based volume viewer written by Chris Cocosco. Has both bytecode as well as the source.
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