The MNI-BIC software distribution page

This is the place to get some of the software developed at the McConnell Brain Imaging Centre of the Montreal Neurological Institute. We will try our best to provide five different formats: tardists for IRIX 6.5 systems, RPMs and Debian binary packages for Linux systems, MacIntosh OS X binaries, as well as the source code. A bit of a disclaimer: the packages will not have been thoroughly tested, and we cannot guarantee that they will always be up to date, though we will try. Some instructions for how to compile the sources are provided as well; we make no guarantee, however, that the process will always be easy and painless. The source has been compiled on SGI IRIX, Linux, and MacIntosh OS X systems, most of it ought to work on any UNIX variant. So, at your own risk (and we make no assurances that these packages won't erase all your files or cause an aardvark infestation in your neighbourhood), download, compile, and play! To download packages, go to packages.bic.mni.mcgill.ca. You will also find a slightly more details below. If you run into any problems please consult our wiki at wiki.bic.mni.mcgill.ca. You may also email minc-users@bic.mni.mcgill.ca.

Table of Contents

IRIX 6.5 binaries

IRIX 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 binaries

We 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 binaries

Binaries 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 Instructions

We 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.

NetCDF

What 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.

MINC

The core to BIC software - both libraries (libminc and volume_io) as well as multiple tools.

Prerequisites:

  • NetCDF

Getopt::Tabular

Not 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 Perllib

Multiple Perl libraries that are extensively used by our Perl scripts. Uses the Perl package mechanism for installation.

BICPL

An extensive collection of algorithms and data-types packaged in a library, written by David MacDonald.

Prerequisites:

  • NetCDF
  • MINC

N3

Non-uniformity correction software written by John Sled.

Prerequisites:

  • NetCDF
  • MINC
  • EBTKS
  • Getopt-Tabular
  • MNI-Perllib

Conglomerate

A very wide variety of tools; most of which are based on the bicpl library. Mostly written by David MacDonald.

Prerequisites:

  • NetCDF
  • MINC
  • BICPL

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

Prerequisites:

  • NetCDF
  • MINC

Inormalize (INSECT)

Tool for intensity normalisation between or within volumes. Written by Alex Zijdenbos. Also part of INSECT.

Prerequisites:

  • NetCDF
  • MINC
  • EBTKS
  • Getopt-Tabular
  • MNI-Perllib

Classify (INSECT)

Tissue classification, written by Alex Zijdenbos. Part of INSECT as well.

Prerequisites:

  • NetCDF
  • MINC
  • EBTKS
  • Getopt-Tabular
  • MNI-Perllib

MNI-autoreg (ANIMAL)

Registration and segmenation package, written by Louis Collins.

Prerequisites:

  • NetCDF
  • MINC
  • Getopt-Tabular
  • MNI-Perllib

MNI-autoreg Models (ANIMAL)

The MNI Average 305 Model to be used by MNI-autoreg.

Register

Visualization and manual registration tool written by David MacDonald.

Prerequisites:

  • NetCDF
  • MINC
  • BICPL

ray_trace

Command line generation of images, written by David MacDonald.

Prerequisites:

  • NetCDF
  • MINC
  • BICPL 1.4.0 or later

Display

Visualization and brain painting tool written by David MacDonald.

Prerequisites:

  • NetCDF
  • MINC
  • BICPL

JIV

A Java based volume viewer written by Chris Cocosco. Has both bytecode as well as the source.