MINC - TOOLKIT (Medical Imaging NetCDF Toolkit)

Introduction

This metaproject bundles multiple MINC-based packages that historically have been developed somewhat independently.

Here is a list of bundled packages:

• libminc - base Medical Imaging NetCDF package, file IO library
• minc-tools - low-level image manipulation tools
• bicpl - BIC programming library, adds supports for 3D objects in terms of io-library and low-level tools
• EBTKS - Everything But The Kitchen Sink library, higher level C++ library for image manipulation
• arguments - helper library for parsing command line arguments
• oobicpl - Object Oriented BIC programming library, provides a higher level C++ interface to bicpl, and some higher level object manipulation tools
• conglomerate - conglomerate of low-level volume and object manipulation tools
• inormalize - intensity normalization tools
• N3 - non-parametric method for correction of intensity non-uniformity in MRI data (http://en.wikibooks.org/wiki/MINC/Tools/N3)
• classify - Tissue classification tools
• mni_autoreg - MNI Automated Registration Package, supports both linear and non-linear registration, implements ANIMAL algorithm
• ray_trace - 3D visualisation tool
• glim_image - voxel-level general linar modelling tool
• bic-pipelines - basic brain MRI processing pipeline
• BEaST - automatic brain extraction tool
• mrisim - MRI simulation tool
• mni-perllib - perl library commonly used in perl scripts developed in BIC-MNI
• EZminc - Eazy MINC - higher level C++ interface to minc, includes distortion correction tool, non-local means filter, markov random field tissue classification tool, modified diffeomorphic demons non-linear registration tool
• register - interactive 3D image viewer and co-registration tool
• Display - interactive 3D image viewer and segmentation tool
• postf - interactive 3D image viewer for statistical results
• ITK - Imaging Tookkit
• minc4itk - MINC to ITK glue library
• c3d - Convert3D multipurpose image processing tool from UPENN
• mincANTS - ANTS nonlinear registration tool from UPENN

Installation

Installing from github, need CMake > 2.8.8

  git clone --recursive git://github.com/BIC-MNI/minc-toolkit.git minc-toolkit
  cd minc-toolkit
  mkdir build && cd build
  ccmake .. # Enter the location of all dependencies, if not detected automatically ..., 
  make && make test && make install

Important: CMAKE_BUILD_TYPE is set to RELEASE by default, if you have older build set it manually or face severe speed degradation of some tools

  cmake -DCMAKE_BUILD_TYPE:STRING=Release .

Dependencies

Following packages are needed to compile all tools:

• Perl - http://www.perl.org/
• BISON - http://www.gnu.org/software/bison/
• FLEX - http://flex.sf.net/
• GLUT - http://freeglut.sourceforge.net/
• libxi
• libxmu

Following packages are optional (i.e thay can be build as part of superbuild)

• zlib - http://zlib.net/ http://zlib.net/zlib-1.2.6.tar.gz
• NETCDF - http://www.unidata.ucar.edu/software/netcdf/ ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.0.1.tar.gz
• HDF5 - http://www.hdfgroup.org/HDF5/ http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.8/src/hdf5-1.8.8.tar.gz
• PCRE - http://www.pcre.org/ http://downloads.sourceforge.net/project/pcre/pcre/8.12/pcre-8.12.tar.gz
• GSL - http://www.gnu.org/software/gsl/ ftp://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz
• FFTW3 - http://www.fftw.org/ http://www.fftw.org/fftw-3.3.2.tar.gz

Installing Building Dependencies on Ubuntu 10.04, 12.04

sudo apt-get install \
 build-essential g++ \
 cmake cmake-curses-gui \
 bison flex \
 freeglut3 freeglut3-dev \
 libxi6 libxi-dev libxmu6 libxmu-dev libxmu-headers

Installing Building Dependencies on Fedora 20

sudo yum install \
 cmake flex bison \
 git \
 freeglut freeglut-devel \
 libXi-devel libXi \
 libXmu libXmu-devel \
 libXrandr libXrandr-devel \
 libXpm-devel libXft-devel \
 libXres-devel libXcomposite-devel \
 redhat-lsb