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:

• zlib - data compression library
• NetCDF - file format library ( used for MINC1)
• HDF5 - another file format library (used for MINC2)
• FFTW - FFT library
• GSL - Gnu Scientific library
• openblas - fast library for linear algebra
• ITK - Insight Toolkti version 4.11
• pcre - perl-compatible regular expressions
• 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 Toolkit https://itk.org/
• c3d - Convert3D multipurpose image processing tool from UPENN http://www.itksnap.org/c3d/
• ANTS - ANTS nonlinear registration tool from UPENN https://github.com/stnava/ANTs
• Elastix - Elastix a toolbox for rigid and nonrigid registration of images. http://elastix.isi.uu.nl/

Installation

Installing from github, need CMake >= 3.1

  To get the latest supported version of minc-toolkit-v2 (1.9.18) 
  git clone --recursive --branch release-1.9.18 https://github.com/BIC-MNI/minc-toolkit-v2.git minc-toolkit-v2
  cd minc-toolkit-v2
  mkdir build && cd build
  ccmake .. # Enter configuration details, recommend not to use any system-provided libraries that are included in minc-toolkit-v2

Following command will configure build system to build all the tools and install them into /opt/minc/1.9.17 on Linux

 cmake .. \
-DCMAKE_BUILD_TYPE:STRING=Release   \
-DCMAKE_INSTALL_PREFIX:PATH=/opt/minc/1.9.18 \
-DMT_BUILD_ABC:BOOL=ON   \
-DMT_BUILD_ANTS:BOOL=ON   \
-DMT_BUILD_C3D:BOOL=ON   \
-DMT_BUILD_ELASTIX:BOOL=ON   \
-DMT_BUILD_IM:BOOL=OFF   \
-DMT_BUILD_ITK_TOOLS:BOOL=ON   \
-DMT_BUILD_LITE:BOOL=OFF   \
-DMT_BUILD_SHARED_LIBS:BOOL=ON   \
-DMT_BUILD_VISUAL_TOOLS:BOOL=ON   \
-DMT_USE_OPENMP:BOOL=ON   \
-DUSE_SYSTEM_FFTW3D:BOOL=OFF   \
-DUSE_SYSTEM_FFTW3F:BOOL=OFF   \
-DUSE_SYSTEM_GLUT:BOOL=OFF   \
-DUSE_SYSTEM_GSL:BOOL=OFF   \
-DUSE_SYSTEM_HDF5:BOOL=OFF   \
-DUSE_SYSTEM_ITK:BOOL=OFF   \
-DUSE_SYSTEM_NETCDF:BOOL=OFF   \
-DUSE_SYSTEM_NIFTI:BOOL=OFF   \
-DUSE_SYSTEM_PCRE:BOOL=OFF   \
-DUSE_SYSTEM_ZLIB:BOOL=OFF 

make && make install

If you have installed minc-toolkit-v2 outside of the default installation ( i.e. changing DCMAKE_INSTALL_PREFIX:PATH within the build above).
source minc-toolkit-config.sh

Dependencies

Following packages are needed to compile all tools:

• Tools without GUI
  • cmake - https://cmake.org/
  • Perl - http://www.perl.org/
  • BISON - http://www.gnu.org/software/bison/
  • FLEX - http://flex.sf.net/
  • bc - http://ftp.gnu.org/gnu/bc/
  • libjpeg or libjpeg-turbo
• More packages for tools with GUI
  • X11 development libraries
  • libxi
  • libxmu
  • libjpeg-dev
  • libgl
  • libglu

Following packages are built internally :

• zlib - http://zlib.net/
• NETCDF - http://www.unidata.ucar.edu/software/netcdf/
• HDF5 - http://www.hdfgroup.org/HDF5/
• PCRE - http://www.pcre.org/
• GSL - http://www.gnu.org/software/gsl/
• FFTW3 - http://www.fftw.org/
• ITK 4.13- http://www.itk.org/
• NIFTI - http://niftilib.sourceforge.net/
• OpenBLAS - http://www.openblas.net/

Installing Build Dependencies on Ubuntu:

sudo apt-get install \
 build-essential g++ bc \
 cmake \
 bison flex \
 libx11-dev x11proto-core-dev \
 libxi6 libxi-dev \
 libxmu6 libxmu-dev libxmu-headers \
 libgl1-mesa-dev libglu1-mesa-dev \
 libjpeg-dev

Installing Build Dependencies on CentOS 7:

yum groupinstall 'Development Tools'  && \
yum install libX11-devel libXmu-devel libXi-devel \
 mesa-libGL-devel mesa-libGLU-devel \
 libjpeg-turbo-devel \
 openssl-devel bc \
 rpm-build-libs rpm-devel redhat-lsb-core