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README.md

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


  git clone --recursive 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/1.9.15 on Linux


 cmake .. \
-DCMAKE_BUILD_TYPE:STRING=Release   \
-DCMAKE_INSTALL_PREFIX:PATH=/opt/minc/1.9.15 \
-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

Dependencies

Following packages are needed to compile all tools:

Following packages are built internally :

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