Created: 2012-03-20 04:07
Updated: 2018-11-08 16:06
License: gpl-3.0


MINC - TOOLKIT (Medical Imaging NetCDF Toolkit)


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


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



Following packages are needed to compile all tools:

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

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 \
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