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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:

  • 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:

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 \
 redhat-lsb

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Metaproject uniting all the available minc tools

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