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 >= 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
  # example configuration for linux to build all the tools and install them into /opt/minc-itk4 :
    CMAKE_BUILD_TYPE:STRING=Release
    CMAKE_INSTALL_PREFIX:PATH=/opt/minc-itk4
    MT_BUILD_ABC:BOOL=ON
    MT_BUILD_ANTS:BOOL=ON
    MT_BUILD_C3D:BOOL=ON
    MT_BUILD_ELASTIX:BOOL=ON
    MT_BUILD_IM:BOOL=OFF
    MT_BUILD_ITK_TOOLS:BOOL=ON
    MT_BUILD_LITE:BOOL=OFF
    MT_BUILD_SHARED_LIBS:BOOL=ON
    MT_BUILD_VISUAL_TOOLS:BOOL=ON
    MT_USE_OPENMP:BOOL=ON
    USE_SYSTEM_FFTW3D:BOOL=OFF
    USE_SYSTEM_FFTW3F:BOOL=OFF
    USE_SYSTEM_GLUT:BOOL=OFF
    USE_SYSTEM_GSL:BOOL=OFF
    USE_SYSTEM_HDF5:BOOL=OFF
    USE_SYSTEM_ITK:BOOL=OFF
    USE_SYSTEM_NETCDF:BOOL=OFF
    USE_SYSTEM_NIFTI:BOOL=OFF
    USE_SYSTEM_PCRE:BOOL=OFF
    USE_SYSTEM_ZLIB:BOOL=OFF
  #
  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/
libxi
libxmu

###Following packages are included :

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 4.9- http://www.itk.org/
NIFTI - http://niftilib.sourceforge.net/ ##Installing Dependencies on Ubuntu:


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

benjamindeleener / minc-toolkit-v2

MINC - TOOLKIT (Medical Imaging NetCDF Toolkit)

Introduction

Installing from github, need CMake >= 3.1

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