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Metaproject uniting all the available minc tools

Octocat-spinner-32 BEaST @ 4cb8cb6 Updated several subprojects
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Octocat-spinner-32 Display @ 8b81ba0 Fixing various small bugs
Octocat-spinner-32 EBTKS @ e3faa1a Updating to new volume_io
Octocat-spinner-32 EZminc @ 1ef5442 Updated EZminc
Octocat-spinner-32 N3 @ 5df4173 new versions
Octocat-spinner-32 Register @ 6c5756d Updated projects
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Octocat-spinner-32 c3d @ 3aa2866 Fixing various small bugs
Octocat-spinner-32 centos Add rpmmacros file and patches
Octocat-spinner-32 classify @ cbba409 Updating to new volume_io
Octocat-spinner-32 cmake-modules Fixed building flags leading to dramatic slow-down in FFTW
Octocat-spinner-32 conglomerate @ 03815c7 Updated versions of subprojects
Octocat-spinner-32 glim_image @ c3be545 Updating to new volume_io
Octocat-spinner-32 inormalize @ 134cef7 Updating to new volume_io
Octocat-spinner-32 libminc @ adb8cd0 Updated libminc and mni_autoreg
Octocat-spinner-32 minc4itk @ 968aae9 new version of minc4itk
Octocat-spinner-32 mincANTS @ 1d86973 New versions of mincANTS
Octocat-spinner-32 minctools @ f5d91cb Updated libminc and minctools, bumped version
Octocat-spinner-32 mni-perllib @ b908472 Changed mnc-perllib
Octocat-spinner-32 mni_autoreg @ d05e813 New version of bic-pipelines and mni_autore
Octocat-spinner-32 mrisim @ 4c60fe6 Refactoring volume_io
Octocat-spinner-32 oobicpl @ 417c7db Fixed libminc and oobicpl
Octocat-spinner-32 perl-modules added command to create intermediate copy of perl modules
Octocat-spinner-32 postf @ 8ea5b48 Refactoring volume_io
Octocat-spinner-32 ray_trace @ 1633738 Updated projects
Octocat-spinner-32 xdisp @ 36d40ca Fixed a problem in mni_autoreg resulting in differences between mac a…
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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 > 2.6 , preferably > 2.8.3


  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

Dependencies

Following packages are needed to compile all tools:

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

Installing 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
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