MINC Toolkit (source: github)

General BIC-wiki
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Contents:

This software repository contains open-source tools developed at the McConnell Brain Imaging Centre, Montreal Neurological Institute The main documentation site for this repository is located at wikibooks

Also, concise man pages for various minc tools are located at bic-mni.github.io/man-pages

Support

Contact @vfonov, @andrewjanke or @rdvincent if you have any questions

MINC Tool Kit

This toolkit contains most of the commonly used minc tools in one precompiled 32 and 64bit binary packages of Debian, Ubuntu, RedHat and Mac OS X. It includes most of the standard minc tools, Display, Register and a basic image processing pipeline based on the one developed for NIHPD project (standard_pipeline.pl) Everything is currently installed in /opt/minc , to avoid conflict with standard /usr/local/bic location.

Notes about versions

  • 1.9.XX - includes the same standard minc-tools as version 1.0.XX, but sometimes with updated parameters (minctracc so far is the only such program). Also includes new experimental software based on ITK 4.XX and latest versions of ANTS,Elastix and C3D. Use this version
  • 1.0.XX - is a legacy version that still includes all the latest versions of the minc tools, and several programs based on ITK 3.20. The standard minc-based programs are kept up-to date, but new experimental software is not included. Use this version if you need only basic minc tools (i.e register/Display/xdisp) or you are running a legacy image processing pipeline that does not require new tools.

V2 Version 1.9.16

This version includes ITK-4.13.0, latest version of Elastix, ANTs and C3D - all with minc support. WARNING some basic tools produce results incompatible with version 1.00.XX Test-suite will fail due to changes in minctracc All files will be installed into /opt/minc-itk4 in order to co-exist with version 1 of minc-toolkit

V1 Version 1.0.09 legacy

Containers

  • Containers based on Ubuntu 16.04 64bit and include R 3.4.3 + tidyverse + RMINC 1.5.1.0 , python 2.7 + pyminc + pyezminc + minc2_simple, and also standard anatomical models and beast templates installed in /opt/minc
    • Docker minc-toolkit-v2 1.9.16: docker pull nistmni/minc-toolkit:1.9.16
    • Docker minc-toolkit-v1 1.0.09: docker pull nistmni/minc-toolkit:1.0.09
    • Singularity minc-toolkit-v2 1.9.16: singularity pull --name minc-toolkit-1.9.16.simg shub://vfonov/minc-toolkit-containers:1.9.16
  • Containers without visual tools (Register, Display and ray_trace are missing) and without anatomical models:
    • Docker minc-toolkit-v2 1.9.16: docker pull nistmni/minc-toolkit-min:1.9.16
    • Singulatity minc-toolkit-v2 1.9.16: singularity pull --name minc-toolkit-1.9.16-min.simg shub://vfonov/vfonov/minc-toolkit-containers:1.9.16-min

Virtual Machine

A virtual machine containing minc-toolkit, as well as a number of tools built upon it is available for download at CoBrALab/MINC-VM It is kept up to date with the latest releases of minc-toolkit and additional tools.

Data files and models

These packages contain anatomical models needed for standard pipeline, all files are installed into /opt/minc/share

Previous versions

Previous versions are archived in Index of /minc-toolkit

Installing

On Debian/Ubuntu

  • install dependencies: sudo apt-get install libc6 libstdc++6 imagemagick perl
  • optional dependency is octave, which is currently used only by xfmavg script.
  • download corresponding binary packages
  • run sudo dpkg -i minc-toolkit-<version>.deb minc-toolkit-testsuite-<version>.deb bic-mni-models-<version>.deb beast-library-<version>.deb . Sometimes it will be necessary to run sudo apt-get install -f afterwards to install missing libraries.
  • Visualization programs : register, display and ray_trace rely on working OpenGL , install appropriate drivers or software emulation sudo apt-get install libgl1-mesa-glx libglu1-mesa

On CentOS / OpenSuse / Fedora

  • install dependencies: sudo yum install glibc libstdc++ ImageMagick perl
  • install downloaded rpm packages

On MacOS X 10.8 and later

  • download and double click on appropriate dmg file, the standard MacOS X installer will start
  • install ImageMagick, either using mac ports - preferred or homebrew

Using

  • Version 1.0.09 (version 1) : source the environment in /opt/minc/1.0.09/minc-toolkit-config.sh for bash or /opt/minc/1.0.09/minc/minc-toolkit-config.csh for tcsh
  • Version 1.9.16 (version 2) : source the environment in /opt/minc/1.9.16/minc-toolkit-config.sh for bash or /opt/minc/1.9.16/minc-toolkit-config.csh for tcsh

Running test suite

Currently Broken Test data is installed in /opt/minc/share/testsuite/ . To run the test, execute /opt/minc/run_tests.sh <prefix> , it will take around an hour on a modern PC, the output will be in <prefix>/00200 and <prefix>/00201 and the log file will be saved in <prefix>/minc-toolkit-test-<date>.log . The results of the local test will be compared to a file containing the results from a baseline test to determine if the tools have been installed and run correctly.

Building from the source

Consult minc-toolkit on github or minc-toolkit-v2 on github for details and to download latest version of the software. The binary builds are now built using docker, see all the scripts here: build_packages on github

Additional software ported to support MINC file format:

ITK-SNAP 3.2