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, @gdevenyi 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/VERSION
, 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 recent versions of ANTS and Elastix. 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 1.9.18
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/1.9.18 in order to co-exist with other versions of minc-toolkit
- 64 bit tools
- 32 bit tools Caveat Emptor Unfortunately, currently
mincbeast
is unable to run in 32bit mode properly, sostandard_pipelene.pl
will fail, also nu_correct produces different results then 64 bit version- Ubuntu
- RPM based
- Source code
- minc-toolkit complete source archive
V1 Version 1.0.09 legacy
All files will be installed into /opt/minc/1.0.09 in order to co-exist with other versions of minc-toolkit
- 64 bit tools
- Ubuntu
- Debian
- RPM based
- MacOS X
- 32 bit tools Caveat Emptor Unfortunately, currently
mincbeast
is unable to run in 32bit mode properly, sostandard_pipelene.pl
will fail (and the test-suite will also fail).- Ubuntu
- RPM based
- Source code
- minc-toolkit complete source archive
- Testsuite (under development)
Older Versions
Older packages are archived at https://packages.bic.mni.mcgill.ca/minc-toolkit/Debian for Ubuntu/Debian and https://packages.bic.mni.mcgill.ca/minc-toolkit/RPM/ for CentOS, Fedora and RedHat
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 1.9.17:
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
- Docker minc-toolkit-v2 1.9.17:
- 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
- Docker minc-toolkit-v2 1.9.16:
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
- BEaST segmentation library, needed to run mincbeast software for brain extraction
- bic-mni-models anatomical template library, includes models from ICBM 2009 template
Previous versions
Previous versions are archived in http://packages.bic.mni.mcgill.ca/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 runsudo 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
- optional dependency is octave, which is currently used only by xfmavg script.
- download corresponding binary packages
- run
for file in minc-toolkit-<version>.deb minc-toolkit-testsuite-<version>.deb bic-mni-models-<version>.deb beast-library-<version>.deb; do gdebi $file; done
.
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 1.9.18 (version 2): source the environment in
/opt/minc/1.9.18/minc-toolkit-config.sh
for bash or/opt/minc/1.9.18/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
- MacOS X
- MacOS X 10.7 - QT 4 version (doesn’t support retina display)
- MacOS X 10.11 - QT 5 version