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

Version 1.0.08 (currently stable)

V2 Version 1.9.11

This version includes ITK-4.9, 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

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 http://packages.bic.mni.mcgill.ca/minc-toolkit/

Installing

On Debian/Ubuntu

On CentOS / OpenSuse / Fedora

On MacOS X 10.7 and 10.9

Using

Running test suite

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.

Additional software ported to support MINC file format

ITK-SNAP 3.2