MINC/Tutorials

MINC in a few less than hard steps

The following set of tutorials are broken into three sections, the first involves all issues with installing MINC. The second running the MINC command line tools and the third concerns using an example pipeline for automated analysis. These tutorials assume that you are using a linux-based system an a "sh" variant shell such as bash, but should be reasonably easy to adapt to other settings.

Installing and configuring MINC

The first step is to install the MINC library itself, this can be done by either compiling from source or by using a binary installer if you happen to be working on a platform that is currently supported. So you can pick either one of the first two tutorials here before progressing to the 3rd and 4th.

SourceInstall - Building the MINC tools from source

BinaryInstalls - How to install a binary MINC package

InstallingPerl - How to install the required perl modules

AddingPaths - Finishing off the installation

Using the MINC command line tools

Tutorials01 - Basic MINC commands from the toolbox

Tutorials02 - Conversion to MINC, the MINC file format, information on files

Programming with the MINC2 toolkit in C

Programming01 - The MINC version of "hello world."

Programming02 - The two MINC coordinate systems.

Programming03 - A fully functional and useful example on using voxel and world coordinates.

Programming04 - Writing volumes to file, with an aside on slice scaling.

Programming05 - Working with hyperslabs.

Programming06 - Hyperslabs part 2: a slice loop with slice scaling

Programming with MINC2 in python

InstallingPyminc - How to install pyminc.

PythonExample - A simple example for manipulating image data in Python.

PythonSliceLoop - How to run a slice loop in python for dealing with large amounts of data.

NumericPyminc - Why use python at all? See here - an illustration of solving the same problem in a bunch of ways.

CVS and how to make a MINC package

CVSandPackaging - Procedure to follow to make a BIC source package and release it

Reading/Writing MINC2.0 images from ITK (Insight Toolkit)

part1 - Build ITK with MINC2.0 options enabled

part2 - How to read/Write MINC2.0 images from ITK