MINC/Tools

=Documentation for MINC Tools=

There are a large number of add-on tools that have been written for MINC, this is an attempt to draw all of the documentation for these into one cohesive place. There is a lot of it out there! The tools are organised into rough sections, feel free to add your own tools in here and add a section if required. Note that the source code for all of these tools is available here: http://packages.bic.mni.mcgill.ca/tgz Some or at least most of these packages will also have binary versions available on http://packages.bic.mni.mcgill.ca/ as well.

Registration (alignment)
Registration is a process whereby two (more) images are aligned to each other. There are a number of methods by which you can do this but most of them involve some form of gradient descent and a matching algorithm.

/mni autoreg/ - A registration framework written by Louis Collins

Intensity Correction
Intensity correction in MRI typically refers to the correction of the B1 field effect, however there is also intensity correction that can occur between different scans of the same subject or indeed different subjects. There can also be intensity differences between slices of a single acquisition.

/iNormalize/ A global intensity correction package by Alex Zijdenbos

/N3/ - An intensity nonuniformity correction package written by John G. Sled

Geometric Distortion Correction
MRI scanners introduce geometric distortions caused by several factors.

/DistortionCorrection/ - a tool for correcting distortions in anatomical images caused by the nonlinearities in imaging gradients.

C Libraries
These libraries have been written in order to extend the functionality of MINC, typically they add certain features to MINC such as a link to an image display library.

/bicpl/ - the BIC "programmers" library

/EBTKS/ - Everything but the kitchen sink

/bicInventor/ - a glue library that allows the use of Inventor/Coin in a MINC program

Virtual Machine
A virtual machine, containing the MINC tools preinstalled and ready to use is available at https://github.com/cobralab/MINC-VM

Interfaces to other Languages
/emma/ - an old, ageing and un-maintained interface to MATLAB (written by an Academy award winner!)