Image Processing

The various image processing applications can be considered the heart of the software at the Brain Imaging Centre. Their dominant goal is the application of various algorithms to medical images. Below is a small list of the most important of these programs and their applications. To reiterate, if the program is in bold and not hyperlinked then no online documentation exists for it.


BEaST is a robust brain extraction method based on a multi-resolution patch-based framework.


CANDLE is a Collaborative Approach for eNhanced Denoising under Low-light Excitation (CANDLE) for the processing of 3D laser scanning multiphoton microscopy images.

Geometric distortion correction

Tools to estimate and correct for geometrical distortions caused by imaging gradient non-linearities


The N3 package, a part of MINC tools, implements a non-parametric method for correction of intensity non-uniformity in MRI data. Its use tends to be an essential first step in any processing sequence.

Registration tools/ANIMAL

This family of algorithms linearly and nonlinearly register two images to each other. The most used, mritotal registers an MRI to standard Talairach space. They are all part of the MNI AutoReg package. ANIMAL is also part of MNI Autoreg and was designed to label the major anatomical regions (the different lobes, corpus callosum, etc.) of a MRI.


INSECT is the algorithm to separate a structural MRI into it’s three tissue types: white matter, gray matter, and CSF. It is available as part of the classify packages in the directory


SEAL stands for “Sulcal Extraction and Labelling” - which pretty much explains its use as well.


RMNMS is a robust multi-modal (T2W and FLAIR) MS lesion segmentation algorithm which exploits pre-segmented training datasets.