There are a number main packages available for statistical analysis of medical images.
glim_image is designed for performing VBM (Voxel Based Morphometry) - in other words, it is useful for examining the changes in segmented tissue matter (white matter, gray matter, CSF) as it relates to a linear model.
EMMA (Extensible MATLAB Medical image Analysis) is a toolkit designed to ease the use of MATLAB in the analysis of medical imaging data. It provides functions for reading and writing MINC files (our local data file format), viewing images, performing ROI operations, and performing several popular analyses. Also, there are toolkits for performing kinetic analysis of dynamic PET rCBF (regional cerebral blood flow) and FDG data.
And lastly fMRI statistical analysis is also done using matlab.