MRIcron
MRIcron is a cross-platform NIfTI format image viewer. It can load multiple layers of images, generate volume renderings and draw volumes of interest. It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics
FreeSurfer is an open source software suite for processing and analyzing (human) brain MRI images.
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data