- SPM Statistical Parametric Mapping for different types of neuro data
- FSL A unix based tool for neuroimaging analysis
- AFNI I’ve only used it for the AlphaSim tool
- conn A toolbox for resting connectivity analysis based in MATLAB
- xjView A simple tool for displaying images and overlays
- xvfb Allows sending graphical output to spot in memory, useful for graphical functionality in cluster environment
- Rdgehdr Used to convert pfiles into text to read header info!
- MRICron a nice tool to have for looking quickly at data, and figuring out orientation. It comes with a package called - dcm2nii that converts DICOM–>NIFTII as well.