Neuroimaging Software and Toolboxes

Structural

Volume-Based Morphometry

• CIVET (human)
• SPM (human)
• MAGeT (subcortical) (human & murine)
• MBMpydiper (murine)
• DCM ANTs & python (human)

Surface-Based Analysis

• CIVET (human)
• Freesurfer (human)
• MAGeT (subcortical) (human & murine)

Statistical analysis

• RMINC (human and murine)

Functional (BOLD) and Connectivity

• SPM (human)
• FSL (human & murine)
• AFNI (human & murine)
• ANTs (human & murine)
• CONN

Diffusion

• MRtrix (human & murine)
• FSL (human & murine)

Graph Theory

• GraphVar
• Brain Connectivity Toolbox

Machine Learning

• GraphVar