3D Slicer

FSL

AFNI/NIfTI/SUMA

SPM - Statistical Parametric Mapping

NITRC

iSurf - iPhone/iPad app

Nipype - Neuroimaging in Python, w/ FreeSurfer interfaces

Mindboggle-101 data - Manually labeled anatomical regions for 101 healthy subjects

MNE - M/EEG data analysis using FreeSurfer meshes and surface registration

Brainstorm - See Integration with FreeSurfer