FreeSurfer is an open-source software suite for processing and analyzing (human) brain MRI images. It can support Skullstripping, Image Registration, Subcortical Segmentation, Cortical Surface Reconstruction, Cortical Segmentation, Cortical Thickness Estimation, Longitudinal Processing, fMRI Analysis, Tractography, FreeView, Visualization GUI and other tasks.
Official Website: Main package, Interoperable Packages & PETsurfer *
Tutorials: Support, Wiki, Step-by-step guide
Reference Paper: Link 1 & Link 2
*PETsurfer is a a tool for performing ROI-based, surface-based, and whole-brain analysis of PET data, including certain kinetic modeling methods, integrated with FreeSurfer anatomical analysis
NMMItools 