ITK: core image processing and SimpleITK.
Image Registration – Advanced Normalization Tools (ANTs) SyN. Compile ANTs.
Image Segmentation – Atropos program (via ANTs). Link to paper. Also Paul Yushkevich’s ITK-SNAP!
Bias Correction – N4 (via ANTs).
Paraview and mricron are useful for visualization.
Other useful tools:
InSANE surface-based visualization and mapping. Compile with these instructions.
Sparse canonical correlation analysis for neuroimaging (SCCAN): Email for info. paper.
Topologically constrained segmentation (via ANTs, git version).
Pipedream depends on ANTs and Camino. A processing pipeline for neuroimaging software: T1, DTI, ASL/CBF and (in development) fMRI. Its longitudinal component was used here.
Here is an evaluation of ANTs affine registration against FSL affine registration: Pretty similar. An in-depth evaluation of ANTs is here, here and here.