Pre-processing steps:
1. AC (anterior commissure)-PC (posterior commisure) alignment.
2. Remove extra-cranial tissue.
3. Segment brain tissue into white matter, gray matter and cerebrospinal fluid.
4. Set the label values for white matter, gray matter and cerebrospinal fluid to 250, 150, 10, respectively.

Running HAMMER:
1. Do the linear registration to remove the global difference.
2. Run HAMMER to estimate the local deformations.

You may use the AC-PC alignment module in 3D Slicer to correct the anterior and posterior commissures. The tutorial and document can be found at (http://www.slicer.org/slicerWiki/index.p...).

You  may use the skull stripping module in 3D Slicer to remove the extra-cranial tissues of brain. The tutorial and document can be found at (http://www.slicer.org/slicerWiki/index.p...).

There are a lot of modules in 3D Slicer for image segmentation. Here we suggest to use the EM segmentation module in 3D Slicer. The document and tutorial can be found at (http://www.slicer.org/slicerWiki/index.p...) and (http://www.slicer.org/slicerWiki/index.p...).

There are a lot of linear registration methods available in 3D Slicer. We suggest to use the affine registration module in 3D slicer. The document and tutorial can be found at (http://www.slicer.org/slicerWiki/index.p...).