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SBIA, Department of Radiology, Upenn

HAMMER is an elastic registration procedure. It is used to warp a template brain image to an individual, and vice versa.

In order to make HAMMER as robust as possible to different acquisition protocols and conditions, we provide a distribution that assumes that images have been skull-stripped and segmented into gray matter, white matter, and ventricular CSF. We have other software tools that can perform these steps, including skull stripping, reorientation and reslicing, and segmentation tools. Importantly, we use 250 for WM, 150 for GM, 50 for Ventricles and 10 for CSF in the tissue-segmented brain images.

Current modules used for group analysis:

-- Labeling subject brain using a manually-labeled brain Model
-- Generating RAVENS map for each tissue (WM, GM, VN)
-- Normalizing subject brain images

NIfTI-1 support
Dinggang Shen, Christos Davatzikos
How to get
Download through web page:
Current version
Current version release date
Sept. 2005
Open source
Available free of charge
At least 1G memory
Technical publications
1. D. Shen, and C. Davatzikos, "Very high-resolution morphometry using mass-preserving deformations and HAMMER elastic registration". Neuroimage, 18(1):28-41, 2003.
2. D. Shen, and C. Davatzikos, "HAMMER: Hierarchical attribute matching mechanism for elastic registration". IEEE Trans on Med. Imaging, 21(11):1421-1439, 2002.
Applications publications

1. Christos Davatzikos, Dinggang Shen, Ruben C. Gur, Xiaoying Wu, Dengfeng Liu, Yong Fan, Paul Hughett, Bruce I., Turetsky, Raquel E., Gur, "Whole-brain morphometric study of schizophrenia reveals a spatially complex set of focal Abnormalities",In press JAMA Archives of General Psychiatry, 2005 .
2.Dinggang Shen, Dengfeng Liu, Hong Liu, Liv Clasen, Jay Giedd and Christos Davatzikos,"Automated Morphometric Study of Brain Variation in XXY Males",NeuroImage, Vol 23(2):648-653, October 2004.
3. Resnick, S.M., Pham, D.L., Kraut, M.A., Zonderman, A.B., Davatzikos, C.: Longitudinal magnetic resonance imaging studies of older adults: a shrinking brain. J. Neurosci. 23(8): 3295-3301, 2003.
Other information
atlas, registration, warping
Linux, SGI
IATR listing last updated
30 Nov 2005