A data set of 41 subjects was obtained from Massachusetts General Hospital (MGH). This data is in freeSurfer format. The following subcortical structures have been segmented in this dataset: amygdala, caudate, hippocampus, pallidus, putamen, thallamus, ventricle. CIS used this dataset to generate a template (left and right) for each structure. The template was generated using large deformation diffeomorphic mapping (LDDMM) techniques. The template represents an average of the 41 subjects. In order to quantify shape change of subcortical structures with disease, subcortical surface data from Alzheimer's Disease Neuroimaging Initiative (ADNI) project, Open Access Series of Imaging Studies (OASIS) as well as freeSurfer data was compared to the templates. The surfaces are first aligned with the templates, then mapped to the templates using lddmm-surface, a CIS tool that maps surfaces to surfaces, using LDDMM methods.

Download Human Subcortical Atlas

A postmortem brain was obtained from the Brain Resource Center, Department of Pathology, Johns Hopkins University. The brain tissues were fixed by 10% formaldehyde for more than two weeks. A section of the brain that included the amygdala, hippocampus and entorhinal cortex was sectioned from the right hemisphere of the brain, and scannned using a Bruker Biospec 11.7T scanner. The b0 modality scan was hand segmented to create amygdala, entorhinal cortex and hippocampus masks, inclduing subfields.

Download 11T Subcortical Structures

A data set of 8 normal canine hearts was obtained from Drs. Patrick A. Helm and Raimond L. Winslow at the Center for Cardiovascular Bioinformatics and Modeling and Dr. Elliot McVeigh at the National Institute of Health. There are two kinds of data: geometry/scalar data and diffusion tensor data. We use the template estimation method developed at CIS to generate a geometry atlas based on geometry data. Then we use LDDMM to map the diffusion tensor data from the subject to the geometry atlas. Finally, the cardiac atlas will have both geometry and diffusion tensor data, which can be used to study shape variation in a population.

Download Canine Heart Atlas


A data set of 8 subjects was obtained from the Laboratory of Dr. Steven Yantis, Department of Psychological and Brain Sciences, Johns Hopkins University. The population is 8 females with a mean age of 21 years. Whole-brain high resolution 3D structural MRI images were acquired from the Phillips 3T scanner using a T1 weighted MPRAGE sequence with a TR of 8.1 ms, TE of 3.8 ms, flip angle of 8 degrees, coronal slice acquisition, time between inversions of 3 seconds, inversion time of 748 ms, and an isotropic resolution of 1 mm. This data is in Analyze format. The following subcortical structures have been segmented in this dataset: amygdala, caudate, hippocampus, pallidus, putamen and thallamus. Download Yantis Eight

Atlas File Formats

Atlas volumes are provided in Analyze 7.5 format. Analyze is an image processing program, written by The Biomedical Imaging resource at the Mayo Foundation. The Analyze data format is used by a wide variety of software including lddmm-volume. The specification for Analyze 7.5 is available at Analyze 7.5 file format

Atlas surfaces are provided in .byu format. This file format was developed at Brigham Young University, for representing 3D polygonal meshes. It is an ASCII format. A description of the format is available at BYU file format