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.
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.
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.