Digimouse:

We have generated a 3D Digital Mouse Atlas -Digimouse- using coregistered CT and cryosection images of a 28g nude normal male mouse resulting a matrix size of 380x992x208 and 0.1mm cubical voxels. The structures segmented from these data are: whole brain, external cerebrum, cerebellum, olfactory bulbs, striatum, medulla, massetter muscles, eyes, lachrymal glands, heart, lungs, liver, stomach, spleen, pancreas, adrenal glands, kidneys, testes, bladder, skeleton and skin. You can get more information on the data acquisition, registration of PET, CT and Cryosection data and the creation of atlas in Digimouse website.

Final Registered PET, CT, Cryosection, Atlas and Overlay images for a coronal slice

PET	CT	Cryosection	Atlas	Overlay

• B. Dogdas, D. Stout, A. Chatziioannou, and R. M. Leahy, "Digimouse: A 3D Whole Body Mouse Atlas from CT and Cryosection Data." Phys Med Biol. 2007 Feb 7; 52 (3): 577-87 website

Skull / Scalp Extraction:

We developed a new technique for segmentation of skull and scalp in human T1-weighted magnetic resonance (MR) images that generates realistic models of the head for EEG and MEG source modeling. Our method performs skull segmentation using a sequence of mathematical morphological operations. Prior to the segmentation of skull, we segment the scalp and the brain from the MR image. The scalp mask allows us to quickly exclude background voxels with intensities similar to those of the skull, while the brain mask obtained from our Brain Surface Extractor algorithm ensures that the brain does not intersect our skull segmentation. We find the inner and the outer skull boundaries using thresholding and morphological closing and opening operations. We then mask the results with the scalp and brain volumes to ensure closed and nonintersecting skull boundaries. We applied our scalp and skull segmentation algorithm to several MR images and validated our method using coregistered CT-MR image data sets. We observe that our method is capable of producing scalp and skull segmentations suitable for MEG and EEG source modeling in 3D T1-weighted human MR images.

The Skull/Scalp Extraction is now a part of BrainSuite.

Segmentation of brain, skull and scalp from MRI and its corresponding CT on transaxial, sagittal and coronal slices respectively. First Row: Original MR Image. Second Row: Original CT data. Third Row: Segmentation of brain, skull and scalp from MRI. Fourth Row: Segmentation of brain, skull and scalp from CT.

Surface tesselations of the scalp, outer skull, inner skull, and brain from a T1 weighted MR Image.

• Belma Dogdas, David W. Shattuck and Richard M. Leahy, "Segmentation of Skull and Scalp in 3D Human MRI Using Mathematical Morphology", Human Brain Mapping, Volume 26, Issue 4, Pages 273 - 285, Dec 2005. pdf

• Belma Dogdas, David W. Shattuck and Richard M. Leahy, "Segmentation of Patient Specific MEG/EEG Skull, Scalp, and Brain Models from MRI", Proceedings of Biomag 2002 Conference, August 2002. pdf

• Belma Dogdas, David W. Shattuck and Richard M. Leahy, "Segmentation of the skull in 3D human MR images using mathematical morphology", Proceedings of SPIE Medical Imaging Conference, vol. 4684, paper 180, pp. 1553-1562, 2002. pdf

Other:

• Belma Dogdas and Orhan Arikan, "A New Approach for Accurate Estimation of Tectonic Velocity Field over the Marmara Region of Turkey", ICASSP 2000, (placed 3rd in Student Poster Presentation)