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Uberti MG, Boska MD, Liu Y. A semi-automatic image segmentation method for extraction of brain volume from in vivo mouse head magnetic resonance imaging using Constraint Level Sets. J Neurosci Methods. May 2009;179(2):338-344.

Full Text – Open Access

Publication Date
May 2009

How Analyze was Used
“The SBRG algorithm in Analyze® (AnalyzeDirect, Lenexa, KS) was used for brain extraction on the optimized T2-wt RARE MRI. A seed was located on the brain tissue of a middle coronal slice. Lower and upper thresholding limits were adjusted to exclude as much non-brain tissue as possible while preserving all of the brain tissue.

“Manual segmentation was performed on the optimized T2-wt RARE MRI in a slice by slice fashion, by three experienced investigators using the ROI function in Analyze® software. Brain contours were manually traced on coronal slices using freehand ROI. To be in accordance with the constraints used in the level sets, paraflocculi and olfactory tubercle were also excluded during manual segmentation.”

Keywords
Algorithms
Animals
Brain/anatomy & histology/physiology
Brain Mapping/methods
Diffusion Magnetic Resonance Imaging
Disease Models, Animal
Image Processing, Computer-Assisted/methods
Magnetic Resonance Imaging (MRI)/methods
Male
Mice
Mice, SCID
Nerve Fibers, Myelinated/physiology/ultrastructure
Organ Size/physiology
Pattern Recognition, Automated/methods
Software
Species Specificity

Author Affiliation(s)
Center for Neurovirology and Neurodegenerative Disorders, University of Nebraska Medical Center, Omaha, NE 68198-5880, US. (MGU, MDB, YL)

Department of Radiology, University of Nebraska Medical Center, Omaha, NE 68198-1045, US. (MGU, MDB, YL)

ID# 1375

Tags: Algorithms, Animal Disease Models, Animals, Automated Pattern Recognition/methods, Brain Mapping/methods, Brain/anatomy & histology/physiology, Computer-Assisted Image Processing/methods, Diffusion Magnetic Resonance Imaging, Magnetic Resonance Imaging (MRI)/methods, Male, Mice, Myelinated Nerve Fibers/physiology/ultrastructure, Organ Size/physiology SCID Mice, Software, Species Specificity