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Proceedings Article

Automatic skull-stripping of rat MRI/DTI scans and atlas building

[+] Author Affiliations
Ipek Oguz, Francois Budin, Ashley Rumple, Matthew McMurray, Josephine Johns, Martin Styner

Univ. of North Carolina at Chapel Hill (USA)

Joohwi Lee, Fulton Crews

Univ. of North Carolina (USA)

Cindy Ehlers

The Scripps Research Institute (USA)

Proc. SPIE 7962, Medical Imaging 2011: Image Processing, 796225 (March 11, 2011); doi:10.1117/12.878405
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From Conference Volume 7962

  • Medical Imaging 2011: Image Processing
  • Benoit M. Dawant; David R. Haynor
  • Lake Buena Vista, Florida | February 12, 2011


3D Magnetic Resonance (MR) and Diffusion Tensor Imaging (DTI) have become important noninvasive tools for the study of animal models of brain development and neuropathologies. Fully automated analysis methods adapted to rodent scale for these images will allow highthroughput studies. A fundamental first step for most quantitative analysis algorithms is skullstripping, which refers to the segmentation of the image into two tissue categories, brain and non-brain. In this manuscript, we present a fully automatic skull-stripping algorithm in an atlasbased manner. We also demonstrate how to either modify an external atlas or to build an atlas from the population itself to present a self-contained approach. We applied our method to three datasets of rat brain scans, at different ages (PND5, PND14 and adult), different study groups (control, ethanol exposed, intrauterine cocaine exposed), as well as different image acquisition parameters. We validated our method by comparing the automated skull-strip results to manual delineations performed by our expert, which showed a discrepancy of less than a single voxel on average. We thus demonstrate that our algorithm can robustly and accurately perform the skull-stripping within one voxel of the manual delineation, and in a fraction of the time it takes a human expert.

© (2011) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

Ipek Oguz ; Joohwi Lee ; Francois Budin ; Ashley Rumple ; Matthew McMurray, et al.
"Automatic skull-stripping of rat MRI/DTI scans and atlas building", Proc. SPIE 7962, Medical Imaging 2011: Image Processing, 796225 (March 11, 2011); doi:10.1117/12.878405; http://dx.doi.org/10.1117/12.878405

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