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A simple rapid process for semi-automated brain extraction from magnetic resonance images of the whole mouse head

Delora, Adam and Gonzales, Aaron and Medina, Christopher S. and Mitchell, Adam and Mohed, Abdul Faheem and Jacobs, Russell E. and Bearer, Elaine L. (2016) A simple rapid process for semi-automated brain extraction from magnetic resonance images of the whole mouse head. Journal of Neuroscience Methods, 257 . pp. 185-193. ISSN 0165-0270. PMCID PMC4910826.

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Background: Magnetic resonance imaging (MRI) is a well-developed technique in neuroscience. Limitations in applying MRI to rodent models of neuropsychiatric disorders include the large number of animals required to achieve statistical significance, and the paucity of automation tools for the critical early step in processing, brain extraction, which prepares brain images for alignment and voxel-wise statistics. New Method: This novel timesaving automation of template-based brain extraction (“skull-stripping”) is capable of quickly and reliably extracting the brain from large numbers of whole head images in a single step. The method is simple to install and requires minimal user interaction. Results: This method is equally applicable to different types of MR images. Results were evaluated with Dice and Jacquard similarity indices and compared in 3D surface projections with other stripping approaches. Statistical comparisons demonstrate that individual variation of brain volumes are preserved. Comparison with Existing Methods: A downloadable software package not otherwise available for extraction of brains from whole head images is included here. This software tool increases speed, can be used with an atlas or a template from within the dataset, and produces masks that need little further refinement. Conclusions: Our new automation can be applied to any MR dataset, since the starting point is a template mask generated specifically for that dataset. The method reliably and rapidly extracts brain images from whole head images, rendering them useable for subsequent analytical processing. This software tool will accelerate the exploitation of mouse models for the investigation of human brain disorders by MRI.

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URLURL TypeDescription CentralArticle
Jacobs, Russell E.0000-0002-1382-8486
Additional Information:© 2015 Elsevier B.V. Received date: 10-8-2015; Revised date: 28-9-2015; Accepted date: 30-9-2015. The authors gratefully acknowledge Vince Calhoun for review of this work, Art Toga for inspiring us to pursue creation of this new processing tool, and technical assistance from Xiaowei Zhang, Sharon Lin, Kevin P. Reagan, Kathleen Kilpatrick, Amber Zimmerman and Frances Chaves. This work is supported by The Harvey Family Endowment (ELB), and the NIH: R01MH087660 and P5OGM08273 (ELB).
Funding AgencyGrant Number
Harvey Family EndowmentUNSPECIFIED
Subject Keywords:Mouse brain extraction; Automated skull stripping; Magnetic resonance imaging; Freeware; Software tools
PubMed Central ID:PMC4910826
Record Number:CaltechAUTHORS:20151019-154045270
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Official Citation:Adam Delora, Aaron Gonzales, Christopher S. Medina, Adam Mitchell, Abdul Faheem Mohed, Russell E. Jacobs, Elaine L. Bearer, A simple rapid process for semi-automated brain extraction from magnetic resonance images of the whole mouse head, Journal of Neuroscience Methods, Available online 9 October 2015, ISSN 0165-0270, (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:61291
Deposited By: Tony Diaz
Deposited On:19 Oct 2015 22:53
Last Modified:03 Oct 2019 09:06

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