title: A simple rapid process for semi-automated brain extraction from magnetic resonance images of the whole mouse head.
abstract: 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.
  
  
  METHODS
  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.
  
  
  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.
authors.affiliation: Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, United States.
authors.forename: Adam
authors.initials: A
authors.lastname: Delora
authors.affiliation: Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, United States.
authors.forename: Aaron
authors.initials: A
authors.lastname: Gonzales
authors.affiliation: Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, United States.
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Medina
authors.affiliation: Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, United States.
authors.forename: Adam
authors.initials: A
authors.lastname: Mitchell
authors.affiliation: Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, United States.
authors.forename: Abdul Faheem
authors.initials: AF
authors.lastname: Mohed
authors.affiliation: Beckman Institute, California Institute of Technology, Pasadena, CA 91125, United States.
authors.forename: Russell E
authors.initials: RE
authors.lastname: Jacobs
authors.affiliation: Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, United States; Division of Biology, California Institute of Technology, Pasadena, CA 91125, United States. Electronic address: ebearer@salud.unm.edu.
authors.forename: Elaine L
authors.initials: EL
authors.lastname: Bearer
mesh_terms: D022126:Access to Information; D000818:Animals; D001921:Brain / Q000033:anatomy & histology*; D066264:Datasets as Topic; D006257:Head / Q000033:anatomy & histology*; D020407:Internet; D008279:Magnetic Resonance Imaging / Q000379:methods*; D051379:Mice / Q000033:anatomy & histology*; D009929:Organ Size; D010363:Pattern Recognition, Automated / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D013995:Time
keywords: Automated skull stripping; Freeware; Magnetic resonance imaging; Mouse brain extraction; Software tools