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Brain Atlases and Neuroanatomic Imaging

  • Allan MacKenzie-Graham
  • Jyl Boline
  • Arthur W. Toga
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 401)

Summary

Quantifying the effect of a genetic manipulation or disease is a complicated process in a population of animals. Probabilistic brain atlases can capture population variability and be used to quantify those variations in anatomy as measured by structural imaging. Minimum deformation atlases (MDAs), a subclass of probabilistic atlases, are intensity-based averages of a collection of scans in a common space unbiased by selection of a single target image. Here, we describe a method for generating an MDA from a set of magnetic resonance microscopy images. First, the images are segmented to remove any non-brain tissue and bias field corrected to remove field inhomogeneities. The corrected images are then linearly aligned to a representative scan, the geometric mean of all the transformations is calculated, and a minimum deformation target (MDT) is produced by averaging the volumes in this new space. The brains are then non-linearly aligned to the MDT to produce the MDA. Finally, the images are linearly aligned to the MDA using a full-affine transformation to spatially and intensity normalize them, removing global differences in size, shape, and position but retaining anatomically significant differences.

Key Words

Mouse MRI probabilistic variability spatial normalization. 

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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Allan MacKenzie-Graham
    • 1
  • Jyl Boline
    • 1
  • Arthur W. Toga
    • 1
  1. 1.Laboratory of Neuro Imaging, Department of NeurologyUniversity of CaliforniaLos Angeles

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