A multidimensional magnetic resonance histology atlas of the Wistar rat brain

NeuroImage

Volumn 62, Issue 3, 2012, Pages 1848-1856

  Johnson, G Allan ^a,b   Calabrese, Evan ^a,b   Badea, Alexandra ^a   Paxinos, George ^d,e   Watson, Charles ^c,d,e  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b Duke University   (United States)

^c CURTIN UNIVERSITY   (Australia)

^d NEUROSCIENCE RESEARCH AUSTRALIA   (Australia)

^e UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

Atlas; Diffusion tensor imaging; MRI; Rat brain

Indexed keywords

ADULT ANIMAL; ANIMAL TISSUE; ARTICLE; BRAIN; DIFFUSION TENSOR IMAGING; HISTOCHEMISTRY; HISTOLOGY; IMAGE ANALYSIS; IMAGE PROCESSING; IMAGE QUALITY; MALE; MULTIDIMENSIONAL MAGNETIC RESONANCE HISTOLOGY; NEUROANATOMY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE IMAGING; NUCLEAR MAGNETIC RESONANCE SCANNER; PRIORITY JOURNAL; RAT; SKULL; THREE DIMENSIONAL IMAGING; WHITE MATTER;

ANATOMY, ARTISTIC; ANIMALS; ATLASES AS TOPIC; BRAIN; DIFFUSION MAGNETIC RESONANCE IMAGING; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MALE; RATS; RATS, WISTAR;

EID: 84863511173     PISSN: 10538119     EISSN: 10959572     Source Type: Journal    
DOI: 10.1016/j.neuroimage.2012.05.041     Document Type: Article

References (51)

1. Aggarwal M., Zhang J., Mori S. Magnetic resonance imaging-based mouse brain atlas and its applications. Methods Mol. Biol. 2011, 711:251-270.
2. Arsigny V., Fillard P., Pennec X., Ayache N. Log-Euclidean metrics for fast and simple calculus on diffusion tensors. Magn. Reson. Med. 2006, 56:411-421.
3. Ashwell K.W.S., Paxinos G. Atlas of the Developing Rat Nervous System 2008, Elsevier Academic Press, San Diego. 3rd edition.
4. Avants B.B., Epstein C.L., Grossman M., Gee J.C. Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. Med. Image Anal. 2008, 12:26-41.
5. Badea A., Ali-Sharief A.A., Johnson G.A. Morphometric analysis of the C57BL/6J mouse brain. NeuroImage 2007, 37:683-693.
6. Bai J., Trinh T.L., Chuang K.H., Qiu A. Atlas-based automatic mouse brain image segmentation revisited: model complexity vs. image registration. Magn. Reson. Imaging 2012, 30:789-798.
7. Basser P.J. Inferring microstructural features and the physiological state of tissues from diffusion-weighted images. NMR Biomed. 1995, 8:333-344.
8. Basser P.J., Jones D.K. Diffusion-tensor MRI: theory, experimental design and data analysis - a technical review. NMR Biomed. 2002, 15:456-467.
9. Basser P.J., Mattiello J., LeBihan D. MR diffusion tensor spectroscopy and imaging. Biophys. J. 1994, 66:259-267.
10. Benveniste H., Kim K., Zhang L., Johnson G.A. Magnetic resonance microscopy of the C57BL mouse brain. NeuroImage 2000, 11:601-611.
11. Chen X.J., Kovacevic N., Lobaugh N.J., Sled J.G., Henkelman R.M., Henderson J.T. Neuroanatomical differences between mouse strains as shown by high-resolution 3D MRI. NeuroImage 2006, 29:99-105.
12. Chuang N., Mori S., Yamamoto A., Jiang H., Ye X., Xu X., Richards L.J., Nathans J., Miller M.I., Toga A.W., Sidman R.L., Zhang J. An MRI-based atlas and database of the developing mouse brain. NeuroImage 2011, 54:80-89.
13. Cross D.J., Minoshima S., Anzai Y., Flexman J.A., Keogh B.P., Kim Y., Maravilla K.R. Statistical mapping of functional olfactory connections of the rat brain in vivo. NeuroImage 2004, 23:1326-1335.
14. Franklin K.B.J., Paxinos G. The Mouse Brain in Stereotaxic Coordinates 2007, Elsevier Academic Press, San Diego. 3rd edition.
15. Hjornevik T., Leergaard T.B., Darine D., Moldestad O., Dale A.M., Willoch F., Bjaalie J.G. Three-dimensional atlas system for mouse and rat brain imaging data. Front. Neuroinform. 2007, 1:4.
16. Jiang Y., Johnson G.A. Microscopic diffusion tensor atlas of the mouse brain. NeuroImage 2011, 56:1235-1243.
17. Johnson G.A., Thompson M.B., Drayer B.P. Three dimensional MR microscopy of the normal rat brain. Magn. Reson. Med. 1987, 4:351-365.
18. Johnson G.A., Benveniste H., Black R.D., Hedlund L.W., Maronpot R.R., Smith B.R. Histology by magnetic resonance microscopy. Magn. Reson. Q. 1993, 9:1-30.
19. Johnson G.A., Cofer G.P., Gewalt S.L., Hedlund L.W. Morphologic phenotyping with MR microscopy: the visible mouse. Radiology 2002, 222:789-793.
20. Johnson G.A., Ali-Sharief A., Badea A., Brandenburg J., Cofer G., Fubara B., Gewalt S., Hedlund L., Upchurch L. High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology. NeuroImage 2007, 37:82-89.
21. Johnson G.A., Badea A., Brandenburg J., Cofer G., Fubara B., Liu S., Nissanov J. Waxholm Space: an image-based reference for coordinating mouse brain research. NeuroImage 2010, 53:365-372.
22. Kochunov P., Lancaster J.L., Thompson P., Woods R., Mazziotta J., Hardies J., Fox P. Regional spatial normalization: toward an optimal target. J. Comput. Assist. Tomogr. 2001, 25:805-816.
23. König J.F.R., Klippel R.A. The rat brain. A Stereotaxic Atlas of the Forebrain and Lower Parts of the Brain Stem 1963, The Williams and Wilkins Company, Baltimore, MD.
24. Leergaard T.B., Bjaalie J.G., Devor A., Wald L.L., Dale A.M. In vivo tracing of major rat brain pathways using manganese-enhanced magnetic resonance imaging and three-dimensional digital atlasing. NeuroImage 2003, 3:1591-1600.
25. Lu H., Scholl C.A., Zuo Y., Demny S., Rea W., Stein E.A., Yang Y. Registering and analyzing rat fMRI data in the stereotaxic framework by exploiting intrinsic anatomical features. Magn. Reson. Imaging 2010, 1:146-152.
26. Ma Y., Hof P.R., Grant S.C., Blackband S.J., Bennett R., Slatest L., McGuigan M.D., Benveniste H. A three-dimensional digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy. Neuroscience 2005, 135:1203-1215.
27. Mai J.K., Paxinos G., Voss T. Atlas of the Human Brain 2008, Elsevier Academic Press, San Diego. 3rd edition.
28. Mori S., Crain B.J., Chacko V.P., van Zijl P.C. Three-dimensional tracking of axonal projections in the brain by magnetic resonance imaging. Ann. Neurol. 1999, 45:265-269.
29. Morin L.P., Wood R.I. A Stereotaxic Atlas of the Golden Hamster Brain 2001, Academic Press, San Diego.
30. Mukherjee P., Berman J.I., Chung S.W., Hess C.P., Hnery R.G. Diffusion tensor MR imaging and fiber tractography: theoretic underpinnings. AJNR Am. J. Neuroradiol. 2008, 4:632-641.
31. Nie B., Hui J., Wang L., Chai P., Gao J., Liu S., Zhang Z., Shan B., Zhao S. Automatic method for tracing regions of interest in rat brain magnetic resonance imaging studies. J. Magn. Reson. Imaging 2010, 32:830-835.
32. Paxinos G., Watson C. The Rat Brain in Stereotaxic Coordinates 1982, Academic Press, Sydney, 152 pp.
33. Paxinos G., Watson C. The Rat Brain in Stereotaxic Coordinates 1986, Academic Press, Sydney, 192 pp. 2nd edition.
34. Paxinos G., Watson C. The Rat Brain in Stereotaxic Coordinates 1997, Academic Press, San Diego. 3rd Edition.
35. Paxinos G., Watson C. The Rat Brain in Stereotaxic Coordinates 1998, Academic Press, San Diego, (Special CD edition). Comprehensive 4th edition.
36. Paxinos G., Watson C. The Rat Brain in Stereotaxic Coordinates: The New Coronal Set 2005, Elsevier Academic Press, San Diego, 209 pp. 5th edition.
37. Paxinos G., Watson C. The Rat Brain in Stereotaxic Coordinates 2007, Elsevier Academic Press, San Diego. 6th Edition.
38. Paxinos G., Halliday G., Watson C., Koutcherov Y., Wang H.Q. Atlas of the Developing Mouse Brain at E17.5, P0, and P6 2007, Elsevier Academic Press, San Diego.
39. Paxinos G., Huang X.-F., Petrides M., Toga A.W. The Rhesus Monkey Brain in Stereotaxic Coordinates 2009, Elsevier Academic Press, San Diego. 2nd edition.
40. Paxinos G., Watson C., Carrive P., Kirkcaldie M., Ashwell K. Chemoarchitectonic Atlas of the Rat Brain 2009, Elsevier Academic Press, San Diego. 2nd edition.
41. Paxinos G., Watson C., Petrides M. The Rhesus Monkey Brain in Stereotaxic Coordinates. Brain Navigator website 2010, Elsevier Academic Press, San Diego, (www.brainnav.com). 3rd edition.
42. Pellegrino L.J., Pellegrino A.A., Cushman A.J. Stereotaxic Atlas of the Rat Brain 1979, Plenum Press, New York, 35 pp.
43. Puelles L., Martinez-de-la-Torre M., Paxinos G., Watson C., Martinez S. The chick brain in stereotaxic coordinates. An Atlas Featuring Neuromeres and Mammalian Homologies 2007, Elsevier Academic Press, San Diego.
44. Ramu J., Bockhorst K.H., Mogatadakala K.V., Narayana P.A. Functional magnetic resonance imaging in rodents: methodology and application to spinal cord injury. J. Neurosci. Res. 2006, 84:1235-1244.
45. Schwarz A.J., Danckaert A., Reese T., Gozzi A., Paxinos G., Watson C., Merlo-Pich E.V., Bifone A. A stereotaxic MRI template set for the rat brain with tissue class distribution maps and co-registered anatomical atlas: application to pharmacological MRI. NeuroImage 2006, 32:538-550.
46. Schweinhardt P., Fransson P., Olson L., Spenger C., Andersson J.L. A template for spatial normalisation of MR images of the rat brain. J. Neurosci. Methods 2003, 129:105-113.
47. Suddarth S.A., Johnson G.A. Three-dimensional MR microscopy with large arrays. Magn. Reson. Med. 1991, 18:132-141.
48. Ting Y.L., Bendel P. Thin-section MR imaging of rat brain at 4.7T. J. Magn. Reson. Imaging 1992, 4:393-399.
49. Valdés-Hernández P.A., Sumiyoshi A., Nonaka H., Haga R., Aubert-Vásquez E., Ogawa T., Iturria-Medina Y., Riera J.J., Kawashima R. An in vivo MRI template set for morphometry, tissue segmentation, and fMRI localization in rats. Front. Neuroinform. 2011, 5:26.
50. Veraart J., Leergaard T.B., Antonsen B.T., Van Hecke W., Blockx I., Jeurissen B., Jiang Y., Van der Linden A., Johnson G.A., Verhoye M., Sijbers J. Population-averaged diffusion tensor imaging atlas of the Sprague Dawley rat brain. NeuroImage 2011, 58:975-983.
51. Watson C., Paxinos G. Chemoarchitectonic Atlas of the Mouse Brain 2010, Elsevier Academic Press, San Diego, 350 pp.