A rat brain MRI template with digital stereotaxic atlas of fine anatomical delineations in paxinos space and its automated application in voxel-wise analysis

Human Brain Mapping

Volumn 34, Issue 6, 2013, Pages 1306-1318

  Nie, Binbin ^a   Chen, Kewei ^b,c,d,e   Zhao, Shujun ^f   Liu, Junhua ^g,h   Gu, Xiaochun ^g,h   Yao, Qunli ^g   Hui, Jiaojie ^h   Zhang, Zhijun ^h   Teng, Gaojun ^g   Zhao, Chunjie ^g,h   Shan, Baoci ^a  

^a INSTITUTE OF HIGH ENERGY PHYSICS   (China)

^b BANNER ALZHEIMER S INSTITUTE   (United States)

^c ARIZONA STATE UNIVERSITY   (United States)

^d UNIVERSITY OF ARIZONA   (United States)

^e ARIZONA ALZHEIMER S CONSORTIUM   (United States)

^f ZHENGZHOU UNIVERSITY   (China)

^g MEDICAL SCHOOL OF SOUTHEAST UNIVERSITY   (China)

^h SOUTHEAST UNIVERSITY   (China)

Author keywords

Co registration; Location; MRI imaging analysis; Normalization; SD rat brain; SPM

Indexed keywords

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; ATLAS; BRAIN; CONTROLLED STUDY; IMAGE ANALYSIS; MIDDLE CEREBRAL ARTERY OCCLUSION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE IMAGING; OLFACTORY BULB; PRIORITY JOURNAL; RAT; STEREOTAXIS;

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

EID: 84876417523     PISSN: 10659471     EISSN: 10970193     Source Type: Journal    
DOI: 10.1002/hbm.21511     Document Type: Article

References (33)

1. Alexander GE, Chen K, Aschenbrenner M, Merkley TL, Santerre-Lemmon LE, Shamy JL, Skaggs WE, Buonocore MH, Rapp PR, Barnes CA ( 2008): Age-related regional network of magnetic resonance imaging gray matter in the rhesus macaque. J Neurosci 28: 2710-2718.
2. Ashburner J, Friston KJ ( 1999): Nonlinear spatial normalization using basis functions. Hum Brain Mapp 7: 254-266.
3. Black KJ, Koller JM, Snyder AZ, Perlmutter JS ( 2001a): Template images for nonhuman primate neuroimaging. II. Macaque. NeuroImage 14: 744-748.
4. Black KJ, Snyder AZ, Koller JM, Gado MH, Perlmutter JS ( 2001b): Template images for nonhuman primate neuroimaging. I. Baboon. NeuroImage 14: 736-743.
5. Chupin M, Mukuna-Bantumbakulu AR, Hasboun D, Bardinet E, Baillet S, Kinkingnehun S, Lemieux L, Dubois B, Garnero L ( 2007): Anatomically constrained region deformation for the automated segmentation of the hippocampus and the amygdala: Method and validation on controls and patients with Alzheimer's disease. NeuroImage 34: 996-1019.
6. Devanand DP, Michaels-Marston KS, Liu X, Pelton GH, Padilla M, Marder K, Bell K, Stern Y, Mayeux R ( 2000): Olfactory deficits in patients with mild cognitive impairment predict Alzheimer's disease at follow-up. Am J Psychiatry 157: 1399-1405.
7. Friston KJ, Ashburner J, Frith CD, Pline J-B, Heather JD, Frachowiak RSJ ( 1995a): Spatial registration and normalization of images. Hum Brain Mapp 2: 89-165.
8. Friston KJ, Ashburner JT, Kiebel SJ, Nichols TE, Penny WD ( 2007): Statistical Parametric Mapping: The Analysis of Functional Brain Images. London: Academic Press.
9. Gonzalez RC, Woods RE, Eddins SL ( 2004): Digital Image Processing Using MATLAB. Beijing, China: Publishing house of electronics industry. pp 305-307.
10. Good CD, Johnsrude IS, Ashburner J, Henson RN, Friston KJ, Frackowiak RS ( 2001): A voxel-based morphometric study of ageing in 465 normal adult human brains. NeuroImage 14( 1 Part 1): 21-36.
11. Jaccard P ( 1912): The distribution of the flora in the alpine zone. New Phytol 11: 37-50.
12. Keller SS, Wilke M, Wieshmann UC, Sluming VA, Roberts N ( 2004): Comparison of standard and optimized voxel-based morphometry for analysis of brain changes associated with temporal lobe epilepsy. NeuroImage 23: 860-868.
13. Lancaster JL, Rainey LH, Summerlin JL ( 1997): Automated labeling of the human brain: A preliminary report on the development and evaluation of a forward transform method. Human brain mapping 5: 1-5.
14. Lin L, Chen K, Alexander GE, He J, Valla J, Galons J-P, Hauss-Wegrzyniak B, Reiman EM ( 2003): Construction of mouse brain MRI templates using SPM99. Modeling and control in biomedical systems. pp 113-118.
15. Longa EZ, Weinstein PR, Carlson S, Cummins R ( 1989): Reversible middle cerebral artery occlusion without craniectomy in rats. Stroke 20: 84-91.
16. Murugavel M, Sullivan JMJr ( 2009): Automatic cropping of MRI rat brain volumes using pulse coupled neural networks. NeuroImage 45: 845-854.
17. Nie B, Hui J, Wang L, Chai P, Gao J, Liu S, Zhang Z, Shan B, Zhao S ( 2010): Automatic method for tracing regions of interest in rat brain magnetic resonance imaging studies. J Magn Reson Imaging 32: 830-835.
18. Pawela CP, Hudetz AG, Ward BD, Schulte ML, Li R, Kao DS, Mauck MC, Cho YR, Neitz J, Hyde JS ( 2008): Modeling of region-specific fMRI BOLD neurovascular response functions in rat brain reveals residual differences that correlate with the differences in regional evoked potentials. NeuroImage 41: 525-534.
19. Paxinos G, Watson C ( 1998): The Rat Brain in Stereotaxic Coordinates, 4th ed. San Diego: Academic Press.
20. Paxinos G, Watson C ( 2005): The Rat Brain in Stereotaxic Coordinates, 5th ed. New York: Academic Press.
21. Peters JM, Hummel T, Kratzsch T, Lotsch J, Skarke C, Frolich L ( 2003): Olfactory function in mild cognitive impairment and Alzheimer's disease: An investigation using psychophysical and electrophysiological techniques. Am J Psychiatry 160: 1995-2002.
22. Poirier C, Vellema M, Verhoye M, Van Meir V, Wild JM, Balthazart J, Van Der Linden A ( 2008): A three-dimensional MRI atlas of the zebra finch brain in stereotaxic coordinates. NeuroImage 41: 1-6.
23. Rodionov R, Chupin M, Williams E, Hammers A, Kesavadas C, Lemieux L ( 2009): Evaluation of atlas-based segmentation of hippocampi in healthy humans. Magn Reson Imaging 27: 1104-1109.
24. Rorden C, Brett M ( 2000): Stereotaxic display of brain lesions. Behav Neurol 12: 191-200.
25. Rubins DJ, Melega WP, Lacan G, Way B, Plenevaux A, Luxen A, Cherry SR ( 2003): Development and evaluation of an automated atlas-based image analysis method for microPET studies of the rat brain. NeuroImage 20: 2100-2118.
26. Sawiak SJ, Wood NI, Williams GB, Morton AJ, Carpenter TA ( 2009): Voxel-based morphometry in the R6/2 transgenic mouse reveals differences between genotypes not seen with manual 2D morphometry. Neurobiol Dis 33: 20-27
27. Schubert CR, Carmichael LL, Murphy C, Klein BE, Klein R, Cruickshanks KJ ( 2008): Olfaction and the 5-year incidence of cognitive impairment in an epidemiological study of older adults. J Am Geriatr Soc 56: 1517-1521.
28. Schwarz AJ, Danckaert A, Reese T, Gozzi A, Paxinos G, Watson C, Merlo-Pich EV, Bifone A ( 2006): A stereotaxic MRI template set for the rat brain with tissue class distribution maps and co-registered anatomical atlas: Application to pharmacological MRI. NeuroImage 32: 538-550.
29. Schwarz AJ, Gozzi A, Bifone A ( 2009): Community structure in networks of functional connectivity: Resolving functional organization in the rat brain with pharmacological MRI. NeuroImage 47: 302-311.
30. Schweinhardt P, Fransson P, Olson L, Spenger C, Andersson JL ( 2003): A template for spatial normalisation of MR images of the rat brain. J Neurosci Methods 129: 105-113.
31. Talairach P, Tournoux J ( 1988): A Stereotactic Coplanar Atlas of the Human Brain. Stuttgart: Thieme.
32. Tzourio-Mazoyer N, Landeau B, Papathanassiou D, Crivello F, Etard O, Delcroix N, Mazoyer B, Joliot M ( 2002): Automated anatomical labeling of activations in SPM using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. NeuroImage 15: 273-89.
33. Zhilkin P, Alexander ME ( 2004): Affine registration: A comparison of several programs. Magn Reson Imaging 22: 55-66.