A multi-atlas based method for automated anatomical rat brain MRI segmentation and extraction of PET activity

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Lancelot, Sophie ^a,b   Roche, Roxane ^c   Slimen, Afifa ^c   Bouillot, Caroline ^c   Levigoureux, Elise ^a,b   Langlois, Jean Baptiste ^c   Zimmer, Luc ^a,b,c   Costes, Nicolas ^c  

^a UNIVERSITÉ LYON 1   (France)

^b HOSPICES CIVILS DE LYON   (France)

^c CERMEP IMAGERIE DU VIVANT   (France)

Author keywords

[No Author keywords available]

Indexed keywords

FLUORODEOXYGLUCOSE F 18;

AMYGDALOID NUCLEUS; ARTICLE; AUTOMATION; BRAIN FOURTH VENTRICLE; BRAIN REGION; BRAIN SIZE; BRAIN STEM; BRAIN THIRD VENTRICLE; CAUDATE NUCLEUS; CEREBELLUM; CINGULATE GYRUS; CONTROLLED STUDY; FRONTAL CORTEX; HIPPOCAMPUS; HYPOTHALAMUS; IMAGE ANALYSIS; LATERAL BRAIN VENTRICLE; LEFT HEMISPHERE; MORPHOMETRICS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE IMAGING; OCCIPITAL CORTEX; PARIETAL CORTEX; POSITRON EMISSION TOMOGRAPHY; PUTAMEN; RAT; RIGHT HEMISPHERE; SPRAGUE DAWLEY RAT; TEMPORAL CORTEX; THALAMUS; VOLUMETRY; WHITE MATTER; ANATOMY AND HISTOLOGY; ANIMAL; BOOK; BRAIN; BRAIN MAPPING; COMPARATIVE STUDY; COMPUTER ASSISTED DIAGNOSIS; EVALUATION STUDY; IMAGE PROCESSING; PHYSIOLOGY; PROCEDURES; SCINTISCANNING; SENSITIVITY AND SPECIFICITY;

RATTUS;

ANIMALS; ATLASES AS TOPIC; BRAIN; BRAIN MAPPING; IMAGE INTERPRETATION, COMPUTER-ASSISTED; IMAGE PROCESSING, COMPUTER-ASSISTED; MAGNETIC RESONANCE IMAGING; POSITRON-EMISSION TOMOGRAPHY; RATS; RATS, SPRAGUE-DAWLEY; SENSITIVITY AND SPECIFICITY;

EID: 84908133397     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0109113     Document Type: Article

References (29)

1. Lancelot S, Zimmer L (2010) Small-animal positron emission tomography as a tool for neuropharmacology. Trends Pharmacol Sci 31: 411-417. Review.
2. Paxinos G, Watson C (1998) The rat brain in stereotaxic coordinates, compact 4th ed. CD-Rom. Academic Press, San Diego.
3. 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.
4. Schwarz AJ, Danckaert A, Reese T, Gozzi A, Paxinos G, et al. (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.
5. Valdés-Hernández PA, Sumiyoshi A, Nonaka H, Haga R, Aubert-Vásquez E, et al. (2011) An in vivo MRI Template Set for Morphometry, Tissue Segmentation, and fMRI Localization in Rats. Front Neuroinform 5: 1-19.
6. Casteels C, Vermaelen P, Nuyts J, Van Der Linden A, Baekelandt V, et al. (2006) Construction and evaluation of multitracer small-animal PET probabilistic atlases for voxel-based functional mapping of the rat brain. J Nucl Med 47: 1858-1866.
7. Nie B, Chen K, Zhao S, Liu J, Gu X, et al. (2013) A rat brain MRI template with digital stereotaxic atlas of fine anatomical delineations in Paxinos space and its automated application in voxel-wise analysis. Hum Brain Mapp 34: 1306-1318.
8. Toga AW, Santori EM, Hazani R, Ambach K (1995) A 3D digital map of rat brain. Brain Res Bull 38: 77-85.
9. Rubins DJ, Melega WP, Lacan G, Way B, Plenevaux A, et al. (2003) Development and evaluation of an automated atlas-based image analysis method for microPET studies of the rat brain. NeuroImage 20: 2100-2118.
10. Johnson GA, Calabrese E, Badea A, Paxinos G, Watson C (2012) A multidimensional magnetic resonance histology atlas of the Wistar rat brain. NeuroImage 62: 1848-1856.
11. Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage. doi:10.1016/j.neuroimage.2014.04.001.
12. Dorr AE, Lerch JP, Spring S, Kabani N, Henkelman RM (2008) High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice. NeuroImage 42: 60-69.
13. Nie B, Hui J, Wang L, Chai P, Gao J, et al. (2010) Automatic method for tracing regions of interest in rat brain magnetic resonance imaging studies. J Magn Reson Imaging 32: 830-835.
14. Swanson LW (2004) Brain Maps: Structure of the Rat Brain. Third edition. Amsterdam, Elsevier. 215 p.
15. Hammers A, Allom R, Koepp MJ, Free SL, Myers R, et al. (2003) Three-dimensional maximum probability atlas of the human brain, with particular reference to the temporal lobe. Hum Brain Mapp 19: 224-247.
16. Hammers A, Koepp MJ, Free SL, Brett M, Richardson MP, et al. (2002) Implementation and application of a brain template for multiple volumes of interest. Hum Brain Mapp 15: 165-174.
17. Ballanger B, Tremblay L, Sgambato-Faure V, Beaudoin-Gobert M, Lavenne F, et al. (2013) A multi-atlas based method for automated anatomical Macaca fascicularis brain MRI segmentation and PET kinetic extraction. NeuroImage 77: 26-43.
18. Constantinescu CC, Mukherjee J (2009) Performance evaluation of an Inveon PET preclinical scanner. Phys Med Biol 54: 2885-2899.
19. Collins DL, Neelin P, Peters TM, Evans AC (1994) Automatic 3D intersubject registration of MR volumetric data in standardized Talairach space. J Comput Assist Tomogr 18: 192-205.
20. Heckemann RA, Hajnal JV, Aljabar P, Rueckert D, Hammers A (2006) Automatic anatomical brain MRI segmentation combining label propagation and decision fusion. NeuroImage 33: 115-126.
21. Dice LR. (1945) Measures of the Amount of Ecologic Association Between Species. Ecology 26: 297-302.
22. Heckemann RA, Keihaninejad S, Aljabar P, Rueckert D, Hajnal JV, et al. (2010) Improving intersubject image registration using tissue-class information benefits robustness and accuracy of multi-atlas based anatomical segmentation. NeuroImage 51: 221-227.
23. Gaser C, Schmidt S, Metzler M, Herrmann KH, Krumbein I, et al. (2012) Deformation-based brain morphometry in rats. NeuroImage 63: 47-53.
24. Ashburner J (2007) A fast diffeomorphic image registration algorithm. NeuroImage 38: 95-113.
25. Kochunov P, Lancaster JL, Thompson P, Woods R, Mazziotta J, et al. (2001) Regional spatial normalization: toward an optimal target. J Comput Assist Tomogr 25: 805-816.
26. Rohlfing T, Brandt R, Menzel R, Maurer CR Jr (2004) Evaluation of atlas selection strategies for atlas-based image segmentation with application to confocal microscopy images of bee brains. NeuroImage 21: 1428-1442.
27. Jia H, Yap PT, Shen D (2012) Iterative multi-atlas-based multi-image segmentation with tree-based registration. NeuroImage 59: 422-430.
28. Chakravarty MM, Steadman P, van Eede MC, Calcott RD, Gu V, et al. (2012) Performing label-fusion-based segmentation using multiple automatically generated templates. Hum Brain Mapp 34: 2635-2654.
29. Aljabar P, Heckemann RA, Hammers A, Hajnal JV, Rueckert D (2009) Multi-atlas based segmentation of brain images: atlas selection and its effect on accuracy. NeuroImage 46: 726-738.