Automatic structural parcellation of mouse brain MRI using multi-atlas label fusion

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Ma, Da ^a   Cardoso, Manuel J ^a   Modat, Marc ^a   Powell, Nick ^a   Wells, Jack ^a   Holmes, Holly ^a   Wiseman, Frances ^b   Tybulewicz, Victor ^c   Fisher, Elizabeth ^b   Lythgoe, Mark F ^a   Ourselin, Sébastien ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL TISSUE; ARTICLE; BRAIN; CONTROLLED STUDY; FACTUAL DATABASE; GOLD STANDARD; IMAGE ANALYSIS; IMAGE PROCESSING; INTERMETHOD COMPARISON; MOUSE; MULTI ATLAS SEGMENTATION PROPAGATION; NEUROANATOMY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE IMAGING; PROCESS OPTIMIZATION;

ANIMALS; ATLASES AS TOPIC; BRAIN; IMAGE PROCESSING, COMPUTER-ASSISTED; MAGNETIC RESONANCE IMAGING; MICE; MICE, TRANSGENIC;

EID: 84900340760     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0086576     Document Type: Article

References (59)

1. Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES (2000) Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction. Genome Res 10: 950-958. (Pubitemid 30609361)
2. Austin CP, Battey JF, Bradley A, Bucan M, Capecchi M, et al. (2004) The Knockout Mouse Project. Nat Genet 36: 921-924. (Pubitemid 351319639)
3. Ma Y, Smith D, Hof PR, Foerster B, Hamilton S, et al. (2008) In Vivo 3D Digital Atlas Database of the Adult C57BL/6J Mouse Brain by Magnetic Resonance Microscopy. Front Neuroanat 2: 1.
4. Richards K, Watson C, Buckley RF, Kurniawan ND, Yang Z, et al. (2011) Segmentation of the mouse hippocampal formation in magnetic resonance images. Neuroimage 58: 732-740.
5. Bai J, Trinh TLH, Chuang K-H, Qiu A (2012) Atlas-based automatic mouse brain image segmentation revisited: model complexity vs. image registration. Magn Reson Imaging 30: 789-798.
6. Lee J, Jomier J, Aylward S, Tyszka M, Moy S, et al. (2009) Evaluation of atlas based mouse brain segmentation. Proc SPIE Int Soc Opt Photonics 7259: 725943.
7. Cleary JO, Modat M, Norris FC, Price AN, Jayakody SA, et al. (2011) Magnetic resonance virtual histology for embryos: 3D atlases for automated high-throughput phenotyping. Neuroimage 54: 769-778.
8. 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. (Pubitemid 44404167)
9. Calmon G, Roberts N (2000) Automatic measurement of changes in brain volume on consecutive 3D MR images by segmentation propagation. Magn Reson Imaging 18: 439-453. (Pubitemid 30228579)
10. Zhuang X, Rhode KS, Razavi RS, Hawkes DJ, Ourselin S (2010) A registration-based propagation framework for automatic whole heart segmentation of cardiac MRI. IEEE Trans Med Imaging 29: 1612-1625.
11. Klein A, Andersson J, Ardekani BA, Ashburner J, Avants B, et al. (2009) Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration. Neuroimage 46: 786-802.
12. Warfield SK, Zou KH, Wells WM (2004) Simultaneous truth and performance level estimation (STAPLE): an algorithm for the validation of image segmentation. IEEE Trans Med Imaging 23: 903-921.
13. Rohlfing T, Russakoff DB, Maurer CR (2004) Performance-based classifier combination in atlas-based image segmentation using expectation-maximization parameter estimation. IEEE Trans Med Imaging 23: 983-994.
14. Aljabar P, Heckemann RA, Hammers A, Hajnal JV, Rueckert D (2007) Classifier selection strategies for label fusion using large atlas databases. Proc MICCAI Int Conf Med Image Comput Comput Assist Interv 4791: 523-531.
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. (Pubitemid 36959351)
16. Fischl B, Salat DH, Busa E, Albert M, Dieterich M, et al. (2002) Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. Neuron 33: 341-355. (Pubitemid 34162530)
17. 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.
18. Rohlfing T, Maurer CR (2007) Shape-based averaging. IEEE Trans Image Process 16: 153-161. (Pubitemid 46437478)
19. Artaechevarria X, Munoz-Barrutia A, Ortiz-de-Solorzano C (2009) Combination strategies in multi-atlas image segmentation: application to brain MR data. IEEE Trans Med Imaging 28: 1266-1277.
20. Leung KK, Barnes J, Ridgway GR, Bartlett JW, Clarkson MJ, et al. (2010) Automated cross-sectional and longitudinal hippocampal volume measurement in mild cognitive impairment and Alzheimer's disease. Neuroimage 51: 1345-1359.
21. Cardoso M, Leung K, Modat M, Keihaninejad S, Cash D, et al. (2013) STEPS: Similarity and Truth Estimation for Propagated Segmentations and its application to hippocampal segmentation and brain parcelation. Med Image Anal 17: 671-684.
22. Agarwal M, Hendriks EA, Stoel BC, Bakker ME, Reiber JHC, et al. (2012) Local SIMPLE multi atlas-based segmentation applied to lung lobe detection on chest CT. Proc SPIE Int Soc Opt Photonics: 831410.
23. Wolz R, Aljabar P, Hajnal JV, Hammers A, Rueckert D (2010) LEAP: learning embeddings for atlas propagation. Neuroimage 49: 1316-1325.
24. Langerak TR, van der Heide UA, Kotte ANTJ, Viergever MA, van Vulpen M, et al. (2010) Label fusion in atlas-based segmentation using a selective and iterative method for performance level estimation (SIMPLE). IEEE Trans Med Imaging 29: 2000-2008.
25. Artaechevarria X, Muñoz-Barrutia A, Ortiz-de-Solórzano C (2008) Efficient classifier generation and weighted voting for atlas-based segmentation: Two small steps faster and closer to the Combination Oracle. Proc SPIE Int Soc Opt Photonics: 69141W-69141W-9.
26. Ma Y, Hof PR, Grant SC, Blackband SJ, Bennett R, et al. (2005) A three-dimensional digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy. Neuroscience 135: 1203-1215. (Pubitemid 41416682)
27. Chakravarty MM, van Eede MC, Lerch JP (2011) Improved segmentation of mouse MRI data using multiple automatically generated templates. Int Soc Magn Reson Med 15: 2011.
28. Bock NA, Nieman BJ, Bishop JB, Mark Henkelman R (2005) In vivo multiple-mouse MRI at 7 Tesla. Magn Reson Med 54: 1311-1316. (Pubitemid 41567215)
29. Natt O, Watanabe T, Boretius S, Radulovic J, Frahm J, et al. (2002) High-resolution 3D MRI of mouse brain reveals small cerebral structures in vivo. J Neurosci Methods 120: 203-209. (Pubitemid 35248169)
30. Scheenstra AEH, Van De Ven RCG, van der Weerd L, van den Maagdenberg AMJM, Dijkstra J, et al. (2009) Automated Segmentation of In Vivo and Ex Vivo Mouse Brain Magnetic Resonance Images. Mol Imaging 8: 35-44.
31. Modat M, Ridgway GR, Taylor ZA, Lehmann M, Barnes J, et al. (2010) Fast free-form deformation using graphics processing units. Comput Methods Programs Biomed 98: 278-284.
32. Ourselin S, Roche A, Prima S, Ayache N (2000) Block matching: A general framework to improve robustness of rigid registration of medical images. Proc MICCAI Int Conf Med Image Comput Comput Assist Interv 1935: 557-566.
33. Sled JG, Zijdenbos AP, Evans AC (1998) A nonparametric method for automatic correction of intensity nonuniformity in MRI data. IEEE Trans Med Imaging 17: 87-97. (Pubitemid 128742012)
34. Kovacević N, Henderson JT, Chan E, Lifshitz N, Bishop J, et al. (2005) A three-dimensional MRI atlas of the mouse brain with estimates of the average and variability. Cereb Cortex 15: 639-645. (Pubitemid 40577479)
35. 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.
36. Chuang N, Mori S, Yamamoto A, Jiang H, Ye X, et al. (2011) An MRI-based atlas and database of the developing mouse brain. Neuroimage 54: 80-89.
37. Badea A, Ali-Sharief AA, Johnson GA (2007) Morphometric analysis of the C57BL/6J mouse brain. Neuroimage 37: 683-693. (Pubitemid 47248321)
38. Jiang Y, Johnson GA (2011) Microscopic diffusion tensor atlas of the mouse brain. Neuroimage 56: 1235-1243.
39. Ullmann JFP, Watson C, Janke AL, Kurniawan ND, Reutens DC (2013) A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex. Neuroimage 78: 196-203.
40. Ullmann JP, Watson C, Janke A, Kurniawan N, Paxinos G, et al. (2013) An MRI atlas of the mouse basal ganglia. Brain Struct Funct: 1-11.
41. Paxinos G, Franklin KBJ (2004) The mouse brain in stereotaxic coordinates.
42. Jones SE, Buchbinder BR, Aharon I (2000) Three-dimensional mapping of cortical thickness using Laplace's Equation. Hum Brain Mapp 11: 12-32.
43. Lerch JP, Carroll JB, Dorr A, Spring S, Evans AC, et al. (2008) Cortical thickness measured from MRI in the YAC128 mouse model of Huntington's disease. Neuroimage 41: 243-251.
44. Maes F, Van Leemput K, DeLisi L, Vandermeulen D, Suetens P (1999) Quantification of Cerebral Grey and White Matter Asymmetry from MRI. Proc MICCAI Int Conf Med Image Comput Comput Assist Interv 1679: 348-357.
45. Liu Y, Collins RT, Rothfus William E (1998) Automatic bilateral symmetry (midsagittal) plane extraction from pathological 3D neuroradiological images. Proc SPIE Int Soc Opt Photonics: 1528-1539.
46. Prima S, Thirion JP, Subsol G, Roberts N (1998) Automatic analysis of normal brain dissymmetry of males and females in MR images. Proc MICCAI Int Conf Med Image Comput Comput Assist Interv 1496: 770-779.
47. Bowden DM, Johnson GA, Zaborsky L, Green WDK, Moore E, et al. (2011) A symmetrical Waxholm canonical mouse brain for NeuroMaps. J Neurosci Methods 195: 170-175.
48. John JP, Wang L, Moffitt AJ, Singh HK, Gado MH, et al. (2006) Inter-rater reliability of manual segmentation of the superior, inferior and middle frontal gyri. Psychiatry Res Neuroimaging 148: 151-163. (Pubitemid 44750586)
49. Sinclair B, Cleary JO, Modat M, Norris VC, Wiseman F, et al. (2011) Tensor-based morphometry on the Tc1 mouse model of Down syndrome highlights previously undetected phenotypes. Proc Intl Soc Mag Reson Med 19: 702.
50. Van Eede MC, Scholz J, Chakravarty MM, Henkelman RM, Lerch JP (2013) Mapping registration sensitivity in MR mouse brain images. Neuroimage 82: 226-236.
51. Rueckert D, Sonoda LI, Hayes C, Hill DL, Leach MO, et al. (1999) Nonrigid registration using free-form deformations: application to breast MR images. IEEE Trans Med Imaging 18: 712-721. (Pubitemid 32262025)
52. Rueckert D, Hayes C, Studholme C, Summers P, Leach MO, et al. (1998) Non-rigid registration of breast MR images using mutual information. Med Image Comput Comput Interv 1496: 1144-1152. (Pubitemid 128152765)
53. Spring S, Lerch JP, Wetzel MK, Evans AC, Henkelman RM (2010) Cerebral asymmetries in 12-week-old C57Bl/6J mice measured by magnetic resonance imaging. Neuroimage 50: 409-415.
54. Kohl MM, Shipton OA, Deacon RM, Rawlins JNP, Deisseroth K, et al. (2011) Hemisphere-specific optogenetic stimulation reveals left-right asymmetry of hippocampal plasticity. Nat Neurosci 14: 1413-1415.
55. Kempton MJ, Underwood TSA, Brunton S, Stylios F, Schmechtig A, et al. (2011) A comprehensive testing protocol for MRI neuroanatomical segmentation techniques: Evaluation of a novel lateral ventricle segmentation method. Neuroimage 58: 1051-1059.
56. Boccardi M, Bocchetta M, Ganzola R, Robitaille N, Redolfi A, et al. (2013) Operationalizing protocol differences for EADC-ADNI manual hippocampal segmentation. Alzheimers Dement J Alzheimers Assoc: 1-11.
57. Nestor SM, Gibson E, Gao F-Q, Kiss A, Black SE (2012) A direct morphometric comparison of five labeling protocols for multi-atlas driven automatic segmentation of the hippocampus in Alzheimer's disease. Neuroimage 66C: 50-70.
58. Sharief AA, Badea A, Dale AMA, Johnson GA (2008) Automated segmentation of the actively stained mouse brain using multi-spectral MR microscopy. Neuroimage 39: 136-145. (Pubitemid 350102215)
59. Ullmann JFP, Keller MD, Watson C, Janke AL, Kurniawan ND, et al. (2012) Segmentation of the C57BL/6J mouse cerebellum in magnetic resonance images. Neuroimage 62: 1408-1414.