Automated parcellation of the brain surface generated from magnetic resonance images

Frontiers in Neuroinformatics

Volumn 7, Issue OCT, 2013, Pages

  Li, Wen ^a,b   Andreasen, Nancy C ^b   Nopoulos, Peg ^b   Magnotta, Vincent A ^a,b  

^a UNIVERSITY OF IOWA   (United States)

^b UNIVERSITY OF IOWA   (United States)

Author keywords

Cerebral cortex; Cortical parcellation; Cytoarchitecture; Magnetic resonance imaging; Spherical demons; Surface registration

Indexed keywords

ACCURACY; ADOLESCENT; ADULT; ALGORITHM; ARTICLE; AUTOMATION; BRAIN CORTEX; BRAIN RADIOGRAPHY; CHILD; CLINICAL ARTICLE; CONTROLLED STUDY; GRAY MATTER; HUMAN; IMAGE PROCESSING; INTERMETHOD COMPARISON; NUCLEAR MAGNETIC RESONANCE IMAGING; NUCLEAR MAGNETIC RESONANCE SCANNER; PARCELLATION; RELIABILITY; SCHOOL CHILD; WHITE MATTER;

EID: 84887054414     PISSN: 16625196     EISSN: None     Source Type: Journal    
DOI: 10.3389/fninf.2013.00023     Document Type: Article

References (43)

1. Auzias, G., Colliot, O., Glaunès, J. A., Perrot, M., Mangin, J. F., Trouvé, A., and Baillet, S. (2011). Diffeomorphic brain registration under exhaustive sulcal constraints. IEEE Trans. Med. Imaging 30, 1214-1227. doi: 10.1109/TMI.2011.2108665.
2. Bookstein, F. L. (1991). Thin-plate splines and the atlas problem for biomedical images. IPMI LNCS 511, 326-342.
3. Brodmann, K. (2006). Brodmann's: Localisation in the Cerebral Cortex, ed L. J. Garey, New York, NY:Springer.
4. Caviness, V. S., Meyer, J., Makris, N., and Kennedy, D. N. (1996). MRI-based topographic parcellation of the human neocortex: an anatomically specified method with estimate of reliability J. Cogn. Neurosci. 8, 566-588. doi: 10.1162/jocn.1996.8.6.566.
5. Cocosco, C. A., Kollokian, V., Kwan, R. K.-S., and Evans, A. C. (1997). BrainWeb: online interface to a 3D MRI simulated brain database. Neuroimage 5, S425.
6. Collins, D. L., Goualher, G. L., and Evans, A. C. (1998). Non-linear cerebral registration with sulcal constraints. MICCAI'98 LNCS 1496, 974-984.
7. Collins, D. L., Zijdenbos, A. P., Baare, W. F. C., and Evans, A. C. (1999). ANIMAL+INSECT: Improved cortical structure segmentation. IPMI'99, LNCS 1613, 210-223.
8. Crespo-Facorro, B., Kim, J. J., Andreasen, N. C., O'Leary, D. S., Wiser, A. K., Bailey, J. M., et al. (1999). Human frontal cortex: an MRI-based parcellation method. Neuroimage 10, 500-519. doi: 10.1006/nimg.1999.0489.
9. Crespo-Facorro, B., Kim, J. J., Andreasen, N. C., O'Leary, D. S., Bockholt, H. J., and Magnotta, V. (2000a). Insular cortex abnormalities in schizophrenia: a structural magnetic resonance imaging study of first-episode patients. Schizophr Res. 46, 35-43, Erratum to: Schizophr. Res. 51, 183-184. doi: 10.1016/S0920-9964(01)00283-3.
10. Crespo-Facorro, B., Kim, J. J., Andreasen, N. C., Spinks, R., O'Leary, D. S., Bockholt, H. J., et al. (2000b). Cerebral cortex: a topographic segmentation method using magnetic resonance imaging. Psychiatry Res. 100, 97-126. doi: 10.1016/S0925-4927(00)00072-X.
11. Desikan, R. S., Segonne, F., Fischl, B., Quinn, B. T., Dickerson, B. C., Blacker, D., et al. (2006). An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. Neuroimage 31, 968-980. doi: 10.1016/j.neuroimage.2006.01.021.
12. Destrieux, C., Fischl, B., Dale, A., and Halgren, E. (2010). Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. Neuroimage53, 1-15. doi: 10.1016/j.neuroimage.2010.06.010.
13. Fischl, B., Sereno, M. I., Tootell, R. B. H., and Dale, A. M. (1999). High-resolution intersubject averaging and a coordinate system for the cortical surface. Hum. Brain Mapp. 8, 272-284. doi: 10.1002/(SICI)1097-0193(1999)8:4<272::AID-HBM10>3.0.CO;2-4.
14. Fischl, B., van der Kouwe, A., Destrieux, C., Halgren, E., Segonne, F., Salat, D. H., et al. (2004). Automatically parcellating the human cerebral cortex. Cereb. Cortex 14, 11-22. doi: 10.1093/cercor/bhg087.
15. Gelas, A., Gouaillard, A., and Megason, S. (2008). Surface meshes incremental decimation framework. Insight J. Available online at:http://hdl.handle.net/1926/1488.
16. Gelas, A., and Gouaillard, A. (2007). Parameterization of discrete surfaces. Insight J. Available online at: http://hdl.handle.net/1926/1315.
17. Goldman, A. L., Pezawas, L., Mattay, V. S., Fischl, B., Verchinski, B. A., Zoltick, B., et al. (2008). Heribability of brain morphology related to schizophrenia: a large-scale automated magnetic resonance imaging segmentation study. Biol. Psychiatry 63, 475-483. doi: 10.1016/j.biopsych.2007.06.006.
18. Heckemann, R. A., Keihaninejad, S., Aljabar, P., Rueckert, D., Hajnal, J. V., and Hammers, A. (2010). Improving intersubject image registration using tissue-class information benefits robustness and accuracy of multi-atlas based anatomical segmentation. Neuroimage 51, 221-227. doi: 10.1016/j.neuroimage.2010.01.072.
19. Jones, B. F., Barnes, J., Uylings, H. B., Fox, N. C., Frost, C., Witter, M. P., et al. (2006). Differential regional atrophy of the cingulate gyrus in Alzheimer disease: a volumetric MRI study. Cereb. Cortex 16, 1701-1708. doi: 10.1093/cercor/bhj105.
20. Joshi, A., Shattuck, D., Thompson, P. M., and Leahy, R. M. (2007a). Surface-constrained volumetric brain registration using harmonic mappings. IEEE Trans. Med. Imaging 26, 1657-1669. doi: 10.1109/TMI.2007.901432.
21. Joshi, A., Shattuck, D. W., Thompson, P. M., and Leahy, R. M. (2007b). A finite element method for elastic parameterization and alignment of cortical surfaces using sulcal constraints. Biomedical Imaging: From Nano to Macro. ISBI 2007. 4th IEEE International Symposium on, (Washington, DC), 640-643. doi: 10.1109/ISBI.2007.356933.
22. Kim, J. J., Crespo-Facorro, B., Andreasen, N. C., O'Leary, D. S., Zhang, B., Harris, G., et al. (2000). An MRI-based temporal lobe parcellation. Neuroimage 11, 271-288. doi: 10.1006/nimg.2000.0543.
23. Kim, J. J., Crespo-Facorro, B., Andreasen, N. C., O'Leary, D. S., Magnotta, V., and Nopoulos, P. (2003). Morphology of the lateral superior temporal gyrus in neuroleptic naïve patients with schizophrenia: relationship to symptoms. Schizophr Res. 60, 173-181. doi: 10.1016/S0920-9964(02)00299-2.
24. Kim, E. Y., and Johnson, H. (2010). Multi-structure segmentation of multi-modal brain images using artificial neural networks. Proc. SPIE Med. Imaging. 7623. doi: 10.1117/12.844613.
25. Klein, A., Mensh, B., Ghosh, S., Tourville, J., and Hirsch, J. (2005). Mindboggle: automated brain labeling with multiple atlases. BMC Med. Imaging. doi: 10.1186/1471-2342-5-7.
26. Li, W., Ibanez, L., Gelas, A., Yeo, B. T. T., Neithammer, M., Andreasen, N. C., et al. (2011). An automated pipeline for cortical surface generation and registration of the cerebral cortex. Proc. SPIE. 7962. doi: 10.1117/12.876509.
27. Liu, T., Shen, D., and Davatzikos, C. (2004). Deformable registration of cortical structures via hybrid volumetric and surface warping. Neuroimage 22, 1790-1801. doi: 10.1016/j.neuroimage.2004.04.020.
28. Lu, W. (2010) A method for Automated Landmark Constellation Detection using Evolutionary Principal Components and Statistical Shape Models, M.S. Thesis, The University of Iowa, Iowa City, Iowa.
29. Nopoulos, P. C., Aylward, E. H., Ross, C. A., Johnson, H. J., Magnotta, V. A., Juhl, A. R., et al. (2010). Cerebral cortex structure in prodromal Huntington disease. Neurobiol. Dis. 40, 544-545. doi: 10.1016/j.nbd.2010.07.014.
30. Ono, M., Kubik, S., and Abernathey, C. D. (1990). Atlas of the Cerebral Sulci, New York, NY: Georg Thieme.
31. Pierson, R., Johnson, H., Harris, G., Keefe, H., Paulsen, J., Andreasen, N., and Magnotta, V. (2011). Fully automated analysis using BRAINS: AutoWorkUp. Neuroimage 54, 328-336. doi: 10.1016/j.neuroimage.2010.06.047.
32. Postelnicu, G., Zollei, L., and Fischl, B. (2009). Combined volumetric and surface registration. IEEE Trans. Med. Imaging 28, 508-522. doi: 10.1109/TMI.2008.2004426.
33. Rademacher, J., Galaburda, A. M., Kennedy, D. N., Filipek, P. A., and Cayiness, V. S. J. (1992). Human cerebral cortex: localization, parcellation and morphometry with magnetic resonance imaging. J. Cogn. Neurosci. 4, 352-374. doi: 10.1162/jocn.1992.4.4.352.
34. Roland, P. E., and Zilles, K. (1998). Structural divisions and functional fields in the human cerebral cortex. Brain Res. Rev. 26, 87-105. doi: 10.1016/S0165-0173(97)00058-1.
35. Sabuncu, M. R., Yeo, B. T. T., Van Leemput, K., Fischl, B., and Golland, P. (2010). A generative model for image segmentation based on label fusion. IEEE Trans. Med. Imaging 29, 1714-1729. doi: 10.1109/TMI.2010.2050897.
36. Schaer, M., Cuadra, M. B., Tamarit, L., Lazeyras, F., Eliez, S., and Thiran, J.-P. (2008). A surface-based approach to quantify local cortical gyrification. IEEE Trans. Med. Imaging 27, 161-170. doi: 10.1109/TMI.2007.903576.
37. Trzesniak, C., Schaufelberger, M. S., Duran, F. L. S., Santos, L. C., Rosa, P. G. P., McGuire, P. K., et al. (2012). Longitudinal follow-up of cavum septum pellucidum and adhesion interthalamica alterations in first-episode psychosis: a population-based MRI study. Psychol. Med. 42 2523-2534. doi: 10.1017/S0033291712000839.
38. Uylings, H. B., Rajkowska, G., Sanz-Arigita, E., Amunts, K., and Zilles, K. (2005). Consequences of large interindividual variability for human brain atlases: converging macroscopical imaging and microscopical neuroanatomy. Anat. Embryol. (Berl.) 210, 423-431. doi: 10.1007/s00429-005-0042-4.
39. Van Essen, D. C. (2005). A population-average, landmark-and surface-based (PALS) atlas of human cerebral cortex. Neuroimage 28, 635-662. doi: 10.1016/j.neuroimage.2005.06.058.
40. Van Essen, D. C., Drury, H. A., Joshi, S., and Miller, M. (1998). Functional and structural mapping of human cerebral cortex: solutions are in the surfaces. Proc. Natl. Acad. Sci. U.S.A. 95, 788-795. doi: 10.1073/pnas.95.3.788.
41. Vercauteren, T., Pennec, X., Perchant, A., and Ayache, N. (2009). Diffeomorphic demons: efficient non-parametric image registration. Neuroimage 45, S61-S72. doi: 10.1016/j.neuroimage.2008.10.040.
42. Yeo, B. T. T., Sabuncu, M. R., Vercauteren, T., Ayache, N., Fischl, B., and Golland, P. (2010). Spherical demons: fast diffeomorphic landmark-free surface registration. IEEE Trans. Med. Imaging 29, 650-668. doi: 10.1109/TMI.2009.2030797.
43. Zwanenburg, J. J., Hendrikse, J., and Luijten, P. R. (2012). Generalized multiple-layer appearance of the cerebral cortex with 3D FLAIR 7.0-T MR imaging. Radiology 262, 995-1001. doi: 10.1148/radiol.11110812.