Atlas-based segmentation of developing tissues in the human brain with quantitative validation in young fetuses

Human Brain Mapping

Volumn 31, Issue 9, 2010, Pages 1348-1358

  Habas, Piotr A ^a   Kim, Kio ^a   Rousseau, Francois ^b   Glenn, Orit A ^a   Barkovich, A James ^a   Studholme, Colin ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

Fetal brain; MRI; Segmentation; Validation

Indexed keywords

ALGORITHM; ARTICLE; BRAIN DEVELOPMENT; BRAIN TISSUE; BRAIN VENTRICLE; FETAL RESEARCH; FETUS; GRAY MATTER; HUMAN; HUMAN EXPERIMENT; KERNEL METHOD; NEUROIMAGING; NORMAL HUMAN; NUCLEAR MAGNETIC RESONANCE IMAGING; PRIORITY JOURNAL; THREE DIMENSIONAL IMAGING; TISSUE CHARACTERIZATION; TISSUE DISTRIBUTION; TISSUE TYPES; WHITE MATTER;

ALGORITHMS; BRAIN; FETUS; HUMANS; IMAGE INTERPRETATION, COMPUTER-ASSISTED; MAGNETIC RESONANCE IMAGING;

EID: 77956276314     PISSN: 10659471     EISSN: 10970193     Source Type: Journal    
DOI: 10.1002/hbm.20935     Document Type: Article

References (39)

1. Bach Cuadra M, Cammoun L, Butz T, Cuisenaire O, Thiran J-P (2005): Comparison and validation of tissue modelization and statistical classification methods in T1-weighted MR brain images. IEEE Trans Med Imaging 24:1548-1565.
2. Battin MR, Maalouf EF, Counsell SJ, Herlihy AH, Rutherford MA, Azzopardi D, Edwards AD (1998): Magnetic resonance imaging of the brain in very preterm infants: Visualization of the germinal matrix, early myelination, and cortical folding. Pediatrics 101:957-962.
3. Brugger PC, Stuhr F, Lindner C, Prayer D (2006): Methods of fetal MR: Beyond T2-weighted imaging. Eur J Radiol 57:172-181. (Pubitemid 43183647)
4. Chandramohan D, Habas PA, Kim K, Glenn OA, Barkovich AJ, Studholme C (2009): Cortical thickness mapping of the human fetal brain in utero from motion-corrected clinical MRI: Preliminary results. 15th Annual Meeting of the Organization for Human Brain Mapping, doi: 10.1016/S1053-8119(09)70081-3.
5. Claude I, Daire J-L, Sebag G (2004): Fetal brain MRI: Segmentation and biometric analysis of the posterior fossa. IEEE Trans Biomed Eng 51:617-626.
6. Coakley FV, Glenn OA, Qayyum A, Barkovich AJ, Goldstein R, Filly RA (2004): Fetal MRI: A developing technique for the developing patient. Am J Roentgenol 182:243-252.
7. Dice LR (1945): Measures of the amount of ecologic association between species. Ecology 26:97-302.
8. Girard N, Raybaud C, Poncet M (1995): In vivo MR study of brain maturation in normal fetuses. Am J Neuroradiol 16:407-413.
9. Glenn OA, Barkovich AJ (2006): Magnetic resonance imaging of the fetal brain and spine: An increasingly important tool in prenatal diagnosis. Am J Neuroradiol 27:1604-1611.
10. Grossman R, Hoffman C, Mardor Y, Biegon A (2006): Quantitative MRI measurements of human fetal brain development in utero. Neuroimage 33:463-470.
11. Guimond A, Meunier J, Thirion J-P (2000): Average brain models: A convergence study. Comput Vis Image Underst 77:192-210.
12. Habas PA, Kim K, Rousseau F, Glenn OA, Barkovich AJ, Studholme C (2008): Atlas-based segmentation of the germinal matrix from in utero clinical MRI of the fetal brain. Med Image Comp Comput-Assisted Interv LNCS 5241:351-358.
13. Habas PA, Kim K, Rousseau F, Glenn OA, Barkovich AJ, Studholme C (2009a): A spatio-temporal atlas of the human fetal brain with application to tissue segmentation. Med Image Comp Comput-Assisted Interv LNCS 5761:289-296.
14. Habas PA, Kim K, Rodriguez-Carranza CE, Glenn OA, Barkovich AJ, Studholme C (2009b): Abnormal sulcal formation in fetuses with ventriculomegaly identified by surface curvature mapping from motion-corrected clinical MRI. 15th Annual Meeting of the Organization for Human Brain Mapping, doi: 10.1016/S1053-8119(09)70072-2.
15. Huppi PS, Warfield SK, Kikinis R, Barnes PD, Zientara GP, Jolesz FA, Tsuji MK, Volpe JJ (1998): Quantitative magnetic resonance imaging of brain development in premature and mature newborns. Ann Neurol 43:224-235.
16. Inder TE, Warfield SK, Wang H, Huppi PS, Volpe JJ (2005): Abnormal cerebral structure is present at term in premature infants. Pediatrics 115:286-294.
17. Jiang S, Xue H, Glover A, Rutherford M, Rueckert D, Hajnal JV (2007): MRI of moving subjects using multislice snapshot images with volume reconstruction (SVR): Application to fetal, neonatal, and adult brain studies. IEEE Trans Med Imaging 26:967-980.
18. Kim K, Habas PA, Rousseau F, Glenn OA, Barkovich AJ, Studholme C (in press): Intersection-based motion correction of multi-slice MRI for 3D in utero fetal brain image formation. IEEE Trans Med Imaging, doi: 10.1109/TMI.2009. 2030679.
19. Kinoshita Y, Okudera T, Tsuru E, Yokota A (2001): Volumetric analysis of the germinal matrix and lateral ventricles performed using MR images of postmortem fetuses. Am J Neuroradiol 22:382-388.
20. Kostovic I, Judas M, Rados M, Hrabac P (2002): Laminar organization of the human fetal cerebrum revealed by histochemical markers and magnetic resonance imaging. Cereb Cortex 12:536-544.
21. Levine D, Stroustrup Smith A, McKenzie C (2003): Tips and tricks of fetal MR imaging. Radiol Clin N Am 41:729-745.
22. Matsuzawa J, Matsui M, Konishi T, Noguchi K, Gur RC, Bilker, W, Miyawaki T (2001): Age-related volumetric changes of brain gray and white matter in healthy infants and children. Cereb Cortex 11:335-342.
23. Murgasova M, Dyet L, Edwards D, Rutherford M, Hajnal J, Rueckert D (2007): Segmentation of brain MRI in young children. Acad Radiol 14:1350-1366.
24. Perkins L, Hughes E, Srinivasan L, Allsop J, Glover A, Kumar S, Fisk N, Rutherford M (2008): Exploring cortical subplate evolution using magnetic resonance imaging of the fetal brain. Dev Neurosci 30:211-220.
25. Prastawa M, Gilmore JH, Lin W, Gerig G (2005): Automatic segmentation of MR images of the developing newborn brain. Med Image Anal 9:457-466.
26. Prayer D, Brugger PC, Prayer L (2004): Fetal MRI: Techniques and protocols. Pediatr Radiol 34:685-693.
27. Prayer D, Kasprian G, Krampl E, Ulm B, Witzani L, Prayer L, Brugger PC (2006): MRI of normal fetal brain development. Eur J Radiol 57:199-216. (Pubitemid 43183650)
28. Rousseau F, Glenn OA, Iordanova B, Rodriguez-Carranza CE, Vigneron D, Barkovich AJ, Studholme C (2008): A novel approach to high resolution fetal brain MR imaging. Med Image Comp Comput-Assisted Interv LNCS 3749:548-555.
29. Rousseau F, Glenn OA, Iordanova B, Rodriguez-Carranza CE, Vigneron DB, Barkovich AJ, Studholme C (2006): Registration-based approach for reconstruction of high-resolution in utero fetal MR brain images. Acad Radiol 13:1072-1081.
30. Rutherford M, Jiang S, Allsop J, Perkins L, Srinivasan L, Hayat T, Kumar S, Hajnal J (2008): MR imaging methods for assessing fetal brain development. Dev Neurobiol 68:700-711.
31. Studholme C, Hill DLG, Hawkes DJ (1999): An overlap invariant entropy measure of 3D medical image alignment. Pattern Recognit 32:71-86.
32. Twickler DM, Magee KP, Caire J, Zaretsky M, Fleckenstein JL, Ramus RM (2003): Second-opinion magnetic resonance imaging for suspected fetal central nervous system abnormalities. Am J Obstet Gynecol 188:492-496.
33. Van Leemput K, Maes F, Vandermeulen D, Suetens P (1999a): Automated model-based bias field correction of MR images of the brain. IEEE Trans Med Imaging 18:885-896. (Pubitemid 32211104)
34. Van Leemput K, Maes F, Vandermeulen D, Suetens P (1999b): Automated model-based tissue classification of MR images of the brain. IEEE Trans Med Imaging 18:897-908. (Pubitemid 32211105)
35. Viola P, Wells WM (1997): Alignment by maximization of mutual information. Int J Comput Vis 24:137-154.
36. Wells WM, Grimson WEL, Kikinis R, Jolesz FA (1996): Adaptive segmentation of MRI data. IEEE Trans Med Imaging 15:429-442.
37. Xue H, Srinivasan L, Jiang S, Rutherford M, Edwards AD, Rueckert D, Hajnal JV (2007): Automatic segmentation and reconstruction of the cortex from neonatal MRI. Neuroimage 38:461-477.
38. Zijdenbos AP, Dawant BM, Margolin RA, Palmer AC (1994): Morphometric analysis of white matter lesions in MR images: Method and validation. IEEE Trans Med Imaging 13:716-724.
39. Zhang J (1992): The mean field theory in EM procedures for Markov random fields. IEEE Trans Signal Process 40:2570-2583.