Accurate cortical tissue classification on MRI by modeling cortical folding patterns

Human Brain Mapping

Volumn 36, Issue 9, 2015, Pages 3563-3574

  Kim, Hosung ^a   Caldairou, Benoit ^b   Hwang, Ji Wook ^b   Mansi, Tommaso ^c   Hong, Seok Jun ^b   Bernasconi, Neda ^b   Bernasconi, Andrea ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b MCGILL UNIVERSITY   (Canada)

^c SIEMENS AG   (Germany)

Author keywords

Inhomogeneity; Local histogram; MRI classification; Myelination; Neocortex; Segmentation

Indexed keywords

ACCURACY; ADULT; ARTICLE; BRAIN CORTEX; BRAIN TISSUE; CEREBROSPINAL FLUID; CLASSIFICATION ALGORITHM; CORTICAL FOLDING PATTERNS; FEMALE; GRAY MATTER; HISTOGRAM; HUMAN; HUMAN EXPERIMENT; MALE; MODEL; MORPHOMETRICS; MYELINATION; NEOCORTEX; NEUROIMAGING; NORMAL HUMAN; NUCLEAR MAGNETIC RESONANCE IMAGING; NUCLEAR MAGNETIC RESONANCE SCANNER; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; WHITE MATTER; ALGORITHM; ANATOMY AND HISTOLOGY; AUTOMATED PATTERN RECOGNITION; CLUSTER ANALYSIS; EVALUATION STUDY; IMAGE PROCESSING; INFORMATION PROCESSING; MYELIN SHEATH; NONPARAMETRIC TEST; PROCEDURES; YOUNG ADULT;

ADULT; ALGORITHMS; CEREBRAL CORTEX; CLUSTER ANALYSIS; DATASETS AS TOPIC; FEMALE; GRAY MATTER; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MAGNETIC RESONANCE IMAGING; MALE; MYELIN SHEATH; PATTERN RECOGNITION, AUTOMATED; STATISTICS, NONPARAMETRIC; WHITE MATTER; YOUNG ADULT;

EID: 84939467419     PISSN: 10659471     EISSN: 10970193     Source Type: Journal    
DOI: 10.1002/hbm.22862     Document Type: Article

References (43)

1. Ashburner J, Friston KJ (2005): Unified segmentation. Neuroimage 26:839-851.
2. Bernhardt BC, Bernasconi N, Concha L, Bernasconi A (2010): Cortical thickness analysis in temporal lobe epilepsy: Reproducibility and relation to outcome. Neurology 74:1776-1784.
3. Bock NA, Hashim E, Janik R, Konyer NB, Weiss M, Stanisz GJ, Turner R, Geyer S (2013): Optimizing T(1)-weighted imaging of cortical myelin content at 3.0T. Neuroimage 65:1-12.
4. Boyes RG, Gunter JL, Frost C, Janke AL, Yeatman T, Hill DLG, Bernstein MA, Thompson PM, Weiner MW, Schuff N, Alexander GE, Killiany RJ, DeCarli C, Jack CR, Fox NC (2008): Intensity non-uniformity correction using N3 on 3-T scanners with multichannel phased array coils. Neuroimage 39:1752-1762.
5. Caldairou B, Passat N, Habas PA, Studholme C, Rousseau F (2011): A non-local fuzzy segmentation method: Application to brain MRI. Pattern Recognit 44:1916-1927.
6. 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.
7. Collins DL, Zijdenbos AP, Baare WFC, Evans AC (1999): ANIMAL+INSECT: Improved cortical structure segmentation. In: Kuba A, editor. Image Processing in Medical Imaging. Springer Verlag, Heidelberg, Cambridge, UK. pp 210-223.
8. Colliot O, Bernasconi N, Khalili N, Antel SB, Naessens V, Bernasconi A (2006): Individual voxel-based analysis of gray matter in focal cortical dysplasia. Neuroimage 29:162-171.
9. Comaniciu D, Meer P (2002): Mean shift: A robust approach toward feature space analysis. IEEE Trans Pattern Anal Mach Intell 24:603-619.
10. Dinse J, Waehnert M, Tardif CL, Schafer A, Geyer S, Turner R, Bazin PL (2013): A histology-based model of quantitative T1 contrast for in-vivo cortical parcellation of high-resolution 7 Tesla brain MR images. Med Image Comput Comput Assist Interv 16:51-58.
11. Eickhoff S, Walters NB, Schleicher A, Kril J, Egan GF, Zilles K, Watson JD, Amunts K (2005): High-resolution MRI reflects myeloarchitecture and cytoarchitecture of human cerebral cortex. Hum Brain Mapp 24:206-215.
12. Eskildsen SF, Coupe P, Fonov V, Manjon JV, Leung KK, Guizard N, Wassef SN, Ostergaard LR, Collins DL (2012): BEaST: Brain extraction based on nonlocal segmentation technique. Neuroimage 59:2362-2373.
13. Fischl B, Salat DH, van der Kouwe AJ, Makris N, Segonne F, Quinn BT, Dale AM (2004): Sequence-independent segmentation of magnetic resonance images. Neuroimage 23(Suppl. 1):S69-S84.
14. Flechsig P (1920): Anatomie des menschlichen Gehirns und Rueckenmarks auf myelogenetischer Grundlage. Leipzig: George Thieme.
15. Geyer S, Weiss M, Reimann K, Lohmann G, Turner R (2011): Microstructural Parcellation of the human cerebral cortex - from Brodmann's post-mortem map to in vivo mapping with high-field magnetic resonance imaging. Front Hum Neurosci 5:19
16. Glasser MF, Van Essen DC (2011): Mapping human cortical areas in vivo based on myelin content as revealed by T1- and T2-weighted MRI. J Neurosci 31:11597-11616.
17. Grabowski TJ, Frank RJ, Szumski NR, Brown CK, Damasio H (2000): Validation of partial tissue segmentation of single-channel magnetic resonance images of the brain. NeuroImage 12:640-656.
18. Hong SJ, Kim H, Schrader D, Bernasconi N, Bernhardt BC, Bernasconi A (2014): Automated detection of cortical dysplasia type II in MRI-negative epilepsy. Neurology 83:48-55.
19. Jenkinson M, Beckmann CF, Behrens TE, Woolrich MW, Smith SM (2012): Fsl. Neuroimage 62:782-790.
20. Joshi M, Cui J, Doolittle K, Joshi S, Van Essen D, Wang L, Miller MI (1999): Brain segmentation and the generation of cortical surfaces. NeuroImage 9:461-476.
21. Kim H, Chupin M, Colliot O, Bernhardt BC, Bernasconi N, Bernasconi A (2012): Automatic hippocampal segmentation in temporal lobe epilepsy: Impact of developmental abnormalities. Neuroimage 59:3178-3186.
22. Kim JS, Singh V, Lee JK, Lerch J, Ad-Dab'bagh Y, MacDonald D, Lee JM, Kim SI, Evans AC (2005): Automated 3-D extraction and evaluation of the inner and outer cortical surfaces using a Laplacian map and partial volume effect classification. Neuroimage 27:210-221.
23. Lerch JP, Pruessner JC, Zijdenbos A, Hampel H, Teipel SJ, Evans AC (2005): Focal decline of cortical thickness in Alzheimer's disease identified by computational neuroanatomy. Cereb Cortex 15:995-1001.
24. Lu GY, Wong DW (2008): An adaptive inverse-distance weighting spatial interpolation technique. Comput Geosci 34:1044-1055.
25. Lyttelton O, Boucher M, Robbins S, Evans A (2007): An unbiased iterative group registration template for cortical surface analysis. Neuroimage 34:1535-1544.
26. Ma C-M, Wan S-Y, Lee J-D (2002): Three-dimensional topology preserving reduction on the 4-subfields. IEEE Trans. Pattern Anal Mach Intell 24:1594-1605.
27. Richard N, Dojat M, Garbay C (2007): Distributed Markovian segmentation: Application to MR brain scans. Pattern Recognit 40:3467-3480.
28. Robbins S, Evans AC, Collins DL, Whitesides S (2004): Tuning and comparing spatial normalization methods. Med Image Anal 8:311-323.
29. Salat DH, Lee SY, van der Kouwe AJ, Greve DN, Fischl B, Rosas HD (2009): Age-associated alterations in cortical gray and white matter signal intensity and gray to white matter contrast. Neuroimage 48:21-28.
30. Sanchez-Panchuelo, R.M, Besle, J, Mougin, O, Gowland, P, Bowtell, R, Schluppeck, D, Francis, S (2014): Regional structural differences across functionally parcellated Brodmann areas of human primary somatosensory cortex. Neuroimage 93(Pt 2):221-230.
31. Scherrer B, Forbes F, Garbay C, Dojat M (2009): Distributed Local MRF Models for Tissue and Structure Brain Segmentation. IEEE Trans Med Imaging 28:1278-1295.
32. Sereno MI, Lutti A, Weiskopf N, Dick F (2013): Mapping the human cortical surface by combining quantitative T(1) with retinotopy. Cereb Cortex 23:2261-2268.
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.
34. Steen RG, Reddick WE, Ogg RJ (2000): More than meets the eye: Significant regional heterogeneity in human cortical T1. Magn Reson Imaging 18:361-368.
35. Tam RC, Traboulsee A, Riddehough A, Sheikhzadeh F, Li DK (2011): The impact of intensity variations in T1-hypointense lesions on clinical correlations in multiple sclerosis. Mult Scler 17:949-957.
36. Tohka J, Zijdenbos A, Evans A (2004): Fast and robust parameter estimation for statistical partial volume models in brain MRI. Neuroimage 23:84-97.
37. Tustison NJ, Avants BB, Cook PA, Zheng Y, Egan A, Yushkevich PA, Gee JC (2010): N4ITK: Improved N3 bias correction. IEEE Trans Med Imaging 29:1310-1320.
38. Vogt BA (1910): Die Myeloarchitektonische Felderung Des Menschlichen Stirnhirns. Psychologie Und Neurologie 15:221-232.
39. Worsley KJ, Andermann M, Koulis T, MacDonald D, Evans AC (1999): Detecting changes in nonisotropic images. Hum Brain Mapp 8:98-101.
40. Worsley KJ, Taylor JE, Carbonell F, Chung MK, Duerden E, Bernhardt B, Lyttelton O, Boucher M, Evans A.C (2009): SurfStat: A Matlab toolbox for the statistical analysis of univariate and multivariate surface and volumetric data using linear mixed effects models and random field theory. NeuroImage 47(Suppl. 1):S102.
41. Zhang Y, Brady M, Smith S (2001): Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm. IEEE Trans Med Imaging 20:45-57.
42. Zheng W, Chee MW, Zagorodnov V (2009): Improvement of brain segmentation accuracy by optimizing non-uniformity correction using N3. Neuroimage 48:73-83.
43. Zhu C, Jiang T (2003): Multicontext fuzzy clustering for separation of brain tissues in magnetic resonance images. NeuroImage 18:685-696.