Volume estimation of the thalamus using FreeSurfer and stereology: Consistency between methods

Neuroinformatics

Volumn 10, Issue 4, 2012, Pages 341-350

  Keller, Simon S ^a,b   Gerdes, Jan S ^a   Mohammadi, Siawoosh ^c   Kellinghaus, Christoph ^d   Kugel, Harald ^a   Deppe, Katja ^a   Ringelstein, E Bernd ^a   Evers, Stefan ^a   Schwindt, Wolfram ^a   Deppe, Michael ^a,d  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b KING'S COLLEGE LONDON   (United Kingdom)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

^d Andreas Bannowsky Ltd   (Germany)

Author keywords

Diffusion tensor imaging; Fractional anisotropy .MR image analysis; FreeSurfer; Stereology; Volume

Indexed keywords

ADULT; ANALYSIS OF VARIANCE; ARTICLE; ATROPHY; BRAIN MAPPING; COMPUTER PROGRAM; FEMALE; HUMAN; INSTRUMENTATION; MALE; MIDDLE AGED; MYELINATED NERVE; MYOCLONUS EPILEPSY; NUCLEAR MAGNETIC RESONANCE IMAGING; PATHOLOGY; STATISTICAL MODEL; STEREOTACTIC PROCEDURE; THALAMUS; THREE DIMENSIONAL IMAGING;

ADULT; ANALYSIS OF VARIANCE; ATROPHY; BRAIN MAPPING; FEMALE; HUMANS; IMAGING, THREE-DIMENSIONAL; LINEAR MODELS; MAGNETIC RESONANCE IMAGING; MALE; MIDDLE AGED; MYOCLONIC EPILEPSY, JUVENILE; NERVE FIBERS, MYELINATED; SOFTWARE; STEREOTAXIC TECHNIQUES; THALAMUS; YOUNG ADULT;

EID: 84868303748     PISSN: 15392791     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12021-012-9147-0     Document Type: Article

References (79)

1. Acer, N., Cankaya, M. N., Isci, O., Bas, O., Camurdanoglu, M., & Turgut, M. (2010). Estimation of cerebral surface area using vertical sectioning and magnetic resonance imaging: a stereological study. Brain Research, 1310, 29-36.
2. Adriano, F., Spoletini, I., Caltagirone, C., & Spalletta, G. (2010). Updated meta-analyses reveal thalamus volume reduction in patients with first-episode and chronic schizophrenia. Schizophrenia Research, 123(1), 1-14.
3. Amini, L., Soltanian-Zadeh, H., Lucas, C., & Gity,M. (2004). Automatic segmentation of thalamus from brain MRI integrating fuzzy clustering and dynamic contours. IEEE Transactions on Biomedical Engineering, 51(5), 800-811. (Pubitemid 38525713)
4. Andreasen, N. C. (1997). The role of the thalamus in schizophrenia. Canadian Journal of Psychiatry, 42(1), 27-33. (Pubitemid 27141613)
5. Bas, O., Acer, N., Mas, N., Karabekir, H. S., Kusbeci, O. Y., & Sahin, B. (2009). Stereological evaluation of the volume and volume fraction of intracranial structures in magnetic resonance images of patients with Alzheimer's disease. Annals of Anatomy, 191(2), 186-195.
6. Basso, M. A., Uhlrich, D., & Bickford, M. E. (2005). Cortical function: a view from the thalamus. Neuron, 45(4), 485-488. (Pubitemid 40249860)
7. Behrens, T. E., Johansen-Berg, H., Woolrich, M. W., Smith, S. M., Wheeler-Kingshott, C. A., Boulby, P. A., Barker, G. J., Sillery, E. L., Sheehan, K., Ciccarelli, O., Thompson, A. J., Brady, J. M., & Matthews, P. M. (2003). Non-invasive mapping of connections between human thalamus and cortex using diffusion imaging. Nature Neuroscience, 6(7), 750-757. (Pubitemid 36792891)
8. Berg, A. T., Berkovic, S. F., Brodie, M. J., Buchhalter, J., Cross, J. H., van Emde, B.W., Engel, J., French, J., Glauser, T. A., Mathern, G. W., Moshe, S. L., Nordli, D., Plouin, P., & Scheffer, I. E. (2010). Revised terminology and concepts for organization of seizures and epilepsies: report of the ILAE Commission on Classification and Terminology, 2005-2009. Epilepsia, 51(4), 676-685.
9. Bonilha, L., Kobayashi, E., Cendes, F., & Min, Li L. (2004). Protocol for volumetric segmentation of medial temporal structures using high-resolution 3-D magnetic resonance imaging. Human Brain Mapping, 22(2), 145-154. (Pubitemid 38738037)
10. Cherbuin, N., Anstey, K. J., Reglade-Meslin, C., & Sachdev, P. S. (2009). In vivo hippocampal measurement and memory: a comparison of manual tracing and automated segmentation in a large community-based sample. PLoS One, 4(4), e5265.
11. Chupin, M., Hammers, A., Liu, R. S., Colliot, O., Burdett, J., Bardinet, E., Duncan, J. S., Garnero, L., & Lemieux, L. (2009). Automatic segmentation of the hippocampus and the amygdala driven by hybrid constraints: method and validation. NeuroImage, 46(3), 749-761.
12. Collins, D. L., & Pruessner, J. C. (2010). Towards accurate, automatic segmentation of the hippocampus and amygdala from MRI by augmenting ANIMAL with a template library and label fusion. NeuroImage, 52(4), 1355-1366.
13. Cowell, P. E., Sluming, V. A.,Wilkinson, I. D., Cezayirli, E., Romanowski, C. A., Webb, J. A., Keller, S. S., Mayes, A., & Roberts, N. (2007). Effects of sex and age on regional prefrontal brain volume in two human cohorts. European Journal of Neuroscience, 25(1), 307-318. (Pubitemid 46096244)
14. Crum, W. R., Scahill, R. I., & Fox, N. C. (2001). Automated hippocampal segmentation by regional fluid registration of serial MRI: validation and application in Alzheimer's disease. NeuroImage, 13(5), 847-855. (Pubitemid 32848330)
15. de Jong, L.W., van der Hiele, K., Veer, I. M., Houwing, J. J.,Westendorp, R. G., Bollen, E. L., de Bruin, P. W., Middelkoop, H. A., van Buchem, M. A., & van der Grond, J. (2008). Strongly reduced volumes of putamen and thalamus in Alzheimer's disease: an MRI study. Brain, 131(Pt 12), 3277-3285.
16. Deppe, M., Kellinghaus, C., Duning, T., Moddel, G., Mohammadi, S., Deppe, K., Schiffbauer, H., Kugel, H., Keller, S. S., Ringelstein, E. B., & Knecht, S. (2008). Nerve fiber impairment of anterior thalamocortical circuitry in juvenile myoclonic epilepsy. Neurology, 71(24), 1981-1985.
17. Dewey, J., Hana, G., Russell, T., Price, J., McCaffrey, D., Harezlak, J., Sem, E., Anyanwu, J. C., Guttmann, C. R., Navia, B., Cohen, R., & Tate, D. F. (2010). Reliability and validity of MRI-based automated volumetry software relative to auto-assisted manual measurement of subcortical structures in HIV-infected patients from a multisite study. NeuroImage, 51(4), 1334-1344.
18. Dom, R., Malfroid, M., & Baro, F. (1976). Neuropathology of Huntington's chorea. Studies of the ventrobasal complex of the thalamus. Neurology, 26(1), 64-68.
19. Douaud, G., Gaura, V., Ribeiro, M. J., Lethimonnier, F., Maroy, R., Verny, C., Krystkowiak, P., Damier, P., Bachoud-Levi, A. C., Hantraye, P., & Remy, P. (2006). Distribution of grey matter atrophy in Huntington's disease patients: a combined ROI-based and voxel-based morphometric study. NeuroImage, 32(4), 1562-1575. (Pubitemid 44332291)
20. Du, H., Zhang, Y., Xie, B., Wu, N., Wu, G., Wang, J., Jiang, T., & Feng, H. (2011). Regional atrophy of the basal ganglia and thalamus in idiopathic generalized epilepsy. Journal of Magnetic Resonance Imaging, 33(4), 817-821.
21. Duvernoy, H. (1999). The human brain. Surface, blood supply and three-dimensional sectional anatomy. New York: New York Springer.
22. Engelborghs, S., Marien, P., Martin, J. J., & De Deyn, P. P. (1998). Functional anatomy, vascularisation and pathology of the human thalamus. Acta Neurologica Belgica, 98(3), 252-265. (Pubitemid 128524570)
23. Eriksen, N., Rostrup, E., Andersen, K., Lauritzen, M. J., Fabricius, M., Larsen, V. A., Dreier, J. P., Strong, A. J., Hartings, J. A., & Pakkenberg, B. (2010). Application of stereological estimates in patients with severe head injuries using CT and MR scanning images. British Journal of Radiology, 83(988), 307-317.
24. Fischl, B., Salat, D. H., Busa, E., Albert, M., Dieterich, M., Haselgrove, C., van der Kouwe, A., Killiany, R., Kennedy, D., Klaveness, S., Montillo, A., Makris, N., Rosen, B., & Dale, A. M. (2002). Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. Neuron, 33(3), 341-355. (Pubitemid 34162530)
25. Garcia-Finana, M., Cruz-Orive, L. M., Mackay, C. E., Pakkenberg, B., & Roberts, N. (2003). Comparison of MR imaging against physical sectioning to estimate the volume of human cerebral compartments. NeuroImage, 18(2), 505-516. (Pubitemid 36269158)
26. Garcia-Finana, M., Keller, S. S., & Roberts, N. (2009). Confidence intervals for the volume of brain structures in Cavalieri sampling with local errors. Journal of Neuroscience Methods, 179(1), 71-77.
27. Gong, G., Concha, L., Beaulieu, C., & Gross, D. W. (2008). Thalamic diffusion and volumetry in temporal lobe epilepsy with and without mesial temporal sclerosis. Epilepsy Research, 80(2-3), 184-193.
28. Gundersen, H. J., & Jensen, E. B. (1987). The efficiency of systematic sampling in stereology and its prediction. Journal of Microscopy, 147(Pt 3), 229-263.
29. Gundersen, H. J., Jensen, E. B., Kieu, K., & Nielsen, J. (1999). The efficiency of systematic sampling in stereology-reconsidered. Journal of Microscopy, 193(Pt 3), 199-211.
30. Hallahan, B. P., Craig, M. C., Toal, F., Daly, E. M., Moore, C. J., Ambikapathy, A., Robertson, D., Murphy, K. C., & Murphy, D. G. (2011). In vivo brain anatomy of adult males with Fragile X syndrome: an MRI study. NeuroImage, 54(1), 16-24.
31. Herrero, M. T., Barcia, C., & Navarro, J. M. (2002). Functional anatomy of thalamus and basal ganglia. Child's Nervous System, 18(8), 386-404. (Pubitemid 36013686)
32. Holmes, M. D., Quiring, J., & Tucker, D. M. (2010). Evidence that juvenile myoclonic epilepsy is a disorder of frontotemporal corticothalamic networks. NeuroImage, 49(1), 80-93.
33. Howard, M. A., Roberts, N., Garcia-Finana, M., & Cowell, P. E. (2003). Volume estimation of prefrontal cortical subfields using MRI and stereology. Brain Research. Brain Research Protocols, 10(3), 125-138. (Pubitemid 36143913)
34. ILAE. (1989). Proposal for revised classification of epilepsies and epileptic syndromes. Commission on Classification and Terminology of the International League Against Epilepsy. Epilepsia, 30(4), 389-399.
35. Jelsing, J., Rostrup, E., Markenroth, K., Paulson, O. B., Gundersen, H. J., Hemmingsen, R., & Pakkenberg, B. (2005). Assessment of in vivo MR imaging compared to physical sections in vitro-a quantitative study of brain volumes using stereology. NeuroImage, 26 (1), 57-65. (Pubitemid 40602885)
36. Johansen-Berg, H., Behrens, T. E., Sillery, E., Ciccarelli, O., Thompson, A. J., Smith, S. M., & Matthews, P. M. (2005). Functionalanatomical validation and individual variation of diffusion tractography-based segmentation of the human thalamus. Cerebral Cortex, 15(1), 31-39. (Pubitemid 40019049)
37. Jovicich, J., Czanner, S., Han, X., Salat, D., van der Kouwe, A., Quinn, B., Pacheco, J., Albert, M., Killiany, R., Blacker, D., Maguire, P., Rosas, D., Makris, N., Gollub, R., Dale, A., Dickerson, B. C., & Fischl, B. (2009). MRI-derived measurements of human subcortical, ventricular and intracranial brain volumes: Reliability effects of scan sessions, acquisition sequences, data analyses, scanner upgrade, scanner vendors and field strengths. NeuroImage, 46(1), 177-192.
38. Kassubek, J., Juengling, F. D., Ecker, D., & Landwehrmeyer, G. B. (2005). Thalamic atrophy in Huntington's disease co-varies with cognitive performance: a morphometric MRI analysis. Cerebral Cortex, 15(6), 846-853. (Pubitemid 40696123)
39. Keller SS, Ahrens T, Mohammadi S, Moddel G, Kugel H, Bernd Ringelstein E, Deppe M. (2011a). Microstructural and volumetric abnormalities of the putamen in juvenile myoclonic epilepsy. Epilepsia In press.
40. Keller, S. S., Baker, G., Downes, J. J., & Roberts, N. (2009). Quantitative MRI of the prefrontal cortex and executive function in patients with temporal lobe epilepsy. Epilepsy & Behavior, 15 (2), 186-195.
41. Keller, S. S., Highley, J. R., Garcia-Finana, M., Sluming, V., Rezaie, R., & Roberts, N. (2007). Sulcal variability, stereological measurement and asymmetry of Broca's area on MR images. Journal of Anatomy, 211(4), 534-555. (Pubitemid 47456840)
42. Keller, S. S., Mackay, C. E., Barrick, T. R., Wieshmann, U. C., Howard, M. A., & Roberts, N. (2002). Voxel-based morphometric comparison of hippocampal and extrahippocampal abnormalities in patients with left and right hippocampal atrophy. NeuroImage, 16(1), 23-31. (Pubitemid 34852469)
43. Keller, S. S., & Roberts, N. (2009). Measurement of brain volume using MRI: software, techniques, choices and prerequisites. J Anthropological Sci, 87, 127-151.
44. Keller, S. S., Roberts, N., Garcia-Finana,M.,Mohammadi, S., Ringelstein, E. B., Knecht, S., & Deppe, M. (2011). Can the Language-dominant Hemisphere Be Predicted by Brain Anatomy? Journal of Cognitive Neuroscience, 23(8), 2013-2029.
45. Keller, S. S., Roberts, N., & Hopkins, W. (2009). A Comparative Magnetic Resonance Imaging Study of the Anatomy, Variability, and Asymmetry of Broca's Area in the Human and Chimpanzee Brain. Journal of Neuroscience, 29(46), 14607-14616.
46. Keller, S. S., Wieshmann, U. C., Mackay, C. E., Denby, C. E., Webb, J., & Roberts, N. (2002). Voxel based morphometry of grey matter abnormalities in patients with medically intractable temporal lobe epilepsy: effects of side of seizure onset and epilepsy duration. Journal of Neurology, Neurosurgery, and Psychiatry, 73(6), 648-655.
47. Keshavan, M. S., Anderson, S., Beckwith, C., Nash, K., Pettegrew, J. W., & Krishnan, K. R. (1995). A comparison of stereology and segmentation techniques for volumetric measurements of lateral ventricles in magnetic resonance imaging. Psychiatry Research, 61(1), 53-60.
48. Kim, J. H., Lee, J. K., Koh, S. B., Lee, S. A., Lee, J. M., Kim, S. I., & Kang, J. K. (2007). Regional grey matter abnormalities in juvenile myoclonic epilepsy: a voxel-basedmorphometry study. NeuroImage, 37(4), 1132-1137. (Pubitemid 47385285)
49. Lee, M. S., & Marsden, C. D. (1994). Movement disorders following lesions of the thalamus or subthalamic region. Movement Disorders, 9(5), 493-507. (Pubitemid 24275065)
50. Lux, S., Keller, S., Mackay, C., Ebers, G., Marshall, J. C., Cherkas, L., Rezaie, R., Roberts, N., Fink, G. R., & Gurd, J. M. (2008). Crossed cerebral lateralization for verbal and visuo-spatial function in a pair of handedness discordant monozygotic twins: MRI and fMRI brain imaging. Journal of Anatomy, 212(3), 235-248. (Pubitemid 351325480)
51. Mackay, C. E., Roberts, N., Mayes, A. R., Downes, J. J., Foster, J. K., & Mann, D. (1998). An exploratory study of the relationship between face recognition memory and the volume of medial temporal lobe structures in healthy young males. Behavioural Neurology, 11(1), 3-20. (Pubitemid 28429902)
52. Mackay, C. E., Webb, J. A., Eldridge, P. R., Chadwick, D. W., Whitehouse, G. H., & Roberts, N. (2000). Quantitative magnetic resonance imaging in consecutive patients evaluated for surgical treatment of temporal lobe epilepsy. Magnetic Resonance Imaging, 18(10), 1187-1199. (Pubitemid 32121435)
53. Mayhew, T. M. (1992). A review of recent advances in stereology for quantifying neural structure. Journal of Neurocytology, 21(5), 313-328.
54. McKeown, M. J., Uthama, A., Abugharbieh, R., Palmer, S., Lewis, M., & Huang, X. (2008). Shape (but not volume) changes in the thalami in Parkinson disease. BMC Neurology, 8, 8.
55. Meador-Woodruff, J. H., Clinton, S.M., Beneyto,M., &McCullumsmith, R. E. (2003).Molecular abnormalities of the glutamate synapse in the thalamus in schizophrenia. Annals of the New York Academy of Sciences, 1003, 75-93. (Pubitemid 38083046)
56. Morey, R. A., Petty, C. M., Xu, Y., Hayes, J. P., Wagner, H. R., 2nd, Lewis, D. V., LaBar, K. S., Styner, M., & McCarthy, G. (2009). A comparison of automated segmentation and manual tracing for quantifying hippocampal and amygdala volumes. NeuroImage, 45 (3), 855-866.
57. Morey, R. A., Selgrade, E. S., Wagner, H. R., 2nd, Huettel, S. A., Wang, L., & McCarthy, G. (2010). Scan-rescan reliability of subcortical brain volumes derived from automated segmentation. Human Brain Mapping, 31(11), 1751-1762.
58. Morra, J. H., Tu, Z., Apostolova, L. G., Green, A. E., Avedissian, C., Madsen, S. K., Parikshak, N., Hua, X., Toga, A. W., Jack, C. R., Jr., Weiner, M. W., & Thompson, P. M. (2008). Validation of a fully automated 3D hippocampal segmentation method using subjects with Alzheimer's disease mild cognitive impairment, and elderly controls. NeuroImage, 43(1), 59-68.
59. Mory, S. B., Betting, L. E., Fernandes, P. T., Lopes-Cendes, I., Guerreiro, M. M., Guerreiro, C. A., Cendes, F., & Li, L. M. (2011). Structural abnormalities of the thalamus in juvenile myoclonic epilepsy. Epilepsy & Behavior, 21(4), 407-411.
60. Natsume, J., Bernasconi, N., Andermann, F., & Bernasconi, A. (2003). MRI volumetry of the thalamus in temporal, extratemporal, and idiopathic generalized epilepsy. Neurology, 60(8), 1296-1300. (Pubitemid 36460985)
61. Pardoe, H. R., Pell, G. S., Abbott, D. F., & Jackson, G. D. (2009). Hippocampal volume assessment in temporal lobe epilepsy: How good is automated segmentation? Epilepsia, 50(12), 2586-2592.
62. Patenaude B, Smith S, Kennedy D, Jenkinson M. (2011). A Bayesian model of shape and appearance for subcortical brain segmentation. Neuroimage.
63. Pruessner, J. C., Li, L. M., Serles, W., Pruessner, M., Collins, D. L., Kabani, N., Lupien, S., & Evans, A. C. (2000). Volumetry of hippocampus and amygdala with high-resolution MRI and threedimensional analysis software: minimizing the discrepancies between laboratories. Cerebral Cortex, 10(4), 433-442. (Pubitemid 30185342)
64. Puddephat, M. (1999). Computer interface for convenient application of stereological methods for unbiased estimation of volume and surface area: studies using MRI with particular reference to the human brain. The Magnetic Resonance and Image Analysis Research Centre (MARIARC). Liverpool: University of Liverpool.
65. Pulsipher, D. T., Seidenberg, M., Guidotti, L., Tuchscherer, V. N., Morton, J., Sheth, R. D., & Hermann, B. (2009). Thalamofrontal circuitry and executive dysfunction in recent-onset juvenile myoclonic epilepsy. Epilepsia, 50(5), 1210-1219.
66. Pulsipher, D. T., Seidenberg, M., Morton, J. J., Geary, E., Parrish, J., & Hermann, B. (2007). MRI volume loss of subcortical structures in unilateral temporal lobe epilepsy. Epilepsy & Behavior, 11(3), 442-449. (Pubitemid 350048495)
67. Qiu, A., Zhong, J., Graham, S., Chia,M. Y.,& Sim, K. (2009). Combined analyses of thalamic volume, shape and white matter integrity in first-episode schizophrenia. NeuroImage, 47(4), 1163-1171.
68. Roberts, N., Puddephat, M. J., & McNulty, V. (2000). The benefit of stereology for quantitative radiology. British Journal of Radiology, 73(871), 679-697. (Pubitemid 30614222)
69. Ronan, L., Doherty, C. P., Delanty, N., Thornton, J., & Fitzsimons, M. (2006). Quantitative MRI: a reliable protocol for measurement of cerebral gyrification using stereology. Magnetic Resonance Imaging, 24(3), 265-272.
70. Salmenpera, T., Kononen, M., Roberts, N., Vanninen, R., Pitkanen, A., & Kalviainen, R. (2005). Hippocampal damage in newly diagnosed focal epilepsy: a prospective MRI study. Neurology, 64(1), 62-68. (Pubitemid 40082938)
71. Sheline, Y. I., Black, K. J., Lin, D. Y., Christensen, G. E., Gado, M. H., Brunsden, B. S., & Vannier, M. W. (1996). Stereological MRI volumetry of the frontal lobe. Psychiatry Research, 67(3), 203-214. (Pubitemid 26344751)
72. Shen, L., Saykin, A. J., Kim, S., Firpi, H. A., West, J. D., Risacher, S. L., McDonald, B. C., McHugh, T. L., Wishart, H. A., & Flashman, L. A. (2010). Comparison of manual and automated determination of hippocampal volumes in MCI and early AD. Brain Imaging and Behavior, 4(1), 86-95.
73. Shrout, P. E., & Fleiss, J. L. (1979). Intraclass correlations: uses in assessing rater reliability. Psychological Bulletin, 86(2), 420-428.
74. Smith, S. M., Zhang, Y., Jenkinson, M., Chen, J., Matthews, P. M., Federico, A., & De Stefano, N. (2002). Accurate, robust, and automated longitudinal and cross-sectional brain change analysis. NeuroImage, 17(1), 479-489.
75. Speedie, L. J., & Heilman, K. M. (1983). Anterograde memory deficits for visuospatial material after infarction of the right thalamus. Archives of Neurology, 40(3), 183-186. (Pubitemid 13139124)
76. Tae, W. S., Kim, S. S., Lee, K. U., Nam, E. C., & Kim, K. W. (2008). Validation of hippocampal volumes measured using a manual method and two automated methods (FreeSurfer and IBASPM) in chronic major depressive disorder. Neuroradiology, 50(7), 569-581.
77. Traynor, C. R., Barker, G. J., Crum, W. R., Williams, S. C., & Richardson, M. P. (2011). Segmentation of the thalamus in MRI based on T1 and T2. NeuroImage, 56(3), 939-950.
78. Williams, D. (1965). The thalamus and epilepsy. Brain, 88(3), 539-556.
79. Xuereb, J. H., Perry, R. H., Candy, J. M., Perry, E. K., Marshall, E., & Bonham, J. R. (1991). Nerve cell loss in the thalamus in Alzheimer's disease and Parkinson's disease. Brain, 114(Pt 3), 1363-1379.