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AJNR Awards, New Junior Editors, and more. Read the latest AJNR updates

Research ArticleSpine Imaging and Spine Image-Guided Interventions
Open Access

Automatic Spinal Cord Gray Matter Quantification: A Novel Approach

C. Tsagkas, A. Horvath, A. Altermatt, S. Pezold, M. Weigel, T. Haas, M. Amann, L. Kappos, T. Sprenger, O. Bieri, P. Cattin and K. Parmar
American Journal of Neuroradiology August 2019, DOI: https://doi.org/10.3174/ajnr.A6157
C. Tsagkas
aFrom the Neurologic Clinic and Policlinic (C.T., M.A., L.K., T.S., K.P.), Department of Medicine and Biomedical Engineering
bTranslational Imaging in Neurology Basel (C.T., A.A., M.A., M.W., L.K., K.P.), Department of Medicine and Biomedical Engineering
eMedical Image Analysis Center (C.T., A.A., M.A.), Basel, Switzerland
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A. Horvath
fDepartment of Biomedical Engineering (A.H., A.A., S.P., M.W., O.B., P.C.), University of Basel, Allschwil, Switzerland
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A. Altermatt
bTranslational Imaging in Neurology Basel (C.T., A.A., M.A., M.W., L.K., K.P.), Department of Medicine and Biomedical Engineering
eMedical Image Analysis Center (C.T., A.A., M.A.), Basel, Switzerland
fDepartment of Biomedical Engineering (A.H., A.A., S.P., M.W., O.B., P.C.), University of Basel, Allschwil, Switzerland
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S. Pezold
fDepartment of Biomedical Engineering (A.H., A.A., S.P., M.W., O.B., P.C.), University of Basel, Allschwil, Switzerland
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M. Weigel
bTranslational Imaging in Neurology Basel (C.T., A.A., M.A., M.W., L.K., K.P.), Department of Medicine and Biomedical Engineering
cDivision of Radiological Physics (M.W., T.H., O.B.), Department of Radiology
fDepartment of Biomedical Engineering (A.H., A.A., S.P., M.W., O.B., P.C.), University of Basel, Allschwil, Switzerland
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T. Haas
cDivision of Radiological Physics (M.W., T.H., O.B.), Department of Radiology
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M. Amann
aFrom the Neurologic Clinic and Policlinic (C.T., M.A., L.K., T.S., K.P.), Department of Medicine and Biomedical Engineering
bTranslational Imaging in Neurology Basel (C.T., A.A., M.A., M.W., L.K., K.P.), Department of Medicine and Biomedical Engineering
dDivision of Diagnostic and Interventional Neuroradiology (M.A.), Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland
eMedical Image Analysis Center (C.T., A.A., M.A.), Basel, Switzerland
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L. Kappos
aFrom the Neurologic Clinic and Policlinic (C.T., M.A., L.K., T.S., K.P.), Department of Medicine and Biomedical Engineering
bTranslational Imaging in Neurology Basel (C.T., A.A., M.A., M.W., L.K., K.P.), Department of Medicine and Biomedical Engineering
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T. Sprenger
aFrom the Neurologic Clinic and Policlinic (C.T., M.A., L.K., T.S., K.P.), Department of Medicine and Biomedical Engineering
gDepartment of Neurology (T.S.), DKD HELIOS Klinik, Wiesbaden, Germany.
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O. Bieri
cDivision of Radiological Physics (M.W., T.H., O.B.), Department of Radiology
fDepartment of Biomedical Engineering (A.H., A.A., S.P., M.W., O.B., P.C.), University of Basel, Allschwil, Switzerland
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P. Cattin
fDepartment of Biomedical Engineering (A.H., A.A., S.P., M.W., O.B., P.C.), University of Basel, Allschwil, Switzerland
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K. Parmar
aFrom the Neurologic Clinic and Policlinic (C.T., M.A., L.K., T.S., K.P.), Department of Medicine and Biomedical Engineering
bTranslational Imaging in Neurology Basel (C.T., A.A., M.A., M.W., L.K., K.P.), Department of Medicine and Biomedical Engineering
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REFERENCES

  1. 1.↵
    1. Ginsberg L
    . Disorders of the spinal cord and roots. Pract Neurol 2011;11:259–67 doi:10.1136/practneurol-2011-000069 pmid:21746716
    FREE Full Text
  2. 2.↵
    1. Cook SA
    . Spinal disease: neoplastic, degenerative, and infective spinal cord diseases and spinal cord compression. April 10, 2015. https://clinicalgate.com/spinal-disease-neoplastic-degenerative-and-infective-spinal-cord-diseases-and-spinal-cord-compression/. Accessed April 4, 2015
  3. 3.↵
    1. Wheeler-Kingshott CA,
    2. Stroman PW,
    3. Schwab JM, et al
    . The current state-of-the-art of spinal cord imaging: applications. Neuroimage 2014;84:1082–93 doi:10.1016/j.neuroimage.2013.07.014 pmid:23859923
    CrossRefPubMedWeb of Science
  4. 4.↵
    1. Kearney H,
    2. Miller DH,
    3. Ciccarelli O
    . Spinal cord MRI in multiple sclerosis: diagnostic, prognostic and clinical value. Nat Rev Neurol 2015;11:327–38 doi:10.1038/nrneurol.2015.80 pmid:26009002
    CrossRefPubMed
  5. 5.↵
    1. Schlaeger R,
    2. Papinutto N,
    3. Panara V, et al
    . Spinal cord gray matter atrophy correlates with multiple sclerosis disability. Ann Neurol 2014;76:568–80 doi:10.1002/ana.24241 pmid:25087920
    CrossRefPubMed
  6. 6.↵
    1. Paquin MÊ,
    2. Mendili MM,
    3. Gros C, et al
    . Spinal cord gray matter atrophy in amyotrophic lateral sclerosis. AJNR Am J Neuroradiol 2018;39:184–92 doi:10.3174/ajnr.A5427 pmid:29122760
    Abstract/FREE Full Text
  7. 7.↵
    1. Weidner N,
    2. Rupp R;
    3. Tansey K
    1. Stroman PW,
    2. Bosma RL
    . Spinal cord imaging. In: Weidner N, Rupp R; Tansey K, eds. Neurological Aspects of Spinal Cord Injury. Cham: Springer International Publishing; 2017:237–57
  8. 8.↵
    1. Stroman PW,
    2. Wheeler-Kingshott C,
    3. Bacon M, et al
    . The current state-of-the-art of spinal cord imaging: methods. Neuroimage 2014;84:1070–81 doi:10.1016/j.neuroimage.2013.04.124 pmid:23685159
    CrossRefPubMedWeb of Science
  9. 9.↵
    1. Yiannakas MC,
    2. Kearney H,
    3. Samson RS, et al
    . Feasibility of grey matter and white matter segmentation of the upper cervical cord in vivo: a pilot study with application to magnetisation transfer measurements. Neuroimage 2012;63:1054–59 doi:10.1016/j.neuroimage.2012.07.048 pmid:22850571
    CrossRefPubMedWeb of Science
  10. 10.↵
    1. Held P,
    2. Dorenbeck U,
    3. Seitz J, et al
    . MRI of the abnormal cervical spinal cord using 2D spoiled gradient echo multiecho sequence (MEDIC) with magnetization transfer saturation pulse: a T2* weighted feasibility study. J Neuroradiol 2003;30:83–90 pmid:12717293
    PubMed
  11. 11.↵
    1. Papinutto N,
    2. Schlaeger R,
    3. Panara V, et al
    . 2D phase-sensitive inversion recovery imaging to measure in vivo spinal cord gray and white matter areas in clinically feasible acquisition times. J Magn Reson Imaging 2015;42:698–708 doi:10.1002/jmri.24819 pmid:25483607
    CrossRefPubMed
  12. 12.↵
    1. Weigel M,
    2. Bieri O
    . A simple and fast approach for spinal cord imaging at 3T with high in-plane resolution and good contrast. In: Proceedings of the Annual Meeting of International Society of Magnetic Resonance in Medicine, Singapore; May 7–13, 2016:4408
  13. 13.↵
    1. Weigel M,
    2. Bieri O
    . Spinal cord imaging using averaged magnetization inversion recovery acquisitions. Magn Reson Med 2018;79:1870–81 doi:10.1002/mrm.26833 pmid:28714105
    CrossRefPubMed
  14. 14.↵
    1. Prados F,
    2. Cardoso MJ,
    3. Yiannakas MC, et al
    . Fully automated grey and white matter spinal cord segmentation. Sci Rep 2016;6:36151 doi:10.1038/srep36151 pmid:27786306
    CrossRefPubMed
  15. 15.↵
    1. Datta E,
    2. Papinutto N,
    3. Schlaeger R, et al
    . Gray matter segmentation of the spinal cord with active contours in MR images. Neuroimage 2017;147:788–99 doi:10.1016/j.neuroimage.2016.07.062 pmid:27495383
    CrossRefPubMed
  16. 16.↵
    1. Dupont SM,
    2. De Leener B,
    3. Taso M, et al
    . Fully-integrated framework for the segmentation and registration of the spinal cord white and gray matter. Neuroimage 2017;150:358–72 doi:10.1016/j.neuroimage.2016.09.026 pmid:27663988
    CrossRefPubMed
  17. 17.↵
    1. De Leener B,
    2. Lévy S,
    3. Dupont SM, et al
    . SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data. Neuroimage 2017;145:24–43 doi:10.1016/j.neuroimage.2016.10.009 pmid:27720818
    CrossRefPubMed
  18. 18.↵
    1. Paragios N,
    2. Duncan J,
    3. Ayache N
    1. Bach Cuadra M,
    2. Duay V,
    3. Thiran JP
    . Atlas-based segmentation. In: Paragios N, Duncan J, Ayache N, eds. Handbook of Biomedical Imaging: Methodologies and Clinical Research. Boston: Springer US; 2015:221–44
  19. 19.↵
    1. Wachinger C,
    2. Golland P
    . Atlas-based under-segmentation. Med Image Comput Comput Assist Interv 2014;17:315–22 pmid:25333133
    PubMed
  20. 20.↵
    1. Yao J,
    2. Vrtovec T,
    3. Zheng G, et al.
    1. Horváth A,
    2. Pezold S,
    3. Weigel M, et al
    . Variational segmentation of the white and gray matter in the spinal cord using a shape prior. In: Yao J, Vrtovec T, Zheng G, et al., eds. Computational Methods and Clinical Applications for Spine Imaging. Cham: Springer International Publishing; 2016:26–37
  21. 21.↵
    1. Yao J,
    2. Glocker B,
    3. Klinder T, et al.
    1. Pezold S,
    2. Fundana K,
    3. Amann M, et al
    . Automatic segmentation of the spinal cord using continuous max flow with cross-sectional similarity prior and tubularity features. In: Yao J, Glocker B, Klinder T, et al., eds. Recent Advances in Computational Methods and Clinical Applications for Spine Imaging. Cham: Springer; 2015:107–18
  22. 22.↵
    1. Hancock ER,
    2. Martin RR,
    3. Sabin MA
    1. Lüthi M,
    2. Albrecht T,
    3. Vetter T
    . Probabilistic modeling and visualization of the flexibility in morphable models. In: Hancock ER, Martin RR, Sabin MA, eds. Mathematics of Surfaces XIII. Berlin: Springer-Verlag; 2009:251–64
  23. 23.↵
    1. Asman AJ,
    2. Smith SA,
    3. Reich DS, et al
    . Robust GM/WM segmentation of the spinal cord with iterative non-local statistical fusion. Med Image Comput Comput Assist Inter 2013;16(Pt 1):759–67 pmid:24505736
    PubMed
  24. 24.↵
    1. Prados F,
    2. Ashburner J,
    3. Blaiotta C, et al
    . Spinal cord grey matter segmentation challenge. Neuroimage 2017;152:312–29 doi:10.1016/j.neuroimage.2017.03.010 pmid:28286318
    CrossRefPubMed
  25. 25.↵
    1. Bhadelia RA,
    2. Bogdan AR,
    3. Kaplan RF, et al
    . Cerebrospinal fluid pulsation amplitude and its quantitative relationship to cerebral blood flow pulsations: a phase-contrast MR flow imaging study. Neuroradiology 1997;39:258–64 doi:10.1007/s002340050404 pmid:9144672
    CrossRefPubMedWeb of Science
  26. 26.↵
    1. Figley CR,
    2. Stroman PW
    . Investigation of human cervical and upper thoracic spinal cord motion: implications for imaging spinal cord structure and function. Magn Reson Med 2007;58:185–89 doi:10.1002/mrm.21260 pmid:17659610
    CrossRefPubMed
  27. 27.↵
    1. Piché M,
    2. Cohen-Adad J,
    3. Nejad MK, et al
    . Characterization of cardiac-related noise in fMRI of the cervical spinal cord. Magn Reson Imaging 2009;27:300–10 doi:10.1016/j.mri.2008.07.019 pmid:18801632
    CrossRefPubMedWeb of Science
  28. 28.↵
    1. Perone CS,
    2. Calabrese E,
    3. Cohen-Adad J
    . Spinal cord gray matter segmentation using deep dilated convolutions. Sci Rep 2018;8:5966 doi:10.1038/s41598-018-24304-3 pmid:29654236
    CrossRefPubMed
  29. 29.↵
    1. Horvath A,
    2. Tsagkas C,
    3. Andermatt S, et al
    . Spinal cord gray matter-white matter segmentation on magnetic resonance AMIRA images with MD-GRU. https://arxiv.org/abs/1808.02408. Accessed August 7, 2018
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C. Tsagkas, A. Horvath, A. Altermatt, S. Pezold, M. Weigel, T. Haas, M. Amann, L. Kappos, T. Sprenger, O. Bieri, P. Cattin, K. Parmar
Automatic Spinal Cord Gray Matter Quantification: A Novel Approach
American Journal of Neuroradiology Aug 2019, DOI: 10.3174/ajnr.A6157

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Automatic Spinal Cord Gray Matter Quantification: A Novel Approach
C. Tsagkas, A. Horvath, A. Altermatt, S. Pezold, M. Weigel, T. Haas, M. Amann, L. Kappos, T. Sprenger, O. Bieri, P. Cattin, K. Parmar
American Journal of Neuroradiology Aug 2019, DOI: 10.3174/ajnr.A6157
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