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Deciphering laminar-specific neural inputs with line-scanning fMRI


Using a line-scanning method during functional magnetic resonance imaging (fMRI), we obtained high temporal (50-ms) and spatial (50-μm) resolution information along the cortical thickness and showed that the laminar position of fMRI onset coincides with distinct neural inputs in rat somatosensory and motor cortices. This laminar-specific fMRI onset allowed us to identify the neural inputs underlying ipsilateral fMRI activation in the barrel cortex due to peripheral denervation-induced plasticity.

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Figure 1: Characterization of the line-scanning fMRI method in rat somatosensory and motor cortex.
Figure 2: Mapping the inputs into the barrel cortex (BC) in a rat model of cortical plasticity.


  1. Ogawa, S., Lee, T.M., Kay, A.R. & Tank, D.W. Proc. Natl. Acad. Sci. USA 87, 9868–9872 (1990).

    Article  CAS  Google Scholar 

  2. Biswal, B., Yetkin, F.Z., Haughton, V.M. & Hyde, J.S. Magn. Reson. Med. 34, 537–541 (1995).

    CAS  Google Scholar 

  3. Friston, K. PLoS Biol. 7, e33 (2009).

    Article  Google Scholar 

  4. Moon, C.H., Fukuda, M. & Kim, S.-G. Neuroimage 64, 91–103 (2013).

    Article  Google Scholar 

  5. Menon, R.S., Ogawa, S., Strupp, J.P. & Ugurbil, K. J. Neurophysiol. 77, 2780–2787 (1997).

    Article  CAS  Google Scholar 

  6. Chen, G., Wang, F., Gore, J.C. & Roe, A.W. Neuroimage 64, 147–155 (2013).

    Article  Google Scholar 

  7. Shmuel, A., Yacoub, E., Chaimow, D., Logothetis, N.K. & Ugurbil, K. Neuroimage 35, 539–552 (2007).

    Article  Google Scholar 

  8. Silva, A.C., Lee, S.P., Iadecola, C. & Kim, S.G. J. Cereb. Blood Flow Metab. 20, 201–206 (2000).

    Article  CAS  Google Scholar 

  9. Silva, A.C. & Koretsky, A.P. Proc. Natl. Acad. Sci. USA 99, 15182–15187 (2002).

    Article  CAS  Google Scholar 

  10. Yu, X. et al. Neuroimage 59, 1451–1460 (2012).

    Article  Google Scholar 

  11. Hutchinson, E.B., Stefanovic, B., Koretsky, A.P. & Silva, A.C. Neuroimage 32, 520–530 (2006).

    Article  Google Scholar 

  12. Siero, J.C., Petridou, N., Hoogduin, H., Luijten, P.R. & Ramsey, N.F. J. Cereb. Blood Flow Metab. 31, 1999–2008 (2011).

    Article  Google Scholar 

  13. Tian, P. et al. Proc. Natl. Acad. Sci. USA 107, 15246–15251 (2010).

    Article  CAS  Google Scholar 

  14. Duvernoy, H.M., Delon, S. & Vannson, J.L. Brain Res. Bull. 7, 519–579 (1981).

    Article  CAS  Google Scholar 

  15. Tucciarone, J. et al. Neuroimage 44, 923–931 (2009).

    Article  Google Scholar 

  16. Yu, X. et al. Neuron 74, 731–742 (2012).

    Article  CAS  Google Scholar 

  17. Frey, S.H., Bogdanov, S., Smith, J.C., Watrous, S. & Breidenbach, W.C. Curr. Biol. 18, 1530–1534 (2008).

    Article  CAS  Google Scholar 

  18. Pelled, G., Chuang, K.H., Dodd, S.J. & Koretsky, A.P. Neuroimage 37, 262–273 (2007).

    Article  Google Scholar 

  19. Lin, F.-H. et al. Neuroimage 78, 372–384 (2013).

    Article  Google Scholar 

  20. Quairiaux, C., Armstrong-James, M. & Welker, E. J. Neurophysiol. 97, 2130–2147 (2007).

    Article  Google Scholar 

  21. Shuler, M.G., Krupa, D.J. & Nicolelis, M.A. J. Neurosci. 21, 5251–5261 (2001).

    Article  CAS  Google Scholar 

  22. Lebedev, M.A., Mirabella, G., Erchova, I. & Diamond, M.E. Cereb. Cortex 10, 23–31 (2000).

    Article  CAS  Google Scholar 

  23. Chakrabarti, S., Zhang, M. & Alloway, K.D. J. Neurophysiol. 100, 50–63 (2008).

    Article  Google Scholar 

  24. Bruno, R.M. & Sakmann, B. Science 312, 1622–1627 (2006).

    Article  CAS  Google Scholar 

  25. Cox, R.W. Comput. Biomed. Res. 29, 162–173 (1996).

    Article  CAS  Google Scholar 

  26. Madsen, M.T. Phys. Med. Biol. 37, 1597–1600 (1992).

    Article  Google Scholar 

  27. Uludağ, K. Proc. Natl. Acad. Sci. USA 107, E23 (2010).

    Article  Google Scholar 

  28. Das, A. & Sirotin, Y.B. Proc. Natl. Acad. Sci. USA 107, E24 (2010).

    Article  CAS  Google Scholar 

  29. Buxton, R.B. Neuroimage 13, 953–958 (2001).

    Article  CAS  Google Scholar 

  30. Marota, J.J. et al. Magn. Reson. Med. 41, 247–252 (1999).

    Article  CAS  Google Scholar 

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This research was supported by the Intramural Research Program of the US National Institutes of Health–NINDS. We thank K. Sharer and N. Bouraoud for technical support.

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Authors and Affiliations



X.Y. and A.P.K. conceived of the line-scanning strategy and designed experiments. X.Y. established the line-scanning method, performed experiments and analyzed the data. C.Q. and D.-y.C. performed blind experiments on the MEMRI tracing and line-scanning fMRI of the plasticity model. S.J.D. provided magnetic resonance technical support and IDL (Interactive Data Language) analytical tools. X.Y. and A.P.K. wrote the paper.

Corresponding authors

Correspondence to Xin Yu or Alan P Koretsky.

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The authors declare no competing financial interests.

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Yu, X., Qian, C., Chen, Dy. et al. Deciphering laminar-specific neural inputs with line-scanning fMRI. Nat Methods 11, 55–58 (2014).

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