Skip to main content
Top

2019 | OriginalPaper | Chapter

Muti-shell Diffusion MRI Harmonisation and Enhancement Challenge (MUSHAC): Progress and Results

Authors : Lipeng Ning, Elisenda Bonet-Carne, Francesco Grussu, Farshid Sepehrband, Enrico Kaden, Jelle Veraart, Stefano B. Blumberg, Can Son Khoo, Marco Palombo, Jaume Coll-Font, Benoit Scherrer, Simon K. Warfield, Suheyla Cetin Karayumak, Yogesh Rathi, Simon Koppers, Leon Weninger, Julia Ebert, Dorit Merhof, Daniel Moyer, Maximilian Pietsch, Daan Christiaens, Rui Teixeira, Jacques-Donald Tournier, Andrey Zhylka, Josien Pluim, Greg Parker, Umesh Rudrapatna, John Evans, Cyril Charron, Derek K. Jones, Chantal W. M. Tax

Published in: Computational Diffusion MRI

Publisher: Springer International Publishing

Activate our intelligent search to find suitable subject content or patents.

search-config
loading …

Abstract

We present a summary of competition results in the multi-shell diffusion MRI harmonisation and enhancement challenge (MUSHAC). MUSHAC is an open competition intended to stimulate the development of computational methods that reduce scanner- and protocol-related variabilities in multi-shell diffusion MRI data across multi-site studies. Twelve different methods from seven research groups have been tested in this challenge. The results show that cross-vendor harmonization and enhancement can be performed by using suitable computational algorithms such as deep convolutional neural networks. Moreover, parametric models for multi-shell diffusion MRI signals also provide reliable performances.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

Literature
1.
go back to reference Vollmar, C., O’Muircheartaigh, J., Barker, G.J., Symms, M.R., Thompson, P., Kumari, V., Duncan, J.S., Richardson, M.P., Koepp, M.J.: Identical, but not the same: intra-site and inter-site reproducibility of fractional anisotropy measures on two 3.0t scanners. NeuroImage 51(4), 1384–1394 (2010)CrossRef Vollmar, C., O’Muircheartaigh, J., Barker, G.J., Symms, M.R., Thompson, P., Kumari, V., Duncan, J.S., Richardson, M.P., Koepp, M.J.: Identical, but not the same: intra-site and inter-site reproducibility of fractional anisotropy measures on two 3.0t scanners. NeuroImage 51(4), 1384–1394 (2010)CrossRef
2.
go back to reference Landman, B.A., Farrell, J.A., Jones, C.K., Smith, S.A., Prince, J.L., Mori, S.: Effects of diffusion weighting schemes on the reproducibility of DTI-derived fractional anisotropy, mean diffusivity, and principal eigenvector measurements at 1.5T. NeuroImage 36(4), 1123–1138 (2007) Landman, B.A., Farrell, J.A., Jones, C.K., Smith, S.A., Prince, J.L., Mori, S.: Effects of diffusion weighting schemes on the reproducibility of DTI-derived fractional anisotropy, mean diffusivity, and principal eigenvector measurements at 1.5T. NeuroImage 36(4), 1123–1138 (2007)
3.
go back to reference Landman, B.A., Huang, A.J., Gifford, A., Vikram, D.S., Lim, I.A.L., Farrell, J.A., Bogovic, J.A., Hua, J., Chen, M., Jarso, S., Smith, S.A., Joel, S., Mori, S., Pekar, J.J., Barker, P.B., Prince, J.L., van Zijl, P.C.: Multi-parametric neuroimaging reproducibility: A 3-T resource study. NeuroImage 54(4), 2854–2866 (2011)CrossRef Landman, B.A., Huang, A.J., Gifford, A., Vikram, D.S., Lim, I.A.L., Farrell, J.A., Bogovic, J.A., Hua, J., Chen, M., Jarso, S., Smith, S.A., Joel, S., Mori, S., Pekar, J.J., Barker, P.B., Prince, J.L., van Zijl, P.C.: Multi-parametric neuroimaging reproducibility: A 3-T resource study. NeuroImage 54(4), 2854–2866 (2011)CrossRef
4.
go back to reference Pohl, K.M., Sullivan, E.V., Rohlfing, T., Chu, W., Kwon, D., Nichols, B.N., Zhang, Y., Brown, S.A., Tapert, S.F., Cummins, K., Thompson, W.K., Brumback, T., Colrain, I.M., Baker, F.C., Prouty, D., Bellis, M.D.D., Voyvodic, J.T., Clark, D.B., Schirda, C., Nagel, B.J., Pfefferbaum, A.: Harmonizing DTI measurements across scanners to examine the development of white matter microstructure in 803 adolescents of the NCANDA study. NeuroImage 130, 194–213 (2016)CrossRef Pohl, K.M., Sullivan, E.V., Rohlfing, T., Chu, W., Kwon, D., Nichols, B.N., Zhang, Y., Brown, S.A., Tapert, S.F., Cummins, K., Thompson, W.K., Brumback, T., Colrain, I.M., Baker, F.C., Prouty, D., Bellis, M.D.D., Voyvodic, J.T., Clark, D.B., Schirda, C., Nagel, B.J., Pfefferbaum, A.: Harmonizing DTI measurements across scanners to examine the development of white matter microstructure in 803 adolescents of the NCANDA study. NeuroImage 130, 194–213 (2016)CrossRef
5.
go back to reference Fortin, J.P., Parker, D., Tun, B., Watanabe, T., Elliott, M.A., Ruparel, K., Roalf, D.R., Satterthwaite, T.D., Gur, R.C., Gur, R.E., Schultz, R.T., Verma, R., Shinohara, R.T.: Harmonization of multi-site diffusion tensor imaging data. NeuroImage 161, 149–170 (2017)CrossRef Fortin, J.P., Parker, D., Tun, B., Watanabe, T., Elliott, M.A., Ruparel, K., Roalf, D.R., Satterthwaite, T.D., Gur, R.C., Gur, R.E., Schultz, R.T., Verma, R., Shinohara, R.T.: Harmonization of multi-site diffusion tensor imaging data. NeuroImage 161, 149–170 (2017)CrossRef
6.
go back to reference Mirzaalian, H., Ning, L., Savadjiev, P., Pasternak, O., Bouix, S., Michailovich, O., Grant, G., Marx, C., Morey, R., Flashman, L., George, M., McAllister, T., Andaluz, N., Shutter, L., Coimbra, R., Zafonte, R., Coleman, M., Kubicki, M., Westin, C., Stein, M., Shenton, M., Rathi, Y.: Inter-site and inter-scanner diffusion MRI data harmonization. NeuroImage 135, 311–323 (2016)CrossRef Mirzaalian, H., Ning, L., Savadjiev, P., Pasternak, O., Bouix, S., Michailovich, O., Grant, G., Marx, C., Morey, R., Flashman, L., George, M., McAllister, T., Andaluz, N., Shutter, L., Coimbra, R., Zafonte, R., Coleman, M., Kubicki, M., Westin, C., Stein, M., Shenton, M., Rathi, Y.: Inter-site and inter-scanner diffusion MRI data harmonization. NeuroImage 135, 311–323 (2016)CrossRef
7.
go back to reference Mirzaalian, H., Ning, L., Savadjiev, P., Pasternak, O., Bouix, S., Michailovich, O., Karmacharya, S., Grant, G., Marx, C.E., Morey, R.A., Flashman, L.A., George, M.S., McAllister, T.W., Andaluz, N., Shutter, L., Coimbra, R., Zafonte, R.D., Coleman, M.J., Kubicki, M., Westin, C.F., Stein, M.B., Shenton, M.E., Rathi, Y.: Multi-site harmonization of diffusion MRI data in a registration framework. Brain Imaging Behav. 12(1), 284–295 (2018)CrossRef Mirzaalian, H., Ning, L., Savadjiev, P., Pasternak, O., Bouix, S., Michailovich, O., Karmacharya, S., Grant, G., Marx, C.E., Morey, R.A., Flashman, L.A., George, M.S., McAllister, T.W., Andaluz, N., Shutter, L., Coimbra, R., Zafonte, R.D., Coleman, M.J., Kubicki, M., Westin, C.F., Stein, M.B., Shenton, M.E., Rathi, Y.: Multi-site harmonization of diffusion MRI data in a registration framework. Brain Imaging Behav. 12(1), 284–295 (2018)CrossRef
8.
go back to reference Karayumak, S.C., Bouix, S., Ning, L., James, A., Crow, T., Shenton, M., Kubicki, M., Rathi, Y.: Retrospective harmonization of multi-site diffusion MRI data acquired with different acquisition parameters. NeuroImage 184, 180–200 (2019)CrossRef Karayumak, S.C., Bouix, S., Ning, L., James, A., Crow, T., Shenton, M., Kubicki, M., Rathi, Y.: Retrospective harmonization of multi-site diffusion MRI data acquired with different acquisition parameters. NeuroImage 184, 180–200 (2019)CrossRef
9.
go back to reference Tax, C., et al.: Cross-vendor and cross-protocol harmonisation of diffusion tensor imaging data: a comparative study. ISMRM-ESMRMB. Number 0471 (2018) Tax, C., et al.: Cross-vendor and cross-protocol harmonisation of diffusion tensor imaging data: a comparative study. ISMRM-ESMRMB. Number 0471 (2018)
10.
go back to reference Tax, C., et al.: Cross-scanner and cross-protocol diffusion mri data harmonisation: a benchmark database and evaluation of algorithms. submitted (2018) Tax, C., et al.: Cross-scanner and cross-protocol diffusion mri data harmonisation: a benchmark database and evaluation of algorithms. submitted (2018)
11.
go back to reference Andersson, J.L., Skare, S., Ashburner, J.: How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging. NeuroImage 20(2), 870–888 (2003)CrossRef Andersson, J.L., Skare, S., Ashburner, J.: How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging. NeuroImage 20(2), 870–888 (2003)CrossRef
12.
go back to reference Andersson, J.L., Sotiropoulos, S.N.: An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging. NeuroImage 125, 1063–1078 (2016)CrossRef Andersson, J.L., Sotiropoulos, S.N.: An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging. NeuroImage 125, 1063–1078 (2016)CrossRef
13.
go back to reference Glasser, M.F., Sotiropoulos, S.N., Wilson, J.A., Coalson, T.S., Fischl, B., Andersson, J.L., Xu, J., Jbabdi, S., Webster, M., Polimeni, J.R., Essen, D.C.V., Jenkinson, M.: The minimal preprocessing pipelines for the human connectome project. NeuroImage 80, 105–124 (2013)CrossRef Glasser, M.F., Sotiropoulos, S.N., Wilson, J.A., Coalson, T.S., Fischl, B., Andersson, J.L., Xu, J., Jbabdi, S., Webster, M., Polimeni, J.R., Essen, D.C.V., Jenkinson, M.: The minimal preprocessing pipelines for the human connectome project. NeuroImage 80, 105–124 (2013)CrossRef
14.
go back to reference Bammer, R., Markl, M., Barnett, A., Acar, B., Alley, M., Pelc, N., Glover, G., Moseley, M.: Analysis and generalized correction of the effect of spatial gradient field distortions in diffusion-weighted imaging. Magn. Reson. Med. 50(3) 560–569CrossRef Bammer, R., Markl, M., Barnett, A., Acar, B., Alley, M., Pelc, N., Glover, G., Moseley, M.: Analysis and generalized correction of the effect of spatial gradient field distortions in diffusion-weighted imaging. Magn. Reson. Med. 50(3) 560–569CrossRef
15.
go back to reference Sotiropoulos, S.N., Jbabdi, S., Xu, J., Andersson, J.L., Moeller, S., Auerbach, E.J., Glasser, M.F., Hernandez, M., Sapiro, G., Jenkinson, M., Feinberg, D.A., Yacoub, E., Lenglet, C., Essen, D.C.V., Ugurbil, K., Behrens, T.E.: Advances in diffusion MRI acquisition and processing in the human connectome project. NeuroImage 80, 125–143 (2013)CrossRef Sotiropoulos, S.N., Jbabdi, S., Xu, J., Andersson, J.L., Moeller, S., Auerbach, E.J., Glasser, M.F., Hernandez, M., Sapiro, G., Jenkinson, M., Feinberg, D.A., Yacoub, E., Lenglet, C., Essen, D.C.V., Ugurbil, K., Behrens, T.E.: Advances in diffusion MRI acquisition and processing in the human connectome project. NeuroImage 80, 125–143 (2013)CrossRef
16.
go back to reference Rudrapatna, S.U., Parker, G.D., Roberts, J., Jones, D.K.: Can we correct for interactions between subject motion and gradient-nonlinearity in diffusion MRI? ISMRM. Number (1206 (2018)) Rudrapatna, S.U., Parker, G.D., Roberts, J., Jones, D.K.: Can we correct for interactions between subject motion and gradient-nonlinearity in diffusion MRI? ISMRM. Number (1206 (2018))
17.
go back to reference Jensen, J.H., Helpern, J.A., Ramani, A., Lu, H., Kaczynski, K.: Diffusional kurtosis imaging: the quantification of non-gaussian water diffusion by means of magnetic resonance imaging. Magn. Reson. Med. 53(6), 1432–1440 (2005)CrossRef Jensen, J.H., Helpern, J.A., Ramani, A., Lu, H., Kaczynski, K.: Diffusional kurtosis imaging: the quantification of non-gaussian water diffusion by means of magnetic resonance imaging. Magn. Reson. Med. 53(6), 1432–1440 (2005)CrossRef
18.
go back to reference Özarslan, E., Koay, C.G., Shepherd, T.M., Komlosh, M.E., Irfanoglu, M.O., Pierpaoli, C., Basser, P.J.: Mean apparent propagator (MAP) MRI: a novel diffusion imaging method for mapping tissue microstructure. NeuroImage 78, 16–32 (2013)CrossRef Özarslan, E., Koay, C.G., Shepherd, T.M., Komlosh, M.E., Irfanoglu, M.O., Pierpaoli, C., Basser, P.J.: Mean apparent propagator (MAP) MRI: a novel diffusion imaging method for mapping tissue microstructure. NeuroImage 78, 16–32 (2013)CrossRef
19.
go back to reference Garyfallidis, E., Brett, M., Amirbekian, B., Rokem, A., Van Der Walt, S., Descoteaux, M., Nimmo-Smith, I., Contributors, D.: Dipy, a library for the analysis of diffusion MRI data. Front. Neuroinformatics 8, 8 (2014)CrossRef Garyfallidis, E., Brett, M., Amirbekian, B., Rokem, A., Van Der Walt, S., Descoteaux, M., Nimmo-Smith, I., Contributors, D.: Dipy, a library for the analysis of diffusion MRI data. Front. Neuroinformatics 8, 8 (2014)CrossRef
20.
go back to reference Cardoso, M.J., Modat, M., Wolz, R., Melbourne, A., Cash, D., Rueckert, D., Ourselin, S.: Geodesic information flows: spatially-variant graphs and their application to segmentation and fusion. IEEE Trans. Med. Imaging 34(9), 1976–1988 (2015)CrossRef Cardoso, M.J., Modat, M., Wolz, R., Melbourne, A., Cash, D., Rueckert, D., Ourselin, S.: Geodesic information flows: spatially-variant graphs and their application to segmentation and fusion. IEEE Trans. Med. Imaging 34(9), 1976–1988 (2015)CrossRef
21.
go back to reference Scherrer, B., Schwartzman, A., Taquet, M., Sahin, M., Prabhu, S.P., Warfield, S.K.: Characterizing brain tissue by assessment of the distribution of anisotropic microstructural environments in diffusion-compartment imaging (DIAMOND). Magn. Reson. Med. 76(3), 963–977 (2016)CrossRef Scherrer, B., Schwartzman, A., Taquet, M., Sahin, M., Prabhu, S.P., Warfield, S.K.: Characterizing brain tissue by assessment of the distribution of anisotropic microstructural environments in diffusion-compartment imaging (DIAMOND). Magn. Reson. Med. 76(3), 963–977 (2016)CrossRef
22.
go back to reference Blumberg, S.B., Tanno, R., Kokkinos, I., Alexander, D.C.: Deeper image quality transfer: training low-memory neural networks for 3D images. In: Frangi, A.F., Schnabel, J.A., Davatzikos, C., Alberola-López, C., Fichtinger, G. (eds.) Medical Image Computing and Computer Assisted Intervention—MICCAI 2018., pp. 118–125 (2018)CrossRef Blumberg, S.B., Tanno, R., Kokkinos, I., Alexander, D.C.: Deeper image quality transfer: training low-memory neural networks for 3D images. In: Frangi, A.F., Schnabel, J.A., Davatzikos, C., Alberola-López, C., Fichtinger, G. (eds.) Medical Image Computing and Computer Assisted Intervention—MICCAI 2018., pp. 118–125 (2018)CrossRef
Metadata
Title
Muti-shell Diffusion MRI Harmonisation and Enhancement Challenge (MUSHAC): Progress and Results
Authors
Lipeng Ning
Elisenda Bonet-Carne
Francesco Grussu
Farshid Sepehrband
Enrico Kaden
Jelle Veraart
Stefano B. Blumberg
Can Son Khoo
Marco Palombo
Jaume Coll-Font
Benoit Scherrer
Simon K. Warfield
Suheyla Cetin Karayumak
Yogesh Rathi
Simon Koppers
Leon Weninger
Julia Ebert
Dorit Merhof
Daniel Moyer
Maximilian Pietsch
Daan Christiaens
Rui Teixeira
Jacques-Donald Tournier
Andrey Zhylka
Josien Pluim
Greg Parker
Umesh Rudrapatna
John Evans
Cyril Charron
Derek K. Jones
Chantal W. M. Tax
Copyright Year
2019
DOI
https://doi.org/10.1007/978-3-030-05831-9_18

Premium Partner