Incorporating the effect of white matter microstructure in the estimation of magnetic susceptibility in ex vivo mouse brain

Anders Dyhr Sandgaard, Valerij G. Kiselev, Rafael Neto Henriques, Noam Shemesh, Sune Nørhøj Jespersen*

*Corresponding author for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review


Purpose: To extend quantitative susceptibility mapping to account for microstructure of white matter (WM) and demonstrate its effect on ex vivo mouse brain at 16.4T. Theory and Methods: Previous studies have shown that the MRI measured Larmor frequency also depends on local magnetic microstructure at the mesoscopic scale. Here, we include effects from WM microstructure using our previous results for the mesoscopic Larmor frequency (Formula presented.) of cylinders with arbitrary orientations. We scrutinize the validity of our model and QSM in a digital brain phantom including (Formula presented.) from a WM susceptibility tensor and biologically stored iron with scalar susceptibility. We also apply susceptibility tensor imaging to the phantom and investigate how the fitted tensors are biased from (Formula presented.). Last, we demonstrate how to combine multi-gradient echo and diffusion MRI images of ex vivo mouse brains acquired at 16.4T to estimate an apparent scalar susceptibility without sample rotations. Results: Our new model improves susceptibility estimation compared to QSM for the brain phantom. Applying susceptibility tensor imaging to the phantom with (Formula presented.) from WM axons with scalar susceptibility produces a highly anisotropic susceptibility tensor that mimics results from previous susceptibility tensor imaging studies. For the ex vivo mouse brain we find the (Formula presented.) due to WM microstructure to be substantial, changing susceptibility in WM up to 25% root-mean-squared-difference. Conclusion: (Formula presented.) impacts susceptibility estimates and biases susceptibility tensor imaging fitting substantially. Hence, it should not be neglected when imaging structurally anisotropic tissue such as brain WM.

Original languageEnglish
JournalMagnetic Resonance in Medicine
Pages (from-to)699-715
Number of pages17
Publication statusPublished - Feb 2024


  • Larmor frequency
  • magnetic microstructure
  • magnetic susceptibility
  • mesoscopic Lorentz sphere
  • modeling
  • quantitative susceptibility mapping


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