Optimized, automated shimming procedure for improved experimental cardiac magnetic resonance imaging and spectroscopy at ultra-high magnetic fields

  • Cristiano José da Silva Barros Amaral (Student)

Student thesis: Master's Thesis


Background: Cardiac magnetic resonance imaging and spectroscopy are tools to non-invasively characterize rodent models of human heart disease. The experiments are typically carried out on dedicated MR systems equipped with ultra-high field magnets (≥ 7 Tesla). One fundamental requirement of MR is the homogeneity of the static magnetic field B0 (Grutter, 1993), and fluctuations of the main magnetic field (B0 inhomogeneities) within the scan region should be less than three parts per million (3 ppm). Inserting a sample inherently increases the field inhomogeneity (due to different degree of magnetization across the sample in response to the B0 field (“magnetic susceptibility”)), which needs to be compensated for (Crijns et al, 2011; Koch et al, 2006). Homogenizing (i.e. shimming) the static magnetic field is crucial for any MR experiment in order to maximize resolution and signal-to-noise. This is particularly important at ultra-high magnetic fields due to linear dependence of magnetic susceptibility. Adjusting the three linear and typically up to 14 higher order shims manually is laborious and subjective. Moreover, this process is particularly challenging where various tissues (i.e. heart and skeletal muscle, bone, lungs and flowing blood) are in close vicinity within the chest, each having different magnetic susceptibilities and relative motions. Auto-shim methods such as FASTMAP or FASTERMAP (Shen et al, 1997), are clinically and experimentally well established in brain tissue, but inevitably fail in the heart due to the ill-defined phase of the MR-signal, particularly inside the ventricles. Based on a technique, previously applied to human brain – implemented a novel approach for the application to mouse hearts in vivo, that is able to homogenize the B0-field in an arbitrarily shaped, but connected region of interest. Aim: The aim of this project is to investigate optimal scan parameters and post-processing approach to optimize and advance an automated shimming procedure for improved experimental cardiac magnetic resonance imaging and spectroscopy at ultra-high magnetic fields. Methods: Mice (n = 5) underwent MR experiments carried out in a 9.4 Tesla (T) horizontal magnet. The image acquisition was performed using fast gradient echo sequences varying the following parameters: resolution, flow compensation on / off, orientation (short-axis / axial), and dimension (2D multislice vs 3D). Three different shim coils’ configurations (shim coils up to the third order) were investigated and optimal MR sequence was assessed. Results: The threshold level of 17% proved to be acceptable for removal of phase discontinuities and hence it was used in subsequent studies. Quantitative analysis of the performance of different phase unwrapping approaches showed that the 3D approach is the most effective in resolving phase discontinuities present in field maps. The application of axial orientation, highest resolution data, absence of compensation flow and the introduction of higher order shim coils showed a significant reduction of B0 inhomogeneities when applied. Conclusions: This project established optimal acquisition parameters and post-processing options to improve the homogeneity of B0, and will aid the validation process in further follow-up studies.
Date of Award2012
Original languageEnglish
Awarding Institution
  • Universidade Católica Portuguesa
SupervisorJürgen Schneider (Supervisor)


  • Mestrado em Engenharia Biomédica

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