Development of a 10-echo GE-SE EPIK sequence for simultaneous T$_2$ and T$_2$* quantification with application to oxygen extraction fraction measurement

  • Entwicklung einer 10-Echo GE-SE EPIK Sequenz zur simultanen T$_2$ und T$_2$* Quantifizierung mit Anwendung der Messung des Sauerstoffextraktionsanteils

Küppers, Fabian; Shah, Nadim Joni (Thesis advisor); Stahl, Achim (Thesis advisor)

Aachen : RWTH Aachen University (2023)
Dissertation / PhD Thesis

Dissertation, RWTH Aachen University, 2023


First discovered in the 1970s, magnetic resonance imaging (MRI) is a non-invasive tomographic imaging modality with a tremendous level of versatility, making it an essential part of modern medical care and treatment. In particular, quantitative MR imaging enables the standardized characterization of biological and physiological properties. In this scope, an important focus of today’s MR research is the development of faster imaging sequences that acquire multiple contrasts simultaneously. These so-called multi-contrast sequences offer an enormous range of applications but are often limited by low spatial image resolution and a small number of measured image time points. Based on the combined acquisition of gradient echo and spin echo contrasts, this PhD thesis develops a novel 10-echo GE-SE EPIK sequence that allows an increased amount of echoes to be obtained with improved resolution while enabling the quantification of transverse relaxation times, T$_2$ and T$_2$*, in the human brain using a single sequence. Due to the optimized data acquisition in the course of the EPIK (EPI with keyhole) method, measurements of 20 slices within one minute become possible with improved temporal stability and good temporal resolution. One focus of this sequence is the measurement of the oxygen extraction fraction (OEF), which could play an essential role in the detection and classification of stroke as well as in the characterization of tumor heterogeneity. This clinically valuable information is offered by a fast imaging sequence with more accurate signal acquisition and higher resolution, leading to improved usability and significance. The new GE-SE EPIK sequence developed in this thesis was evaluated with regard to the reconstructed image quality, and improvements in its implementation over other methods were demonstrated. In particular, the developed GE-SE EPIK sequence outperforms its competitors in terms of spatial resolution (128×128 matrix size) and the number of acquired data points (10). Furthermore, a processing routine was developed that simultaneously quantifies T$_2$ and T$_2$* values from the measured image information and additionally corrects potential signal corruptions due to erroneous RF pulses in the sequence. This data evaluation was examined for its robustness to various factors. Another focus of the performed research was the validation of the quantified relaxation times against reference methods in the course of phantom and in vivo measurements. A good agreement between the resulting T$_2$ and T$_2$* times with corresponding reference methods was complemented by a reproducibility study showing a deviation of under 3% between repeated measurements. The sequence was finally applied to quantify OEF, and an initial study of the method’s sensitivity was based on experiments under breath-holds. The agreement of obtained baseline OEF values with those from the literature, as well as the sensitivity of the method to task-induced changes, lays the foundation for a promising application of the developed sequence for the rapid and simultaneous quantification of T$_2$, T$_2$* and OEF in clinically relevant areas.


  • Department of Physics [130000]
  • Chair of Experimental Physics III B [133510]
  • [535000-5]