Optimization of the fat-water separation for muscle imaging at 7 T with application in quantitative Na23/K39 MRI

Type: MA thesis

Status: finished

Date: December 1, 2020 - June 1, 2021

Supervisors: Lena Gast, Armin Nagel, Andreas Maier

Magnetic Resonance Imaging (MRI) is a noninvasive imaging method, without ionizing radiation, which
has the ability to particularly resolve soft tissue such as muscle, fat, and connective tissue. Numerous
studies have shown the ability of MRI to detect alterations in skeletal muscle structure and composition,
for example, patients with Duchenne Muscular Dystrophy (DMD) [1]. The muscle destruction observed
in muscle dystrophy patients is associated with ion homeostasis dysregulation and chronic in
which leads ultimately to bro-fatty replacement of muscle tissue [2]. An increase in total sodium
concentration (TSC) has been observed in these patients in addition to elevated intra-cellular weighted
sodium signal (ICwS) based on an inversion recovery (IR) method. [3] Na23/K39 MRI detects a muscular
Na+ overload in these patients and thus it could depict early changes in the ion homeostasis in skeletal
muscle tissue of these patients. [2]
In this thesis, we aim to optimize the Na23/K39 quanti cation in muscle tissue by combining Na23/K39
MRI data with fat fractions (the proportion of the acquired signal derived from fat protons) obtained
by H1 MRI. As sodium and particularly potassium concentrations are strongly reduced in fat tissue
compared to muscle tissue, the Na23/K39 quanti cation in fat in ltrated muscles is generally distorted.
Thus, a fat correction needs to be applied to obtain the real ion concentrations of muscle tissue. This
can be achieved by applying the Multiple point Dixon technique for Water/Fat decomposition on the
H1 MRI Images acquired at 7T. The original fat quanti cation is based on the fact that fat and water
possess di erent resonance frequencies in MRI, which is called the Chemical Shift. Using a gradient
echo-based Dixon acquisition with very closely spaced echo times, the fat and water from these images
can be successfully separated using Dixon’s fat water separation algorithm [4]. It is based on the
principle that the signal in the image acquired when the water and fat have the same phase, interfere
constructively whereas the images acquired when water and fat are in opposed phase they interfere
destructively. Thus fat in ltration in the muscle tissue of a muscle dystrophy patient could be studied
using the Fat fraction [5].
The goal of the thesis is to create an image processing protocol at 7T correctly maps the fat and
water in the calf muscles and generate a fat-fraction which can further be used on the Na23 images where
both the 1H and Na23 images are acquired at a 7T MRI. Currently, no such protocols exist at 7T, and
adapting them from 3T comes with various challenges. This thesis aims to e ectively facilitate easy and
early diagnosis for various muscular dystrophies.
The following points will be covered in this thesis:
1. Design and production of a measurement phantom
(a) Prerequisites: Multiple compartments (e.g. cylinders) containing di erent fat-water fractions,
size tting into 1H knee coil @ 7T (and other typical 1H coils, e.g. @3T)
(b) Research on typical fat-fractions in muscle tissue/materials suitable for achieving di erent
fat fractions/phantoms used in other publications on fat-water imaging; and thereby design
the phantom.
2. Optimization of measurement protocol for fat-water imaging at 7T
(a) Compare and evaluate existing H1 MRI acquisition protocols for fat-water separation at 3T,
choose the most suitable .rotocol to be translated to 7T.
(b) Optimize multiple-echo acquisition protocols by calculating optimized TEs for fat-water separation
at 7T.
3. Optimization of post-processing for fat-water imaging
(a) Comparison of di erent algorithms for fat-water separation using the ISMRM fat-water toolbox.
(b) Study e ects of B0 inhomogeneities using di erent B0 shimming protocols to resolve phase
wrapping artifacts.
4. Application of fat-water imaging in vivo
Application of optimized fat-water imaging protocol to healthy subjects (approx. 5); Quanti cation
of fat fraction in healthy muscle tissue and comparison of results to literature; Maybe (towards
the end of thesis): application to patients with muscular dystrophies
5. Comparison of fat-water imaging at di erent eld strengths
Optimize protocol (or use existing protocols from literature) for di erent eld strengths, e.g.3T
and 7T; Compare resulting fat fraction values in phantom and in vivo measurements (healthy

[1] Erika L. Finanger, Barry Russman, Sean C. Forbes, William D. Rooney, Glenn A.Walter, and Krista
Vandenborne. Use of skeletal muscle mri in diagnosis and monitoring disease progression in duchenne
muscular dystrophy. Physical medicine and rehabilitation clinics of North America, 23(1):1{ix, 2012.
[2] Teresa Gerhalter, Lena V. Gast, Benjamin Marty, Jan Martin, Regina Trollmann, Stephanie
Schussler, Frank Roemer, Frederik B. Laun, Michael Uder, Rolf Schroder, Pierre G. Carlier, and
Armin M. Nagel. 23na mri depicts early changes in ion homeostasis in skeletal muscle tissue of patients
with duchenne muscular dystrophy. Journal of Magnetic Resonance Imaging, 50(4):1103{1113,
[3] Armin M. Nagel, Marc-Andre Weber, Arijitt Borthakur, and Ravinder Reddy. Skeletal Muscle MR
Imaging Beyond Protons: With a Focus on Sodium MRI in Musculoskeletal Applications, pages
115{133. Springer Berlin Heidelberg, Berlin, Heidelberg, 2014.
[4] W. T. Dixon. Simple proton spectroscopic imaging. Radiology, 153(1):189{94, 1984.
[5] T. J. Bray, M. D. Chouhan, S. Punwani, A. Bainbridge, and M. A. Hall-Craggs. Fat fraction mapping
using magnetic resonance imaging: insight into pathophysiology. Br J Radiol, 91(1089):20170344,