Mumuni, Abdul Nashirudeen

350 Pages·2013·7.33 MB·English

Mumuni, Abdul Nashirudeen (2013) Investigation of brain tissue water
NMR response by optimised quantitative single-voxel proton magnetic
resonance spectroscopy. PhD thesis.

http://theses.gla.ac.uk/4717/

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Glasgow Theses Service
http://theses.gla.ac.uk/
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Investigation of Brain Tissue Water NMR
Response by Optimised Quantitative Single-voxel
Proton Magnetic Resonance Spectroscopy

Abdul Nashirudeen Mumuni
B.Sc, M.Sc

A thesis submitted in partial fulfilment of the requirements for
the Degree of Doctor of Philosophy

Department of Clinical Physics
College of Medical, Veterinary and Life Sciences
University of Glasgow

June 2013

© Abdul Nashirudeen Mumuni, 2013
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Abstract

Nuclear Magnetic Resonance (NMR) is a phenomenon in which certain nuclei in
the presence of a magnetic field and radiofrequency (RF) radiation emit a
certain amount of signal at a frequency equal to that of the RF radiation.
Proton Magnetic Resonance Spectroscopy (1H-MRS) is an NMR technique capable
of measuring the chemical composition, often referred to as metabolites, of
the human body non-invasively and in vivo. It is commonly used as a research
tool in the investigation of neurological disorders such as multiple sclerosis,
brain tumors, stroke, clinical depression, and schizophrenia. Accurate
quantification of the metabolites of interest requires a reference standard of
known and fixed concentration.

Brain tissue water has been previously reported to have a fairly constant and
known concentration, and so has been suggested to be a suitable reference
concentration in absolute quantitative 1H-MRS of the human brain. In practice,
however, it is challenging to measure the actual tissue water concentration;
hence, some studies choose to use estimates of tissue water concentration
from the literature. These literature values are usually averages from a healthy
study group. There are however indications that brain tissue water content
could vary widely in certain disease conditions such as in brain tumors and
inflammation. In such situations, absolute metabolite quantification using the
literature estimates of tissue water content will be inaccurate while the
measurement of cerebral water content using the available techniques will be
impractical for the patients due to scanning time considerations. It is therefore
necessary to develop a technique that can be used to quantify both the
reference water and metabolite concentrations, simultaneously without
subject tolerance issues.

The main objective of this thesis was to investigate the response of water NMR
signal from human brain tissue under various measurement conditions using the
single-voxel 1H-MRS technique. As part of the investigation, the thesis also
focused on the development of methods for the absolute quantification of
cerebral water and metabolite concentrations.
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A standard 1H-MRS water-suppressed acquisition on the General Electric (GE)
MR scanner acquires some unsuppressed-water spectra at the beginning of the
PRESS pulse sequence. Using the Spectroscopy Analysis by GE (SAGE) software
package (version 7), this thesis developed methods to optimise the
unsuppressed-water and suppressed-water signals from which, respectively,
cerebral water and metabolite concentrations were estimated.

The unsuppressed-water signal response characteristics were investigated in
experiments at 3 T that involved: 1) variation of the MRS voxel position over a
three-dimensional RF field within an eight-channel head coil; 2) measurement
of the relaxation times of brain tissue water using standard saturation recovery
and multi spin-echo MRS techniques; 3) measurement of brain tissue water
content in peripheral inflammation; and 4) estimation of the BOLD effect on
the water spectral peak.

The stability of the MR scanner used for all the investigations was assessed.
Over the project period, the worst precision measurements of the scanner (for
both water and metabolite signals) were observed to be about 12 % and 26 % in
serial phantom and human studies, respectively. The MRI/MRS scanner was
therefore found to measure water and metabolite signals with good precision,
both in vivo and in vitro.

By recording the water NMR signal responses at various locations within the
phased-array head coil, RF sensitivity profile (voxel position-dependent)
equations of the head coil were obtained. The coordinates of any in vivo voxel
could be substituted into an appropriate profile equation to estimate an
unsuppressed-water signal area that could be used as a reference signal to
quantify brain tissue water content. This novel technique of quantifying
cerebral water content is superior to the previous techniques of performing
multi-echo unsuppressed-water signal acquisitions. The method does not
require extra unsuppressed-water acquisitions, or corrections for variations in
the sensitivity of the eight-channel head coil as both the in vivo and reference
signals are acquired from the same voxel position.
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Brain tissue water content was subsequently quantified accurately using the
newly developed method of referencing. In frontal brain voxels, the average
water content, WC of grey matter, GM was found to be higher than that of
white matter, WM (GM/WM WC ± SE = 46.37 ± 2.58/42.86 ± 2.46 mol/kg; p =
0.02); parietal voxels also showed a similar comparison (GM/WM WC ± SE =
37.23 ± 1.70/34.14 ± 2.02 mol/kg; p = 0.03). These findings were consistent
with previous reports of cerebral water content. For regions of mixed
proportions of grey and white matter tissues, the average water contents of
each tissue type considered separately (by voxel segmentation) and together
were found to compare with literature estimates. Using data from five voxel
positions, average brain tissue water content was observed to be uniformly
distributed across the human brain by one-way ANOVA (p = 0.60), and did not
vary significantly with gender (p > 0.05) and age (p > 0.05).

For the first time, cerebral water content was observed in this thesis to remain
fairly constant in psoriatic arthritis, a peripheral inflammatory condition (one-
way ANOVA, p = 0.63). Among five brain metabolites quantified in the psoriasis
patients, only the mean concentration of creatine, Cr was found to be
significantly lower in the frontal grey matter voxels of the patients, PsA
compared to healthy controls, HC at baseline (PsA/HC ± SE = 6.34 ± 0.38/7.78 ±
0.38 mM/kg; p = 0.01) and post-TNF-a blockade medication (PsA/HC ± SE =
6.69 ± 0.25/7.78 ± 0.38 mM/kg; p = 0.03). None of the metabolite
concentrations, including Cr (p = 0.27), changed significantly with medication.
The condition of PsA was not observed to affect the mood of the patients, as
indicated by their BDI scores. The significant finding of Cr concentration
alteration in psoriatic arthritis thus suggests that Cr may not be a reliable
denominator in studies of psoriasis that express the metabolite levels as ratios.

The T and T relaxation times of water and the metabolites were measured in
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the prefrontal grey matter (T /T ± SE = 1574 ± 61/147 ± 6 ms) and bilateral
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Hippocampi (T /T ± SE; left = 1475 ± 68/178 ± 83 ms, right = 1389 ± 58/273 ±
1 2
98 ms). The relaxation time estimates for the metabolites were in agreement
with literature values; relaxation times for water however were measured for
the first time in those regions and at 3 T. The measured relaxation times were
used to correct the water and metabolite signals for relaxation effects during
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their absolute quantification, and could as well serve the same purpose in
future studies.

There is increasing interest in the BOLD response of cerebral metabolites and
water during tasks. This thesis thus also assessed changes in brain tissue
metabolite and water contents while a subject experienced a visual stimulus.
In the presence of the visual stimulus, the BOLD effects on the metabolite and
water spectral peaks were found to be comparable, as has been observed in
previous studies. For the first time, this thesis further investigated the impact
of temporal resolution (determined by NEX) on the amount of the BOLD signal
acquired from cerebral water and metabolites. In a single visual activation
paradigm, the BOLD effect resulted in increased water peak area which
differed significantly between NEX values of 2 and 8 (p < 0.01); this observation
also was true for NAA and Glu. The findings thus suggest that temporal
resolution of the MRS data could result in significant differences in the results
of functional MRS studies.

In conclusion, by its detailed investigations of the water signal characteristics
and newly developed methods for the absolute quantification of cerebral water
and metabolite concentrations, this thesis has corroborated the suitability of
the brain tissue water signal as a reference and has also improved on the
accuracy of quantitative MRS using the endogenous water signal as a reference
standard. The techniques presented in this thesis can thus be applied in future
1H-MRS brain studies where the endogenous unsuppressed-water signal is
required.
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Table of Contents

Abstract ............................................................................................................ 2
Table of Contents ............................................................................................. 6
List of Tables .................................................................................................. 15
List of Figures ................................................................................................. 18
Acknowledgements ........................................................................................ 23
Author’s Declaration ....................................................................................... 25
List of Abbreviations/Definitions ...................................................................... 27
Chapter 1: Introduction ................................................................................... 32
1.1 Overview of MR Spectroscopy as Applied in this Thesis ...................... 32
1.1.1 Advances in MR Spectroscopy ....................................................... 32
1.1.2 MR Spectroscopy in Practice ......................................................... 34
1.1.3 Overview and Objective of this Thesis ............................................ 35
1.2 The Role of Water in Neurophysiology .................................................. 38
1.3 The Relevance of Tissue Water in MRI ................................................. 41
1.3.1 Proton Density ................................................................................ 41
1.3.2 Proton Relaxation ........................................................................... 42
1.3.3 Tissue-bound Protons .................................................................... 42
1.3.4 BOLD Contrast ............................................................................... 45
1.4 The Relevance of Tissue Water in MRS ............................................... 46
1.4.1 Reference Standard ....................................................................... 46
1.4.2 MRS Thermometry ......................................................................... 48
1.4.3 Eddy current correction .................................................................. 49
1.4.4 Signal Weighting in Phased-Array Coil Data Combination ............. 51
1.5 Structure and Outline of this Thesis ...................................................... 52
Chapter 2: Background ................................................................................... 54
2.1 Principles of Nuclear Magnetic Resonance ........................................... 54
2.1.1 Origin of the NMR Signal ................................................................ 55
2.1.1.1 Alignment of Magnetic Spins in B ........................................... 55
0
2.1.1.2 Irradiation of the B -aligned Spins with an RF Pulse ................ 57
0
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2.1.1.3 Generation of the NMR Signal ................................................. 59
2.1.2 Relaxation of the NMR Signal ........................................................ 60
2.1.2.1 T Relaxation ........................................................................... 61
1
2.1.2.2 T Relaxation ........................................................................... 62
2
2.1.2.3 T * Relaxation .......................................................................... 63
2
2.1.3 Methods of Measuring Relaxation .................................................. 64
2.1.3.1 Measurement of T Relaxation Time ........................................ 64
1
2.1.3.2 Measurement of T Relaxation Time ........................................ 67
2
2.2 Principles of MR Spectroscopy ............................................................. 69
2.2.1. Chemical Shift ............................................................................... 69
2.2.2 Spin-Spin Coupling ......................................................................... 71
2.2.3 Water Suppression and MRS Pulse Sequences ............................ 71
2.2.3.1 CHEmical Shift Selective (CHESS) Preparation ...................... 72
2.2.3.2 Point-RESolved Spectroscopy (PRESS) ................................. 73
2.2.3.3 STimulated Echo Acquisition Mode (STEAM) .......................... 75
2.2.4 Types of MRS Localisation ............................................................. 77
2.2.5 Echo Times .................................................................................... 78
2.2.6 Neurohistology, Brain Tissue Water and Metabolites ..................... 80
2.2.6.1 Water ....................................................................................... 81
2.2.6.2 myo-Inositol.............................................................................. 82
2.2.6.3 Choline-Containing Compounds .............................................. 83
2.2.6.4 Creatine ................................................................................... 84
2.2.6.5 Glutamate and Glutamine ........................................................ 85
2.2.6.6 N-Acetyl Aspartate ................................................................... 86
2.2.6.7 Lactate ..................................................................................... 87
2.2.6.8 Lipids and Macromolecules...................................................... 88
2.2.7 Challenges of in vivo MRS ............................................................. 88
2.2.7.1 Static Field Inhomogeneity ....................................................... 88
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2.2.7.2 Detection Sensitivity ................................................................. 89
2.2.7.3 Solvent Signal .......................................................................... 89
2.2.7.4 Eddy Currents .......................................................................... 90
2.2.7.5 Phase Detection ....................................................................... 91
2.2.7.6 Motion ...................................................................................... 91
2.3 Materials and Methods .......................................................................... 92
2.3.1 Overview of Spectral Analysis ........................................................ 92
2.3.1.1 Spectral Fitting in LC Model ..................................................... 95
2.3.1.2 Spectral Fitting in SAGE .......................................................... 96
2.3.1.3 Quantification of Water-suppressed and Unsuppressed-water
Spectra ................................................................................................ 98
2.3.2 Spectral Fitting Software used in this Thesis ................................ 100
2.3.3 The MRI Scanner, Head Coil and MRS Phantom......................... 100
2.3.4 Statistics in this Thesis ................................................................. 101
2.3.5 Ethical Approval of Human Studies .............................................. 103
Chapter 3: Reproducibility Measurements of Water and Metabolites ........... 105
3.1 Introduction and Objectives ................................................................. 105
3.2 Methods .............................................................................................. 107
3.2.1 PRESS versus STEAM ................................................................ 107
3.2.2 Reproducibility Studies ................................................................. 108
3.2.2.1 Phantom Studies .................................................................... 108
3.2.2.2 Human Studies ...................................................................... 109
3.2.3 Spectral Analyses in Reproducibility Studies ................................ 110
3.2.4 Assessment of Reproducibility ..................................................... 111
3.3 Results and Discussion ....................................................................... 111
3.3.1 PRESS versus STEAM SNRs Compared .................................... 111
3.3.2 Reproducibility Results ................................................................. 113
3.3.2.1 In vitro Measurements ........................................................... 113
3.3.2.2 Temperature Effect on in vitro Measurements ....................... 116
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3.3.2.3 In vivo Measurements ............................................................ 117
3.4 Summary and Conclusions ................................................................. 122
Chapter 4: RF Field Mapping Using the Unsuppressed-Water Signal .......... 124
4.1 Overview and Objectives .................................................................... 124
4.1.1 Absolute versus Relative Quantitative MRS ................................. 125
4.1.2 Internal versus External Referencing ............................................ 126
4.1.3 Spatial Sensitivity of the RF Coil................................................... 128
4.2 Methods .............................................................................................. 129
4.2.1 Sensitivity mapping along the RL axis .......................................... 130
4.2.2 Sensitivity mapping along the AP axis .......................................... 131
4.2.3 Sensitivity mapping along the SI axis ........................................... 132
4.2.4 Sensitivity mapping in the RL-AP plane along the SI axis ............ 132
4.2.5 Data Analysis ............................................................................... 134
4.2.6 Derivation of Sensitivity Maps ...................................................... 135
4.3 Results and Discussion ....................................................................... 135
4.3.1 RF Field Maps along the Principal Axes of the RF Coil ................ 135
4.3.2 Inter-slice RF Field Maps along the SI Axis of the RF Coil ........... 137
4.4 Use of RF Field Maps in Cerebral Water Quantification ...................... 143
4.5 Summary and Conclusions ................................................................. 143
Chapter 5: Corrections for Relaxation and Partial Volume Effects ............... 145
5.1 Overview and Objectives .................................................................... 145
5.1.1 NMR Relaxation Effects ............................................................... 146
5.1.2 Partial Recovery of Longitudinal Magnetisation of Water ............. 147
5.1.3 Partial Volume Effect .................................................................... 149
5.1.4 Objectives ..................................................................................... 151
5.2 Methods .............................................................................................. 152
5.2.1 Measurement of NMR Relaxation Times in the Brain ................... 152
5.2.1.1 Subjects ................................................................................. 152
5.2.1.2 MR Imaging............................................................................ 152