Refine
Has Fulltext
- yes (19)
Is part of the Bibliography
- yes (19)
Year of publication
Document Type
- Doctoral Thesis (19)
Language
- English (19) (remove)
Keywords
- Kernspintomografie (19) (remove)
Institute
- Physikalisches Institut (9)
- Graduate School of Life Sciences (8)
- Institut für diagnostische und interventionelle Radiologie (Institut für Röntgendiagnostik) (2)
- Deutsches Zentrum für Herzinsuffizienz (DZHI) (1)
- Graduate School of Science and Technology (1)
- Klinik und Poliklinik für Psychiatrie, Psychosomatik und Psychotherapie (1)
- Medizinische Klinik (bis 2004) (1)
Sonstige beteiligte Institutionen
Myocardial infarction (MI) is a leading cause of death worldwide. Timely restoration of coronary blood flow to ischemic myocardium significantly reduces acute infarct mortality and attenuates ventricular remodeling. However, surviving MI patients frequently develop heart failure, which is associated with reduced quality of life, high mortality rate (10% annually), as well as high healthcare expenditures. The main processes involved in the evolution of heart failure post-MI are the great loss of contractile cardiomyocytes during ischemia-reperfusion and the subsequent complex structural and functional alterations, which are rooted in modifications at molecular and cellular levels in both the infarcted and non-infarcted myocardium. However, we still lack efficient treatments to prevent the development and progression of left ventricular remodeling. The improved survival rate of acute MI patients combined with the lack of effective therapy for post-MI remodeling contributes to the high prevalence of heart failure. Cardiac Magnetic Resonance Imaging (MRI) is an important tool for diagnosis and assessment of MI. With the advancement of this technology, the frontier of MRI has been extended to probing molecular and cellular events in vivo and non-invasively. In combination with assessment of morphology and function, the visualization of essential molecular and cellular markers in vivo could provide comprehensive, multifaceted views of the healing process in infarcted hearts, which might give new insight for the treatment of acute MI. In this thesis, molecular and cellular cardiac MRI methods were established to visualize and investigate inflammation and calcium flux in the healing process of acute MI in vivo, in a clinically relevant rat model.
This work considered the frequency-modulated balanced steady-state free precession (fm-bSSFP) sequence as a tool to provide banding free bSSFP MR images. The sequence was implemented and successfully applied to suppress bandings in various in vitro and in vivo examples. In combination with a radial trajectory it is a promising alternative for standard bSSFP applications. First, two specialized applications were shown to establish the benefits of the acquisition strategy in itself. In real time cardiac imaging, it was shown that the continuous shift in frequency causes a movement of the bandings across the FOV. Thus, no anatomical region is constantly impaired, and a suitable timeframe can be found to examine all important structures. Furthermore, a combination of images with different artifact positions, similar to phase-cycled acquisitions is possible. In this way, fast, banding-free imaging of the moving heart was realized. Second, acquisitions with long TR were shown. While standard bSSFP suffers from increasing incidence of bandings with higher TR values, the frequency-modulated approach provided banding free images, regardless of the TR.
A huge disadvantage of fm-bSSFP, in combination with the radial trajectory, is the decrease in signal intensity. In this work a specialized reconstruction method, the multifrequency reconstruction for frequency-modulated bSSFP (Muffm), was established, which successfully compensated that phenomena. The application of Muffm to several anatomical sites, such as inner ear, legs and cardiac acquisitions, proofed the advantageous SNR of the reconstruction.
Furthermore, fm-bSSFP was applied to the clinically highly relevant task of water-fat separation. Former approaches of a phase-sensitive separation procedure in combination with standard bSSFP showed promising results but failed in cases of high inhomogeneity or high field strengths where banding artifacts become a major issue. The novel approach of using the fm-bSSFP acquisition strategy with the separation approach provided robust, reliable images of high quality. Again, losses in signal intensity could be regained by Muffm, as both approaches are completely compatible.
Opposed to conventional banding suppression techniques, like frequency-scouts or phase-cycling, all reconstruction methods established in this work rely on a single radial acquisition, with scan times similar to standard bSSFP scans. No prolonged measurement times occur and patient time in the scanner is kept as short as possible, improving patient comfort, susceptibility to motion or physiological noise and cost of one scan.
All in all, the frequency-modulated acquisition in combination with specializes reconstruction methods, leads to a completely new quality of images with short acquisition times.
The subject of this work was to develop, implement, optimize and apply methods for quantitative MR imaging of tumors. In the context of functional and physiological characterization, this implied transferring techniques established in tumor model research to human subjects and assessing their feasibility for use in patients. In the context of the morphologic assessment and parameter imaging of tumors, novel concepts and techniques were developed, which facilitated the simultaneous quantification of multiple MR parameters, the generation of “synthetic” MR images with various contrasts, and the fast single-shot acquisition of purely T2-weighted images.
This work deals with the acceleration of cardiovascular MRI for the assessment
of functional information in steady-state contrast and for viability assessment
during the inversion recovery of the magnetization. Two approaches
are introduced and discussed in detail. MOCO-MAP uses an exponential
model to recover dynamic image data, IR-CRISPI, with its low-rank plus
sparse reconstruction, is related to compressed sensing.
MOCO-MAP is a successor to model-based acceleration of parametermapping
(MAP) for the application in the myocardial region. To this end, it
was augmented with a motion correction (MOCO) step to allow exponential
fitting the signal of a still object in temporal direction. Iteratively, this
introduction of prior physical knowledge together with the enforcement of
consistency with the measured data can be used to reconstruct an image
series from distinctly shorter sampling time than the standard exam (< 3 s
opposed to about 10 s). Results show feasibility of the method as well as
detectability of delayed enhancement in the myocardium, but also significant
discrepancies when imaging cardiac function and artifacts caused already by
minor inaccuracy of the motion correction.
IR-CRISPI was developed from CRISPI, which is a real-time protocol
specifically designed for functional evaluation of image data in steady-state
contrast. With a reconstruction based on the separate calculation of low-rank
and sparse part, it employs a softer constraint than the strict exponential
model, which was possible due to sufficient temporal sampling density via
spiral acquisition. The low-rank plus sparse reconstruction is fit for the use on
dynamic and on inversion recovery data. Thus, motion correction is rendered
unnecessary with it.
IR-CRISPI was equipped with noise suppression via spatial wavelet filtering.
A study comprising 10 patients with cardiac disease show medical
applicability. A comparison with performed traditional reference exams offer
insight into diagnostic benefits. Especially regarding patients with difficulty
to hold their breath, the real-time manner of the IR-CRISPI acquisition provides
a valuable alternative and an increase in robustness.
In conclusion, especially with IR-CRISPI in free breathing, a major acceleration
of the cardiovascular MR exam could be realized. In an acquisition
of less than 100 s, it not only includes the information of two traditional
protocols (cine and LGE), which take up more than 9.6 min, but also allows
adjustment of TI in retrospect and yields lower artifact level with similar
image quality.
In Magnetic Resonance Imaging (MRI), acquisition of dynamic data may be highly complex due to rapid changes occurred in the object to be imaged. For clinical diagnostic, dynamic MR images require both high spatial and temporal resolution. The speed in the acquisition is a crucial factor to capture optimally dynamics of the objects to obtain accurate diagnosis. In the 90’s, partially parallel MRI (pMRI) has been introduced to shorten scan times reducing the amount of acquired data. These approaches use multi-receiver coil arrays to acquire independently and simultaneously the data.
Reduction in the amount of acquired data results in images with aliasing artifacts. Dedicated methods as such Sensitivity Encoding (SENSE) and Generalized Autocalibrating Partially Parallel Acquisition (GRAPPA) were the basis of a series of algorithms in pMRI.
Nevertheless, pMRI methods require extra spatial or temporal information in order to optimally reconstruct the data. This information is typically obtained by an extra scan or embedded in the accelerated acquisition applying a variable density acquisition scheme.
In this work, we were able to reduce or totally eliminate the acquisition of the training data for kt-SENSE and kt-PCA algorithms obtaining accurate reconstructions with high temporal fidelity.
For dynamic data acquired in an interleaved fashion, the temporal average of accelerated data can generate an artifact-free image used to estimate the coil sensitivity maps avoiding the need of extra acquisitions. However, this temporal average contains errors from aliased components, which may lead to signal nulls along the spectra of reconstructions when methods like kt-SENSE are applied. The use of a GRAPPA filter applied to the temporal average reduces these errors and subsequently may reduce the null components in the reconstructed data. In this thesis the effect of using temporal averages from radial data was investigated. Non-periodic artifacts performed by undersampling radial data allow a more accurate estimation of the true temporal average and thereby avoiding undesirable temporal filtering in the reconstructed images. kt-SENSE exploits not only spatial coil sensitivity variations but also makes use of spatio-temporal correlations in order to separate the aliased signals. Spatio-temporal correlations in kt-SENSE are learnt using a training data set, which consists of several central k-space lines acquired in a separate scan. The scan of these extra lines results in longer acquisition times even for low resolution images. It was demonstrate that limited spatial resolution of training data set may lead to temporal filtering effects (or temporal blurring) in the reconstructed data.
In this thesis, the auto-calibration for kt-SENSE was proposed and its feasibility was tested in order to completely eliminate the acquisition of training data. The application of a prior TSENSE reconstruction produces the training data set for the kt-SENSE algorithm. These training data have full spatial resolution. Furthermore, it was demonstrated that the proposed auto-calibrating method reduces significantly temporal filtering in the reconstructed images compared to conventional kt-SENSE reconstructions employing low resolution training images. However, the performance of auto-calibrating kt-SENSE is affected by the Signal-to-Noise Ratio (SNR) of the first pass reconstructions that propagates to the final reconstructions.
Another dedicated method used in dynamic MRI applications is kt-PCA, that was first proposed for the reconstruction of MR cardiac data. In this thesis, kt-PCA was employed for the generation of spatially resolved M0, T1 and T2 maps from a single accelerated IRTrueFISP or IR-Snapshot FLASH measurement. In contrast to cardiac dynamic data, MR relaxometry experiments exhibit signal at all temporal frequencies, which makes their reconstruction more challenging. However, since relaxometry measurements can be represented by only few parameters, the use of few principal components (PC) in the kt-PCA algorithm can significantly simplify the reconstruction. Furthermore, it was found that due to high redundancy in relaxometry data, PCA can efficiently extract the required information from just a single line of training data.
It has been demonstrated in this thesis that auto-calibrating kt-SENSE is able to obtain high temporal fidelity dynamic cardiac reconstructions from moderate accelerated data avoiding the extra acquisition of training data. Additionally, kt-PCA has been proved to be a suitable method for the reconstruction of highly accelerated MR relaxometry data.
Furthermore, a single central training line is necessary to obtain accurate reconstructions. Both reconstruction methods are promising for the optimization of training data acquisition and seem to be feasible for several clinical applications.
Fulminant myocarditis is rare but a potentially life-threatening disease. Acute or mild myocarditis following acute ischemia is generally associated with a profound activation of the host’s immune system. On one hand this is mandatory to protect the host’s heart by fighting the invading agents (i.e., bacteria, viruses or other microbial agents) and/or to induce healing and repair processes in the damaged myocardium. On other hand, uncontrolled activation of the immune system may result in the generation of auto-reactive (not always beneficial) immune cells.
Myocarditis or inflammatory cardiomyopathy is characterized by focal or diffuse infiltrates, myocyte necrosis and/or apoptosis and subsequent fibrotic replacement of the heart muscle. In humans, about 30% of the myocarditis-patients develop dilated cardiomyopathy. As the clinical picture of myocarditis is multifaceted, it is difficult to diagnose the disease. Therefore, the main goal of the present work was to test and further develop novel non-invasive methods for the detection of myocardial inflammation by employing both contrast enhanced MRI techniques as well as novel nuclear tracers that are suitable for in vivo PET/ SPECT imaging.
As a part of this thesis, a pre-clinical animal model was successfully established by immunizing female Lewis rats with whole-porcine cardiac myosin (CM). Induction of Experimental Autoimmune Myocarditis (EAM) is considered successful when anti-myosin antibody titers are increased more than 100-fold over control animals and pericardial effusion develops. In addition, cardiac tissues from EAM-rats versus controls were analyzed for the expression of various pro-inflammatory and fibrosis markers. To further exploit non-invasive MRI techniques for the detection of myocarditis, our EAM-rats were injected either with (1) ultra-small Paramagnetic iron oxide particles (USPIO’s; Feraheme®), allowing for in vivo imaging , (2) micron sized paramagnetic iron oxide particles (MPIO) for ex vivo inflammatory cell-tracking by cMRI, or (3) with different radioactive nuclear tracers (67gallium citrate, 68gallium-labeled somatostatin analogue, and 68gallium-labeled cyclic RGD-peptide) which in the present work have been employed for autoradiographic imaging, but in principle are also suitable for in vivo nuclear imaging (PET/SPECT). In order to compare imaging results with histology, consecutive heart sections were stained with hematoxylin & eosin (HE, for cell infiltrates) and Masson Goldner trichrome (MGT, for fibrosis); in addition, immuno-stainings were performed with anti-CD68 (macrophages), anti-SSRT2A (somatostatin receptor type 2A), anti-CD61 (β3-integrins) and anti-CD31 (platelet endothelial cell adhesion molecule 1).
Sera from immunized rats strongly reacted with cardiac myosin. In immunized rats, echocardiography and subsequent MRI revealed huge amounts of pericardial effusion (days 18-21). Analysis of the kinetics of myocardial infiltrates revealed maximal macrophage invasion between days 14 and 28. Disappearance of macrophages resulted in replacement-fibrosis in formerly cell-infiltrated myocardial areas. This finding was confirmed by the time-dependent differential expression of corresponding cytokines in the myocardium. Immunized animals reacted either with an early or a late pattern of post-inflammation fibrosis. Areas with massive cellular infiltrates were easily detectible in autoradiograms showing a high focal uptake of 67gallium-citrate and 68gallium labeled somatostatin analogues (68Ga DOTA-TATE). Myocardium with a loss of cardiomyocytes presented a high uptake of 68gallium labeled cyclic RGD-peptide (68Ga NOTA-RGD). MRI cell tracking experiments with Feraheme® as the contrast-agent were inconclusive; however, strikingly better results were obtained when MPIOs were used as a contrast-agent: histological findings correlated well with in vivo and ex vivo MPIO-enhanced MRI images.
Imaging of myocardial inflammatory processes including the kinetics of macrophage invasion after microbial or ischemic damage is still a major challenge in, both animal models and in human patients. By applying a broad panel of biochemical, histological, molecular and imaging methods, we show here that different patterns of reactivity may occur upon induction of myocarditis using one and the same rat strain. In particular, immunized Lewis rats may react either with an early or a late pattern of macrophage invasion and subsequent post-inflammation fibrosis. Imaging results achieved in the acute inflammatory phase of the myocarditis with MPIOs, 67gallium citrate and 68gallium linked to somatostatin will stimulate further development of contrast agents and radioactive-nuclear tracers for the non-invasive detection of acute myocarditis and in the near future perhaps even in human patients.
Magnetic Resonance Imaging (MRI) is a non-invasive medical imaging technique, that is rou- tinely used in clinical practice for detection and diagnosis of a wide range of different diseases. In MRI, no ionizing radiation is used, making even repeated application unproblematic. This is an important advantage over other common imaging methods such as X-rays and Computer To- mography. One major drawback of MRI, however, are long acquisition times and associated high costs of experiments. Since the introduction of MRI, several important technical developments have been made to successfully reduce acquisition times. In this work, novel approaches were developed to increase the efficiency of MRI acquisitions.
In Chapter 4, an improved radial turbo spin-echo (TSE) combined acquisition and reconstruction strategy was introduced. Cartesian turbo spin-echo sequences [3] are widely used especially for the detection and diagnosis of neurological pathologies, as they provide high SNR images with both clinically important proton density and T2 contrasts. TSE acquisitions combined with radial sampling are very efficient, since it is possible to obtain a number of ETL images with different contrasts from a single radial TSE measurement [56–58]. Conventionally, images with a particular contrast are obtained from both radial and Cartesian TSE acquisitions by combining data from different echo times into a single image. In the radial case, this can be achieved by employing k-space weighted image contrast (KWIC) reconstruction. In KWIC, the center region of k-space is filled exclusively with data belonging to the desired contrast while outer regions also are assembled with data acquired at other echo times. However, this data sharing leads to mixed contrast contributions to both Cartesian and radial TSE images. This is true especially for proton density weighted images and therefore may reduce their diagnostic value.
In the proposed method, an adapted golden angle reordering scheme is introduced for radial TSE acquisitions, that allows a free choice of the echo train length and provides high flexibility in image reconstruction. Unwanted contrast contaminations are greatly reduced by employing a narrow-band KWIC filter, that restricts data sharing to a small temporal window around the de- sired echo time. This corresponds to using fewer data than required for fully sampled images and consequently leads to images exhibiting aliasing artifacts. In a second step, aliasing-free images are obtained using parallel imaging. In the neurological examples presented, the CG-SENSE algorithm [42] was chosen due to its stable convergence properties and its ability to reconstruct arbitrarily sampled data. In simulations as well as in different in vivo neurological applications, no unwanted contrast contributions could be observed in radial TSE images reconstructed with the proposed method. Since this novel approach is easy to implement on today’s scanners and requires low computational power, it might be valuable for the clinical breakthrough of radial TSE acquisitions.
In Chapter 5, an auto-calibrating method was introduced to correct for stimulated echo contribu- tions to T2 estimates from a mono-exponential fit of multi spin-echo (MSE) data. Quantification of T2 is a useful tool in clinical routine for the detection and diagnosis of diseases as well as for tis- sue characterization. Due to technical imperfections, refocusing flip angles in a MSE acquisition deviate from the ideal value of 180○. This gives rise to significant stimulated echo contributions to the overall signal evolution. Therefore, T2 estimates obtained from MSE acquisitions typically are notably higher than the reference. To obtain accurate T2 estimates from MSE acquisitions, MSE signal amplitudes can be predicted using the extended phase graph (EPG, [23, 24]) algo- rithm. Subsequently, a correction factor can be obtained from the simulated EPG T2 value and applied to the MSE T2 estimates. However, EPG calculations require knowledge about refocus- ing pulse amplitudes, T2 and T1 values and the temporal spacing of subsequent echoes. While the echo spacing is known and, as shown in simulations, an approximate T1 value can be assumed for high ratios of T1/T2 without compromising accuracy of the results, the remaining two parameters are estimated from the data themselves. An estimate for the refocusing flip angle can be obtained from the signal intensity ratio of the second to the first echo using EPG. A conventional mono- exponential fit of the MSE data yields a first estimate for T2. The T2 correction is then obtained iteratively by updating the T2 value used for EPG calculations in each step. For all examples pre- sented, two iterations proved to be sufficient for convergence. In the proposed method, a mean flip angle is extracted across the slice. As shown in simulations, this assumption leads to greatly reduced deviations even for more inhomogeneous slice profiles. The accuracy of corrected T2 values was shown in experiments using a phantom consisting of bottles filled with liquids with a wide range of different T2 values. While T2 MSE estimates were shown to deviate significantly from the spin-echo reference values, this is not the case for corrected T2 values. Furthermore, applicability was demonstrated for in vivo neurological experiments.
In Chapter 6, a new auto-calibrating parallel imaging method called iterative GROG was pre- sented for the reconstruction of non-Cartesian data. A wide range of different non-Cartesian schemes have been proposed for data acquisition in MRI, that present various advantages over conventional Cartesian sampling such as faster acquisitions, improved dynamic imaging and in- trinsic motion correction. However, one drawback of non-Cartesian data is the more complicated reconstruction, which is ever more problematic for non-Cartesian parallel imaging techniques. Iterative GROG uses Calibrationless Parallel Imaging by Structured Low-Rank Matrix Completion (CPI) for data reconstruction. Since CPI requires points on a Cartesian grid, it cannot be used to directly reconstruct non-Cartesian data. Instead, Grappa Operator Gridding (GROG) is employed in a first step to move the non-Cartesian points to the nearest Cartesian grid locations. However, GROG requires a fully sampled center region of k-space for calibration. Combining both methods in an iterative scheme, accurate GROG weights can be obtained even from highly undersampled non-Cartesian data. Subsequently, CPI can be used to reconstruct either full k- space or a calibration area of arbitrary size, which can then be employed for data reconstruction with conventional parallel imaging methods.
In Chapter 7, a new 2D sampling scheme was introduced consisting of multiple oscillating effi- cient trajectories (MOET), that is optimized for Compressed Sensing (CS) reconstructions. For successful CS reconstruction of a particular data set, some requirements have to be met. First, ev- ery data sample has to carry information about the whole object, which is automatically fulfilled for the Fourier sampling employed in MRI. Additionally, the image to be reconstructed has to be sparse in an arbitrary domain, which is true for a number of different applications. Last, data sam- pling has to be performed in an incoherent fashion. For 2D imaging, this important requirement of CS is difficult to achieve with conventional Cartesian and non-Cartesian sampling schemes. Ra- dial sampling is often used for CS reconstructions of dynamic data despite the streaking present in undersampled images. To obtain incoherent aliasing artifacts in undersampled images while at the same time preserving the advantages of radial sampling for dynamic imaging, MOET com- bines radial spokes with oscillating gradients of varying amplitude and alternating orientation orthogonal to the readout direction. The advantage of MOET over radial sampling in CS re- constructions was demonstrated in simulations and in in vivo cardiac imaging. MOET provides superior results especially when used in CS reconstructions with a sparsity constraint directly in image space. Here, accurate results could be obtained even from few MOET projections, while the coherent streaking artifacts present in the case of radial sampling prevent image recovery even for smaller acceleration factors. For CS reconstructions of dynamic data with sparsity constraint in xf-space, the advantage of MOET is smaller since the temporal reordering is responsible for an important part of incoherency. However, as was shown in simulations of a moving phantom and in the reconstruction of ungated cardiac data, the additional spatial incoherency provided by MOET still leads to improved results with higher accuracy and may allow reconstructions with higher acceleration factors.
The noninvasive magnetic resonance imaging technique allows for the investigation of functional processes in the living plant. For this purpose during this work, different NMR imaging methods were further developed and applied.
For the localisation of the intrusion of water into the germinating rape seed with the simultaneous depiction of the lipid-rich tissue via a 3D rendering, in Chap. 5 the technique of interleaved chemical selective acquisition of water and lipid was used in the germinating seed. The utilization of high-resolution MR images of germinated seeds enabled the localization of a predetermined water gap in the lipid-rich aleurone layer, which resides directly under the seed coat. The for a long time in biology prevalent discussion, whether such a gap exists or the seed soaks up the water from all sides, rather like a sponge, could hereby, at least for the rapeseed seed, be answered clearly. Furthermore, the segmentation and 3D visualization of the vascular tissue in the rapeseed seeds was enabled by the high-resolution datasets, a multiply branched structure preconstructed in the seed could be shown. The water is directed by the vascular tissue and thus awakens the seed gradually to life. This re-awakening could as well be tracked by means of invasive imaging via an oxygen sensor. In the re-awakened seeds, the lipid degradation starts, other than expected, not in the lipid-rich cotyledons but in the residual endosperm remaining from seed development and in the aleurone layer which previously protected the embryo. Within this layer, the degradation could be verified in the high-resolution MR datasets.
The method presented in Chap. 6 provides a further characteristic trait for phenotyping of seeds and lipid containing plants in general. The visualization of the compounds of fatty acids in plant seeds and fruits could be achieved by the distinct utilization of chemical shift-selective imaging techniques. Via the application of a CSI sequence the fatty acid compounds in an olive were localized in a 2D slice. In conjunction with an individually adjusted CHESS presaturation module Haa85 the high-resolution 3D visualization of saturated and unsaturated fatty acid compounds in different seeds was achieved. The ratio maps calculated from these datasets allow to draw conclusions from the developmental stage or the type of seed. Furthermore, it could be shown that the storage condition of two soybean seeds with different storage time durations lead to no degradation of the fatty acid content.
Additional structural information from inside of dry seeds are now accessible via MRI. In this work the imaging of cereal seeds could be significantly improved by the application of the UTE sequence. The hitherto existing depictions of the lipid distribution, acquired with the spin echo sequence, were always sufficient for examinations of the lipid content, yet defects in the starchy endosperm or differences in the starch concentration within the seed remained constantly unseen with this technique. In a direct comparison of the datasets acquired with the previous imaging technique (spin echo) and with UTE imaging, the advantage of data acquisition with UTE could be shown. By investigating the potential seed compounds (starch, proteins, sugar) in pure form, the constituent parts contributing to the signal could be identified as bound water (residual moisture) and starch. The application of a bi-exponential fit on the datasets of the barley seed enabled the separate mapping of magnetization and of relaxation time of two components contributing to the NMR signal. The direct comparison with histological stainings verified the previous results, thus this technique can be used for the selective imaging of starch in dry seeds.
Conclusions on the translocation characteristics in plants can be drawn by the technique proposed in Chap. 8. The associated translocation velocities can now, even in the range of several um/h, be determined in the living plant. Based on calculated concentrations of an MR contrast agent, which was taken up by the plant, these translocation velocities were estimated both in longitudinal direction, thus along the vascular bundle, and in horizontal direction, thus out of the bundle. The latter velocity is located below the contrast agent's velocity value of free diffusion. By adjusting a dynamic contrast-enhancing imaging technique (DCE-Imaging, Tof91) the acquisition duration of a T1-map was significantly reduced. By means of these maps, local concentrations of the contrast agent in plant stems and the siliques of the rapeseed plant could be determined.
Numerous questions in plant science can only be answered by non-invasive techniques such as MRI. For this reason, besides the experimental results achieved in this work, further NMR methods were tested and provided for the investigation of plants.
As an example, the study on the imaging of magnetic exchange processes are mentioned, which provided the groundwork for a possible transfer of CEST experiments (Chemical Exchange Saturation Transfer) to the plant. The results are presented in the bachelor thesis of A. Jäger Jae17, which was performed under my supervision, they find great interest under biologists.
The development of new technologies, which extend the possibilities for the investigation of living organisms, is of great importance. For this reason, I have contributed to the development of the currently unpublished method RACETE (Refocused Acquisition of Chemical Exchange Transferred Excitations [Jak17, Reu17, Gut18a]). By rephasing the transferred magnetization the utilization of properties which have not been available in chemical "`exchange"' experiments is enabled. With this method a positive contrast is generated, thus a reference experiment is not mandatory. Furthermore, the image phase, which in classical experiments contains no information about the exchanged protons, can be used for the distinct identification of multiple substances which have been excited simultaneously.
This recently at the Department of Experimental Physics V developed method can be used in particular for the identification of lipids and for the localization of sugars and amino acids, thus it can serve the enhancement and improvement of non-invasive analytical methods.
Morphological and Functional Ultrashort Echo Time (UTE) Magnetic Resonance Imaging of the Human Lung
(2019)
In this thesis, a 3D Ultrashort echo time (3D-UTE) sequence was introduced in the Self-gated Non-Contrast-Enhanced Functional Lung Imaging (SENCEFUL) framework. The sequence was developed and implemented on a 3 Tesla MR scanner. The 3D-UTE technique consisted of a nonselective RF pulse followed by a koosh ball quasi-random sampling order of the k-space. Measurements in free-breathing and without contrast agent were performed in healthy subjects and a patient with lung cancer.
A gating technique, using a combination of different coils with high signal correlation, was evaluated in-vivo and compared with a manual approach of coil selection. The gating signal offered an estimation of the breathing motion during measurement and was used as a reference to segment the acquired data into different breathing phases.
Gradient delays and trajectory errors were corrected during post-processing using the Gradient Impulse Response Function. Iterative SENSE was then applied to determine the fully sampled data.
In order to eliminate signal changes caused by motion, a 3D image registration was employed, and the results were compared to a 2D image registration method.
Ventilation was assessed in 3D and regionally quantified by monitoring the signal changes in the lung parenchyma. Finally, image quality and quantitative ventilation values were compared to the standard 2D-SENCEFUL technique.
3D-UTE, combined with an automatic gating technique and SENCEFUL MRI, offered ventilation maps with high spatial resolution and SNR. Compared to the 2D method, UTE-SENCEFUL greatly improved the clinical quality of the structural images and the visualization of the lung parenchyma.
Through‐plane motion, partial volume effects and ventilation artifacts were also reduced with a three-dimensional method for image registration.
UTE-SENCEFUL was also able to quantify regional ventilation and presented similar results to previous studies.
Acceleration is a central aim of clinical and technical research in magnetic resonance imaging (MRI) today, with the potential to increase robustness, accessibility and patient comfort, reduce cost, and enable entirely new kinds of examinations. A key component in this endeavor is image reconstruction, as most modern approaches build on advanced signal and image processing. Here, deep learning (DL)-based methods have recently shown considerable potential, with numerous publications demonstrating benefits for MRI reconstruction. However, these methods often come at the cost of an increased risk for subtle yet critical errors. Therefore, the aim of this thesis is to advance DL-based MRI reconstruction, while ensuring high quality and fidelity with measured data. A network architecture specifically suited for this purpose is the variational network (VN). To investigate the benefits these can bring to non-Cartesian cardiac imaging, the first part presents an application of VNs, which were specifically adapted to the reconstruction of accelerated spiral acquisitions. The proposed method is compared to a segmented exam, a U-Net and a compressed sensing (CS) model using qualitative and quantitative measures. While the U-Net performed poorly, the VN as well as the CS reconstruction showed good output quality. In functional cardiac imaging, the proposed real-time method with VN reconstruction substantially accelerates examinations over the gold-standard, from over 10 to just 1 minute. Clinical parameters agreed on average.
Generally in MRI reconstruction, the assessment of image quality is complex, in particular for modern non-linear methods. Therefore, advanced techniques for precise evaluation of quality were subsequently demonstrated.
With two distinct methods, resolution and amplification or suppression of noise are quantified locally in each pixel of a reconstruction. Using these, local maps of resolution and noise in parallel imaging (GRAPPA), CS, U-Net and VN reconstructions were determined for MR images of the brain. In the tested images, GRAPPA delivers uniform and ideal resolution, but amplifies noise noticeably. The other methods adapt their behavior to image structure, where different levels of local blurring were observed at edges compared to homogeneous areas, and noise was suppressed except at edges. Overall, VNs were found to combine a number of advantageous properties, including a good trade-off between resolution and noise, fast reconstruction times, and high overall image quality and fidelity of the produced output. Therefore, this network architecture seems highly promising for MRI reconstruction.