B1+-mapping and B1+ inhomogeneity correction at high field

Magnetic resonance images acquired at the highest strength of the main magnetic field B0 are of interest since they highly benefit from an increased signal to noise ratio. At ultra high field strengths (B0 > 7 Tesla) images with more contrast and higher resolution can thus be obtained, opening new insights into the understanding of organ structures and disease evolutions. One of the main challenges of ultra high field MR imaging is that the wavelength of MR radiations starts to be shorter than the typical organs of interest. At such wavelength, the transmit magnetic field B1+ used to manipulate the magnetization in MR imaging is subject to constructive and destructive interferences and becomes position dependent. This inhomogeneity in the B1+ field leads to signal and contrast variations in the anatomical images which are prone to misinterpretation. This thesis is about measuring and correcting the inhomogeneous B1+ field at 7 Tesla. To be able to correct the B1+ inhomogeneity, it is necessary to measure it first. An appropriate B1+-mapping sequence should provide accurate measurements in a wide range of B1+ values in a short amount of time since the acquisition of the B1+ distribution can be considered as an adjustment step. The SA2RAGE sequence was developed according to these criteria, allowing a typical three-dimensional B1+ map to be acquired in less than 2min. The next challenge was to correct the B1+ inhomogeneity observed across the brain at 7 Tesla. To obtain results of high quality, RF pulses were designed to generate the desired magnetization profile. It was already known that kT-point pulses designed in the small tip angle (STA) approximation provided substantial B1+ inhomogeneity correction. In this thesis, a methodology expressing the Bloch equations in a linear form was developed for the design of kT-point pulses beyond the STA regime. Excitation, inversion and refocusing pulses were designed and significant improvements were observed in the associated magnetization profiles when compared to the results found in the STA regime. The last part of the thesis was dedicated to the design of kT-points for a turbo spin echo (TSE) sequence in order to remove the effect of the B1+ inhomogeneity on T2-weighted imaging at 7 Tesla. In the first approach, a kT-point pulse was designed in the STA regime to make the excitation profile as homogeneous as possible. It was demonstrated that a symmetric kT-point pulse designed in the STA regime still generates an homogeneous excitation profile for flip angles as high as 120°. A unique symmetric kT-point pulse was designed in the STA regime and used to replace all the original hard pulses of a TSE sequence (static design). By adding parallel transmission, anatomical images largely devoid of artifacts resulting from the common B1+ inhomogeneity at 7 Tesla were acquired. To be able to acquire T2-weighted images with signal and contrast homogeneity by using a more efficient TSE sequence protocol, a specific kT-point waveform was optimized for each pulse of the TSE sequence (dynamic design). It was demonstrated that, although at a cost of an increase of the specific absorption rate, the dynamic outperforms the static kT-point design in terms of signal and contrast homogeneity obtained in the acquired T2-weighted images. The use of dynamic kT-points to obtain such a quality in T2-weighted imaging is thus promising for clinical applications at ultra high field.

3D T 2-weighted imaging at 7T using dynamic kT-points on single-transmit MRI systems

Florent Eggenschwiler, Daniel Gallichan, Rolf Gruetter, José Pedro Rebelo Ferreira Marques

OBJECTIVES: For turbo spin echo (TSE) sequences to be useful at ultra-high field, they should ideally employ an RF pulse train compensated for the B 1 + inhomogeneity. Previously, it was shown that a single kT-point pulse designed in the small tip-angle regime can replace all the pulses of the sequence (static kT-points). This work demonstrates that the B 1 + dependence of T 2-weighted imaging can be further mitigated by designing a specific kT-point pulse for each pulse of a 3D TSE sequence (dynamic kT-points) even on single-channel transmit systems MATERIALS AND METHODS: By combining the spatially resolved extended phase graph formalism (which calculates the echo signals throughout the sequence) with a gradient descent algorithm, dynamic kT-points were optimized such that the difference between the simulated signal and a target was minimized at each echo. Dynamic kT-points were inserted into the TSE sequence to acquire in vivo images at 7T. RESULTS: The improvement provided by the dynamic kT-points over the static kT-point design and conventional hard pulses was demonstrated via simulations. Images acquired with dynamic kT-points showed systematic improvement of signal and contrast at 7T over regular TSE-especially in cerebellar and temporal lobe regions without the need of parallel transmission. CONCLUSION: Designing dynamic kT-points for a 3D TSE sequence allows the acquisition of T 2-weighted brain images on a single-transmit system at ultra-high field with reduced dropout and only mild residual effects due to the B 1 + inhomogeneity.

Springer Verlag2016

Fat navigators based retrospective motion correction strategies for brain magnetic resonance imaging

Frédéric Gretsch

Magnetic resonance resonance (MRI) is a widely used modality to obtain in vivo tissue information. Clinical applications are near countless, and almost all body parts can be examined using an MR scanner. As the method is non invasive, does not use ionizing radiation and provides excellent soft tissue contrast, it also appears as an excellent tool for neuroscience research. The major drawback of MRI remains the relatively long acquisition times, of the order of several minutes. During the measurement, the subject must stay still and avoid moving at all costs, as otherwise image artefacts will appear and potentially render the acquired data (partially) unusable. As higher image resolution imply longer acquisition time, probing finer anatomical details imply ultimately requires dealing with said motion. While some research goes in the way of reducing the acquisition time, it necessarily comes at the price of lower sensitivity and hence inherently diminishes the achievable gain for high- resolution imaging as the signal is weaker to start with. In this work, the focus is to try and compensate for motion during brain imaging using a navigator method. This amounts to measure not only the desired image, but also other MR based information, called navigator, at regular intervals during the scan. A modeling step then establishes a link between the navigators samples and the head position change. Incorporating the motion information into the main image reconstruction framework helps to retrospectively reduce the impact of said motion and the associated incoherences which would appear during the standard reconstruction. Brain imaging is probably the easiest case of motion correction in MRI, as the motion can readily be well approximated as rigid. The navigator methods developed and investigated in this work, called FatNavs, are based on the fat signal, which in head imaging is very sparse in space and therefore can be imaged rapidly. They also present the advantage of reduced impact on the main image water signal. Several implementation strategies were tested as, due to the versatility of MRI, all image contrasts cannot be ideally navigated using a single general implementation. Applications to inversion recovery based sequences (MP2RAGE) used a well separated navigator and image acquisition scheme. This method being routinely acquired, comparison to Moir Ìe Phase Tracking, the current gold standard for motion tracking and correction, was also performed in collaboration with Hendrik Mattern from the Magdeburg University. For gradient-echo imaging sequences (GRE), on which time-of-flight angiography and susceptibil- ity induced contrasts are based, both separate and mixed acquisition schemes were tested. Further- more, for imaging protocols using long echo time, the fluctuation of the magnetic field during the scan can also induce severe artefacts. Therefore, extension of the FatNavs to a dual-echo field-mapping version was also explored. Finally, combination of FatNavs with FID navigators, which lack spatial information but have much higher temporal resolution, was investigated for both motion and field fluctuation retrospective correction.

EPFL2020

Application of CMOS image sensors in optical sectioning and polarization microscopy

Jelena Mitic

In this thesis new imaging approaches for optical microscopy are proposed and studied. They are based on the use of dynamic structured illumination in combination with a demodulation detection concept employing CMOS image detectors. Two particular implementations are suggested: real-time optical sectioning microscopy and whole field quantitative polarization microscopy. Optical sectioning, i.e depth resolved imaging, allows observation of thin sections in volumetric samples. In its classical configuration the wide-field microscope does not allow optical sectioning of the investigated objects. In this thesis the optical sectioning in a wide-field microscope is achieved by illuminating the sample with a continuously moving single spatial frequency pattern, which temporarily modulates the signal obtained on the photodetector. Only the object parts that are in the focus have a good contrast and consequently generate stronger signal on the detector. The optically sectioned images are obtained employing a CMOS image detector, which demodulates the time-dependent component of the image. Two different systems for real-time acquisition of optically sectioned images are proposed. The first one is based on a specially designed smart-pixel-detector-array (SPDA), which allows performing the signal processing by an electronic circuit integrated to each pixel of the sensor. The second system utilizes a commercial CMOS image sensor. Here, the images are treated by a digital signal processor (DSP) integrated into the camera (iMVS-155). Both approaches provide real-time acquisition of optically sectioned images. The proof of principle for the new method is demonstrated by imaging artificial three-dimensional reflective samples. The optical sectioning imaging of biological samples in bright-field mode and in fluorescence mode is also demonstrated. The optical sectioning performances of the studied systems are similar to that of the confocal microscope. However the new method has some advantages over the classical confocal system: e.g. the difficulties with the alignment and the post-processing inherent to the confocal system are avoided. The theoretical framework presented in the thesis describes the image formation in structured illumination for both reflective and fluorescent samples. The influence of longitudinal chromatic aberration and spherical aberration caused by specimen induced index mismatch on depth discrimination property are studied. In extension to the work related to optically sectioned microscopy, the quantitative polarization microscopy imaging method is proposed as a new application for CMOS detectors. The polarization state of the illuminating light is dynamically changed and the demodulation detection approach is employed to extract the retardance and azimuth of the birefringent sample in real-time; for a whole field of view. Examples of polarization sensitive measurements for different samples are presented. The theoretical analysis is performed using the Jones formalism. Finally, the potentials and limitations of the CMOS detectors for applications in optical microscopy are discussed. Thanks to constant advancements in CMOS technology, the acquisition speed, resolution and sensitivity of new CMOS detectors generations have been improved. This will allow adapting the methods proposed in this thesis for investigations of fast dynamic process where high temporal and spatial resolution is required.