Mitigating susceptibility-induced distortions in high-resolution 3DEPI fMRI at 7T

Geometric distortion is a major limiting factor for spatial specificity in high-resolution fMRI using EPI readouts and is exacerbated at higher field strengths due to increased B0 field inhomogeneity. Prominent correction schemes are based on B0 field-mapping or acquiring reverse phase-encoded (reversed-PE) data. However, to date, comparisons of these techniques in the context of fMRI have only been performed on 2DEPI data, either at lower field or lower resolution. In this study, we investigate distortion compensation in the context of sub-millimetre 3DEPI data at 7T. B0 field-mapping and reversed-PE distortion correction techniques were applied to both partial coverage BOLD-weighted and whole brain MT-weighted 3DEPI data with matched distortion. Qualitative assessment showed overall improvement in cortical alignment for both correction techniques in both 3DEPI fMRI and whole-brain MT-3DEPI datasets. The distortion-corrected MT-3DEPI images were quantitatively evaluated by comparing cortical alignment with an anatomical reference using dice coefficient (DC) and correlation ratio (CR) measures. These showed that B0 field-mapping and reversed-PE methods both improved correspondence between the MT-3DEPI and anatomical data, with more substantial improvements consistently obtained using the reversed-PE approach. Regional analyses demonstrated that the largest benefit of distortion correction, and in particular of the reversed-PE approach, occurred in frontal and temporal regions where susceptibility-induced distortions are known to be greatest, but had not led to complete signal dropout. In conclusion, distortion correction based on reversed-PE data has shown the greater capacity for achieving faithful alignment with anatomical data in the context of high-resolution fMRI at 7T using 3DEPI

B0 shimming of the human brain at ultrahigh field MRI with a multi-coil shim setup

Magnetic resonance imaging (MRI) is widely used for contemporary diagnostics and research. Higher static magnetic field enables imaging with a higher resolution because of the increased signal-to-noise-ratio in comparison to low field MRI. However, this benefit is not cost-free. Less B1+ field uniformity, higher B0 inhomogeneity, higher specific absorption rate (SAR), and shortened T2 and T2* are some of the challenges of measurement at ultrahigh-field (UHF). The aim of this thesis is to address higher B0 inhomogeneity at a magnet with a strength of 9.4 tesla. To this end, the shimming hardware and software required for homogenization of the B0 field were designed, and the performance of the constructed setups has been validated by simulation and in vivo measurements. The first part of the thesis (Chapter 1) describes the source of B0 inhomogeneity, how it changes the FID signal, its consequences, and why UHF intensifies the B0 inhomogeneity. Then, the process of field homogenization, known as shimming, is introduced, and shimming with spherical harmonics is explained. Next, the standard method for B0 field measurement and inhomogeneity quantification is presented, and least squares minimization is described in order to optimal currents calculation for a constrained shimming. Then, dynamic slice-wise shimming is introduced as an approach to achieve a better B0 uniformity by breaking VOI to sub-volumes. Finally, the multi-coil shim setup is presented which benefits from small local coils for a more efficient shimming. The second part of the thesis (Chapter 2) focuses on construction and application of multi-coil shim setup as achievements of this thesis. First, the construction process of the setup and comparison with spherical harmonic basis sets are provided. Later, the impact of the improved B0 uniformity with the dynamic multi-coil shimming on fMRI contrast is studied. Finally, a novel multi-coil design approach is presented in which a multi-coil shim setup is optimized for shimming of the human brain. Sections 3.4 and 3.5 present a summary of the collaborations in other related projects. First, a novel method to design the shim coils’ wiring pattern based on stream function is introduced which allows higher order shimming with limited number of the coils to be achieved. Next, an application of the small local coils for parallel imaging is demonstrated. Small local coils are employed for a local modulation of the magnetic field and superimpose a unique phase variation to the spin distribution that can be used to disentangle different part of the object. The last part of the thesis starts with conclusions and outlook. Later, the resultant publications are listed, and the relevant publications are appended at the end. Next, an application of the small local coils for parallel imaging is demonstrated. Small local coils are employed for a local modulation of the magnetic field and superimpose a unique phase variation to the spin distribution that can be used to disentangle different part of the object. The last part of the thesis starts with conclusions and outlook. Later, the resultant publications are listed, and the relevant publications are appended at the end

Motion simulation and correction validation using MR tagging

Involuntary subject motion is a well-known problem in MR imaging. Motion simulation is an important step to evaluate correction performance and motion induced artifacts. Here we introduce a new approach based on MR tagging to simulate desired motion pattern on a plain phantom. We employed SPAMM method to generate grid tags with a specified orientation and position. Grid tags were rotated and shifted with a desired pattern per TR. Correspondingly, the imaging slice followed the pattern to compensate the rotation and translation of the tags. Employing this approach, we could simulate motion in 5 DOF

Improving performance of linear field generation with multi-coil setup by optimizing coils position

Purpose/Introduction: Recent publications[1],[2] report a high capability of a multi-coil setup to generate equivalent linear fields. Hence, the spatial encoding which is performed by scanner’s built-in linear gradient, can be accomplished with a multi-coil setup and therefore can be used for imaging in parallel with shimming[3]. The accuracy of the linear field produced by multi-coil is the benchmark key factor. Increasing the number of individual coils brings more degrees of freedom and a better generation of linear fields with the cost of a more complex setup to fabricate and maintain. Here, it is demonstrated how optimization of coil position results in generating superior linear fields with a limited number of coils. Subjects and Methods: Recent reports[1],[2] have used 48 and 84 coils which were arranged with a layout of 6*8 and 6*14 respectively. For comparison, we simulated a local multi-coil setup with 16, 24, 32, 48 and 84 circular shaped coils. All coils are placed on a cylinder with a diameter/length of 360/300 mm which is large enough to house an RF coil. We used optimization-based search of coil positions that result in three linear orthogonal fields for the FOV of 200*200*200 mm around the isocenter. Simulation started from arranging individual coils in a regular fashion on the cylinder surface. The magnetic field for each coil was calculated using the Biot–Savart law with no constraint for the floating current in the coils. The optimization was performed using the fmincon function in MATLAB. Results: As an initial position for the optimization, we placed the coils in a symmetric configuration such that they cover the whole cylinder surface. Figure 1 shows the arrangement of 16 individual coils before and after optimization to produce the linear field. Figure 2 demonstrates a comparison between the ideal linear fields, the generated linear field from 16 symmetrically positioned coils and the generated linear fields from 16 position-optimized coils. Figure 3 illustrates how position optimization can improve the quality of the linear fields generated by a multi-coil setup. As a cost function, we used cross-correlation between optimized field and the ideal linear field and also the l2-norm of their difference. Discussion/Conclusion: According to Fig. 3, position optimized arrangement for 16, 24 and 32 coils can bring the same or even better quality compared to the symmetric arrangement for 32, 48 and 84 coils respectively. This proves the importance of the optimal coil configuration to acquire high fidelity linear field with less coils

Prospective Head Motion Correction Using Multiple Tracking Modalities

Purpose/Introduction: Motion artifacts are a major problem for functional and anatomical MRI. The state of the art in head motion correction is prospective motion correction using a tracking modality of choice while updating slice positions and orientations in real-time during the acquisition.1 This work explores the possibility of using simultaneous tracking with multiple modalities. They can be used to supplement each other or provide an alternative when the tracking update from one method is lost or erroneous. Subjects and Methods: Two tracking methods were used to track and prospectively correct2 for head motion simultaneously: Optical tracking with Moire´ Phase Tracking (MPT)3 (Kineticor Inc, HI, USA) and motion tracking using four 19F NMR field probes4,5,6,7. The MR scanner used in this experiment was a 9.4 T human scanner (Siemens, Erlangen, Germany). The subject was scanned with a gradient echo sequence (Resolution 0.8 9 0.8 9 1.6 mm, TR 80 ms, TE 4 ms, FA 20). The MPT marker was attached to a subject specific bite-bar in order to have line of sight to the camera inside a shielded coil. The field probes (FP) were attached to the nose bridge and the temples of the subject. To simulate tracking dropouts of the MPT system, the subject was asked to obscure the marker for short periods of time. To still achieve continuous motion correction the tracking source was switched to field probes in those time intervals. Results: The in vivo measurements in Fig. 1 show a reference image (a) and the different types of prospective motion correction with small head motion (s. also Fig. 2). The image quality for single modality tracking (b,c) is comparable to the reference case for both modalities. With induced tracking dropouts the quality is visibly reduced (d) but can be improved again when field probe tracking is enabled as a fallback method (e). The motion trajectories measured with both systems for the two measurements with tracking dropouts are shown in Fig. 2. Motion range and pattern are very similar in both measurements. Discussion/Conclusion: The quality of the prospectively corrected images is improved when the fallback is enabled compared to the case when there are tracking dropouts and only one system is used. However, the remaining difference to the images with single source correction has to be investigated further. Further applications might include averaging of the motion estimates of multiple tracking systems or using the other tracking source to cross-validate the plausibility of measured motion

Joint dynamic shimming using the scanner’s spherical harmonic shim combined with a local multi-coil shim array

In this work, we combined scanner's spherical harmonic shim coils with a local multi-coil shim array to work in parallel for dynamic shimming of the human brain at 9.4 T. Performance of the combined method is compared with global shimming with scanner's built-in shim setup, global shimming with multi-coil and dynamic shimming with multi-coil