2016 — 2017 |
Stockmann, Jason P |
K99Activity Code Description: To support the initial phase of a Career/Research Transition award program that provides 1-2 years of mentored support for highly motivated, advanced postdoctoral research scientists. |
Improved Imaging of Deep Brain Nuclei With 7 Tesla Mri Using Comprehensive Magnetic Field Monitoring and Compensation @ Massachusetts General Hospital
Project Summary/Abstract: Networks of small nuclei in the meso and diencephalon (thalamus, hypothalamus, brainstem, etc.) and their connections to the cortex are critical to understanding consciousness and the onset of sedation during anesthesia. Yet despite their importance for daily survival, the functional connections among nuclei and between nuclei and cortex remain poorly understood. Ultra high field MRI at or above 7 Tesla (7T) provides several benefits for studying deep brain nuclei in humans, including improved image Signal to Noise Ratio (SNR) and improved contrast (CNR) for susceptibility based structural (SWI) and functional (BOLD) imaging as well as greater T1-dispersion. In addition to problems stemming from their small size, the study of nuclei at 7T is impeded by both static and dynamic variations in the background magnet field (B0) at these locations. These B0 variations cause image artifacts such as ghosting, signals voids, blurring, and geometric distortion. ?B0 order and cannot compensate dynamic ?B0. In the current project, we propose a comprehensive field Innovation: Standard B0 shim coils on commercial MRI scanners can only compensate static up to 2nd monitoring and control system to null high spatial order static and dynamic field variations at 7T. The system will use integrated RF-shim coil elements for maximum shimming and RF efficiency, NMR field probes for field monitoring, and feedback control for real-time shim updating. We are the first to combine these technologies in a unified system capable of largely overcoming the obstacle of ?B0 in 7T MR imaging. Validation: We use the proposed system to (a.) reduce the standard deviation of B0 inhomogeneity on a slice-optimized basis over the whole brain; (b.) stabilize the phase of EPI time-series data; (c.) mitigate ghosting in multi-shot EPI; (d.) image and identify known functional networks between the brainstem and cortex in single subjects; and (e.) test a hypothesis based on animal models about the action of the anesthetic dexmedotomidine on a brainstem circuit involving three specific nuclei. Clinical benefit: By providing a new tool for studying the activity of brainstem nuclei during sedation, this project paves the way for future efforts to improve our understanding of neural circuits, develop safer site-specific anesthetic drugs, and potentially reduce post-operative delirium and cognitive impairment. Training: I am fortunate to be a part of the exceptionally rich neuroimaging environment at the MGH Martinos Center, one of the premier environments in the world for developing and validating the proposed field control technology. My K99/R00 proposal is designed to help me pivot from a MRI physicist into an independent investigator with enough background in neurobiology to ask clinically significant questions involving deep brain circuits and then develop targeted high-field MRI technology to answer them. To this end, I will require additional training, coursework, and mentorship in the K99 phase focusing on fMRI, neuroscience, physiology, and pharmacology. Structured training will include coursework, tutorials, workshops, neuroimaging seminars, and clinical exposure. The training plan includes the following: 1. Continued MR physics and hardware mentorship from Dr. Lawrence Wald 2. Training in functional MRI data acquisition and analysis, guidance by Drs. Jonathan Polimeni and Marta Bianciardi on ultra-high field fMRI data, and help from Drs. Randy Buckner and Vitaly Napadow in functional connectivity analysis. 3. Courses on neuroscience and physiology as well as guided study of brainstem nuclei and associated circuits in the arousal pathway, led by Drs. Emery Brown, Brian Edlow, and Vitaly Napadow. 4. Coursework in pharmacology and mentorship by Dr. Brown in designing and conducting anesthesia studies and understanding drug action on the brainstem in the broader context of human physiology. 5. Annual conference attendance including ISMRM and HBM. 6. Participation in the BrainMap neuroimaging seminar series and MGH Radiology Grand Rounds. 7. Career guidance from my primary mentors, including advice on grant-writing and the faculty job search. I am confident that this foundation will enable me to collaborate effectively with neuroscientists and clinicians in neuroimaging studies that depict brainstem anatomy and function in unprecedented detail. Transition to independence: My strong background in hardware and MRI physics, combined with my training and mentorship plan, will enable the success of this project and my subsequent transition to independence. I will emerge from the K99 phase with a combination of engineering and neurophysiology knowledge that neither of my mentors possesses, allowing me to separate from them and occupy a niche bridging technology and brainstem neurophysiology. Using technology developed and validated in Aims 1, 2 and 3.2, and leveraging early clinical findings of Aim 3.2, I will submit an R01 grant during the R00 phase. The grant is expected to be a more in-depth use of sedative drugs with neuroimaging to probe the role of deep brain nuclei in supporting consciousness. Given the compelling need to better understand these nuclei, and the enormous potential of 7T MRI for enabling this understanding, I anticipate that I will emerge in the R00 phase a highly competitive candidate for faculty positions either at MGH or elsewhere.
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2018 — 2020 |
Stockmann, Jason P |
R00Activity Code Description: To support the second phase of a Career/Research Transition award program that provides 1 -3 years of independent research support (R00) contingent on securing an independent research position. Award recipients will be expected to compete successfully for independent R01 support from the NIH during the R00 research transition award period. |
Improved Imaging of Deep Brain Nuclei With 7 Tesla Mri Using Comprehensive Magnetic Field Monitoring @ Massachusetts General Hospital
Project Summary/Abstract: Networks of small nuclei in the meso and diencephalon (thalamus, hypothalamus, brainstem, etc.) and their connections to the cortex are critical to understanding consciousness and the onset of sedation during anesthesia. Yet despite their importance for daily survival, the functional connections among nuclei and between nuclei and cortex remain poorly understood. Ultra high field MRI at or above 7 Tesla (7T) provides several benefits for studying deep brain nuclei in humans, including improved image Signal to Noise Ratio (SNR) and improved contrast (CNR) for susceptibility based structural (SWI) and functional (BOLD) imaging as well as greater T1-dispersion. In addition to problems stemming from their small size, the study of nuclei at 7T is impeded by both static and dynamic variations in the background magnet field (B0) at these locations. These B0 variations cause image artifacts such as ghosting, signals voids, blurring, and geometric distortion. ?B0 order and cannot compensate dynamic ?B0. In the current project, we propose a comprehensive field Innovation: Standard B0 shim coils on commercial MRI scanners can only compensate static up to 2nd monitoring and control system to null high spatial order static and dynamic field variations at 7T. The system will use integrated RF-shim coil elements for maximum shimming and RF efficiency, NMR field probes for field monitoring, and feedback control for real-time shim updating. We are the first to combine these technologies in a unified system capable of largely overcoming the obstacle of ?B0 in 7T MR imaging. Validation: We use the proposed system to (a.) reduce the standard deviation of B0 inhomogeneity on a slice-optimized basis over the whole brain; (b.) stabilize the phase of EPI time-series data; (c.) mitigate ghosting in multi-shot EPI; (d.) image and identify known functional networks between the brainstem and cortex in single subjects; and (e.) test a hypothesis based on animal models about the action of the anesthetic dexmedotomidine on a brainstem circuit involving three specific nuclei. Clinical benefit: By providing a new tool for studying the activity of brainstem nuclei during sedation, this project paves the way for future efforts to improve our understanding of neural circuits, develop safer site-specific anesthetic drugs, and potentially reduce post-operative delirium and cognitive impairment. Training: I am fortunate to be a part of the exceptionally rich neuroimaging environment at the MGH Martinos Center, one of the premier environments in the world for developing and validating the proposed field control technology. My K99/R00 proposal is designed to help me pivot from a MRI physicist into an independent investigator with enough background in neurobiology to ask clinically significant questions involving deep brain circuits and then develop targeted high-field MRI technology to answer them. To this end, I will require additional training, coursework, and mentorship in the K99 phase focusing on fMRI, neuroscience, physiology, and pharmacology. Structured training will include coursework, tutorials, workshops, neuroimaging seminars, and clinical exposure. The training plan includes the following: 1. Continued MR physics and hardware mentorship from Dr. Lawrence Wald 2. Training in functional MRI data acquisition and analysis, guidance by Drs. Jonathan Polimeni and Marta Bianciardi on ultra-high field fMRI data, and help from Drs. Randy Buckner and Vitaly Napadow in functional connectivity analysis. 3. Courses on neuroscience and physiology as well as guided study of brainstem nuclei and associated circuits in the arousal pathway, led by Drs. Emery Brown, Brian Edlow, and Vitaly Napadow. 4. Coursework in pharmacology and mentorship by Dr. Brown in designing and conducting anesthesia studies and understanding drug action on the brainstem in the broader context of human physiology. 5. Annual conference attendance including ISMRM and HBM. 6. Participation in the BrainMap neuroimaging seminar series and MGH Radiology Grand Rounds. 7. Career guidance from my primary mentors, including advice on grant-writing and the faculty job search. I am confident that this foundation will enable me to collaborate effectively with neuroscientists and clinicians in neuroimaging studies that depict brainstem anatomy and function in unprecedented detail. Transition to independence: My strong background in hardware and MRI physics, combined with my training and mentorship plan, will enable the success of this project and my subsequent transition to independence. I will emerge from the K99 phase with a combination of engineering and neurophysiology knowledge that neither of my mentors possesses, allowing me to separate from them and occupy a niche bridging technology and brainstem neurophysiology. Using technology developed and validated in Aims 1, 2 and 3.2, and leveraging early clinical findings of Aim 3.2, I will submit an R01 grant during the R00 phase. The grant is expected to be a more in-depth use of sedative drugs with neuroimaging to probe the role of deep brain nuclei in supporting consciousness. Given the compelling need to better understand these nuclei, and the enormous potential of 7T MRI for enabling this understanding, I anticipate that I will emerge in the R00 phase a highly competitive candidate for faculty positions either at MGH or elsewhere.
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0.91 |
2019 — 2021 |
Stockmann, Jason P |
U24Activity Code Description: To support research projects contributing to improvement of the capability of resources to serve biomedical research. |
Open-Source Software and Hardware Tools For Local B0 Field Control @ Massachusetts General Hospital
Project Summary/Abstract Multi-coil (MC) shim arrays have emerged as a promising and flexible tool for improving MRI image quality. Arrays of small, independently-driven loops placed close to the body provide an efficient way to generate rapidly-switchable magnetic field offsets (?B0) that can be shaped to provide useful field profiles inside the body. MC arrays were originally proposed for dynamically-switchable, high spatial order ?B0 shimming? in the body to null subject-specific perturbations of the static background B0 field. The improved shimming reduces geometric distortion in echo planar imaging (widely used for functional and diffusion MRI) and line broadening in MR spectroscopy. However, in the past few years, a surge of new uses for MC arrays have been proposed, including supplementary spatial encoding, improved lipid suppression, zoomed imaging, and reduced flip angle (B1+) inhomogeneity. This diverse and growing set of methods ? which we classify as local field control ? exploit two core features of MC arrays: (1) the ability of non-orthogonal ?B0 basis sets to generate field profiles that can not be created with linear gradients; and (2) the ability to rapidly update shim currents without causing artifacts. Unfortunately, MC local field control research has been slow to spread beyond a small handful of sites due to limited availability of instrumentation as well as control software. Commercial shim amplifiers with dynamic switching capability are rare, and those that do exist are cost-prohibitive for most applications (>$1,000/channel). At the same time, there is no readily-available software for controlling shim amplifiers and interfacing with the scanner host computer. Moreover, there is a lack of software tools using convex optimization to efficiently solve for shim current amplitudes for tailored local field control. We will break down these barriers to entry by developing an open-source resource called AFFECT (Automated Flexible Field Encoding and Control Toolkit). We will refine and disseminate our previously-validated low-cost ($100- 150/channel), low-voltage shim amplifier that is scalable up to 64-channels. We will also upgrade and package a graphical-user-interface (GUI) used to process B0 field maps and compute optimal shim currents. The GUI will be made modular to allow users to plug in their own custom shim optimization tools. Finally, we will create a seamless interface between the GUI and the scanner host computer to improve workflow. More than 10 research groups have already contacted us asking to use our open-source shim amplifiers. However, further work is required to prepare both the hardware and software for dissemination. The goal of this project is to translate our prototypes into robust, user-extensible tools that are packaged and documented. To expedite dissemination, we will provide up to 10 research groups with 32-channel amplifier setups free of charge. Users will also be free to download schematics and fabricate the circuit boards on their own.
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0.91 |
2020 — 2021 |
Bilgic, Berkin Stockmann, Jason P |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Advanced Neuroimaging Through Novel Encoding Strategies and Hardware Design @ Massachusetts General Hospital
Project Summary/Abstract Recent large-scale studies have employed MRI to gain a deeper understanding of how our brain works in health and disease. Human Connectome Project (HCP) and UK Biobank initiatives use Echo Planar Imaging (EPI) to examine brain connectivity as revealed by functional (fMRI) and diffusion MRI (dMRI). Although EPI empowers neuroscience with the necessary fast encoding, it is plagued by distortion artifacts that severely affect regions with poor B0 field homogeneity, such as the temporal and frontal lobes. While Simultaneous MultiSlice (SMS) imaging is routinely used for more efficient sampling, high MultiBand (MB) factors leave little encoding power in existing acquisition methods for in-plane acceleration. This lets the image distortion remain unchecked to hamper brain regions that regulate decision-making, emotions and semantic memory. Further, neuroimaging protocols often employ inefficient structural imaging scans that consume a large portion of the allotted time, which could have been used for additional fMRI and dMRI sampling. We propose synergistic hardware, acquisition and reconstruction strategies to provide multiplicative gains in image distortion, while mitigating signal voids and T2*-related voxel blurring in EPI. We will design and build a 64-channel ?AC/DC? combined receive and shim brain array to provide >2× more uniform B0 field and improved parallel imaging capability. On the pulse sequence side, we will develop ?wave-CAIPI? trajectories for EPI and optimally utilize the encoding power of our AC/DC array to push the in-plane acceleration to 5-fold. This will combine multiplicatively with the gain from dynamic shimming to yield >10-fold distortion reduction, while retaining the ability to perform 2-fold SMS acceleration. Even at extreme MB factors (e.g. 8-fold), we will still allow for a >3× reduction in distortion to target hard-to-image regions with fast fMRI. We will also develop ?BUDA? acquisition to sample 2-shots of EPI with alternating phase encoding directions, and incorporate a B0 map in the reconstruction to eliminate distortion in high-resolution dMRI. We will build on these technologies and develop a suite of EPI-based quantitative structural imaging scans for whole-brain T1 and T2 parameter mapping with high geometric fidelity at 1mm isotropic resolution in 90 sec. These will empower longitudinal studies and leave more time for fMRI and dMRI acquisitions. Finally, we will validate the improvements in fMRI and dMRI by focusing on the ventromedial prefrontal cortex and the brain reward circuity, both placed in challenging regions due to their proximity to air/tissue interfaces. We will compare the developed rapid T1- and T2-weighted acquisitions against conventional T1- MPRAGE and T2-FSE scans by performing morphometric analysis. We will strive to disseminate our developments to fuel the next generation of neuroimaging projects, simply by plugging in our coil and installing our sequences.
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