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  1. Article ; Online: Residual RAKI: A hybrid linear and non-linear approach for scan-specific k-space deep learning.

    Zhang, Chi / Moeller, Steen / Demirel, Omer Burak / Uğurbil, Kâmil / Akçakaya, Mehmet

    NeuroImage

    2022  Volume 256, Page(s) 119248

    Abstract: ... MRI) in part due to its easy inclusion into routine acquisitions. In k-space based parallel imaging ... reconstruction, sub-sampled k-space data are interpolated using linear convolutions. At high acceleration rates ... we present an extension of Robust Artificial-neural-networks for k-space Interpolation (RAKI), called ...

    Abstract Parallel imaging is the most clinically used acceleration technique for magnetic resonance imaging (MRI) in part due to its easy inclusion into routine acquisitions. In k-space based parallel imaging reconstruction, sub-sampled k-space data are interpolated using linear convolutions. At high acceleration rates these methods have inherent noise amplification and reduced image quality. On the other hand, non-linear deep learning methods provide improved image quality at high acceleration, but the availability of training databases for different scans, as well as their interpretability hinder their adaptation. In this work, we present an extension of Robust Artificial-neural-networks for k-space Interpolation (RAKI), called residual-RAKI (rRAKI), which achieves scan-specific machine learning reconstruction using a hybrid linear and non-linear methodology. In rRAKI, non-linear CNNs are trained jointly with a linear convolution implemented via a skip connection. In effect, the linear part provides a baseline reconstruction, while the non-linear CNN that runs in parallel provides further reduction of artifacts and noise arising from the linear part. The explicit split between the linear and non-linear aspects of the reconstruction also help improve interpretability compared to purely non-linear methods. Experiments were conducted on the publicly available fastMRI datasets, as well as high-resolution anatomical imaging, comparing GRAPPA and its variants, compressed sensing, RAKI, Scan Specific Artifact Reduction in K-space (SPARK) and the proposed rRAKI. Additionally, highly-accelerated simultaneous multi-slice (SMS) functional MRI reconstructions were also performed, where the proposed rRAKI was compred to Read-out SENSE-GRAPPA and RAKI. Our results show that the proposed rRAKI method substantially improves the image quality compared to conventional parallel imaging, and offers sharper images compared to SPARK and ℓ
    MeSH term(s) Algorithms ; Artifacts ; Deep Learning ; Humans ; Image Processing, Computer-Assisted/methods ; Magnetic Resonance Imaging ; Neural Networks, Computer
    Language English
    Publishing date 2022-04-27
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 1147767-2
    ISSN 1095-9572 ; 1053-8119
    ISSN (online) 1095-9572
    ISSN 1053-8119
    DOI 10.1016/j.neuroimage.2022.119248
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Accelerated coronary MRI with sRAKI: A database-free self-consistent neural network k-space reconstruction for arbitrary undersampling.

    Hosseini, Seyed Amir Hossein / Zhang, Chi / Weingärtner, Sebastian / Moeller, Steen / Stuber, Matthias / Ugurbil, Kamil / Akçakaya, Mehmet

    PloS one

    2020  Volume 15, Issue 2, Page(s) e0229418

    Abstract: ... Methods: Self-consistent robust artificial-neural-networks for k-space interpolation (sRAKI) performs ...

    Abstract Purpose: To accelerate coronary MRI acquisitions with arbitrary undersampling patterns by using a novel reconstruction algorithm that applies coil self-consistency using subject-specific neural networks.
    Methods: Self-consistent robust artificial-neural-networks for k-space interpolation (sRAKI) performs iterative parallel imaging reconstruction by enforcing self-consistency among coils. The approach bears similarity to SPIRiT, but extends the linear convolutions in SPIRiT to nonlinear interpolation using convolutional neural networks (CNNs). These CNNs are trained individually for each scan using the scan-specific autocalibrating signal (ACS) data. Reconstruction is performed by imposing the learned self-consistency and data-consistency, which enables sRAKI to support random undersampling patterns. Fully-sampled targeted right coronary artery MRI was acquired in six healthy subjects. The data were retrospectively undersampled, and reconstructed using SPIRiT, l1-SPIRiT and sRAKI for acceleration rates of 2 to 5. Additionally, prospectively undersampled whole-heart coronary MRI was acquired to further evaluate reconstruction performance.
    Results: sRAKI reduces noise amplification and blurring artifacts compared with SPIRiT and l1-SPIRiT, especially at high acceleration rates in targeted coronary MRI. Quantitative analysis shows that sRAKI outperforms these techniques in terms of normalized mean-squared-error (~44% and ~21% over SPIRiT and [Formula: see text]-SPIRiT at rate 5) and vessel sharpness (~10% and ~20% over SPIRiT and l1-SPIRiT at rate 5). Whole-heart data shows the sharpest coronary arteries when resolved using sRAKI, with 11% and 15% improvement in vessel sharpness over SPIRiT and l1-SPIRiT, respectively.
    Conclusion: sRAKI is a database-free neural network-based reconstruction technique that may further accelerate coronary MRI with arbitrary undersampling patterns, while improving noise resilience over linear parallel imaging and image sharpness over l1 regularization techniques.
    MeSH term(s) Adult ; Algorithms ; Coronary Vessels/anatomy & histology ; Female ; Follow-Up Studies ; Heart/anatomy & histology ; Humans ; Image Processing, Computer-Assisted/methods ; Magnetic Resonance Imaging/methods ; Male ; Neural Networks, Computer ; Prospective Studies ; Retrospective Studies
    Language English
    Publishing date 2020-02-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0229418
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Scan-specific robust artificial-neural-networks for k-space interpolation (RAKI) reconstruction: Database-free deep learning for fast imaging.

    Akçakaya, Mehmet / Moeller, Steen / Weingärtner, Sebastian / Uğurbil, Kâmil

    Magnetic resonance in medicine

    2018  Volume 81, Issue 1, Page(s) 439–453

    Abstract: Purpose: To develop an improved k-space reconstruction method using scan-specific deep learning ... that is trained on autocalibration signal (ACS) data.: Theory: Robust artificial-neural-networks for k ... nonlinear estimation of missing k-space lines from acquired k-space data with improved noise resilience ...

    Abstract Purpose: To develop an improved k-space reconstruction method using scan-specific deep learning that is trained on autocalibration signal (ACS) data.
    Theory: Robust artificial-neural-networks for k-space interpolation (RAKI) reconstruction trains convolutional neural networks on ACS data. This enables nonlinear estimation of missing k-space lines from acquired k-space data with improved noise resilience, as opposed to conventional linear k-space interpolation-based methods, such as GRAPPA, which are based on linear convolutional kernels.
    Methods: The training algorithm is implemented using a mean square error loss function over the target points in the ACS region, using a gradient descent algorithm. The neural network contains 3 layers of convolutional operators, with 2 of these including nonlinear activation functions. The noise performance and reconstruction quality of the RAKI method was compared with GRAPPA in phantom, as well as in neurological and cardiac in vivo data sets.
    Results: Phantom imaging shows that the proposed RAKI method outperforms GRAPPA at high (≥4) acceleration rates, both visually and quantitatively. Quantitative cardiac imaging shows improved noise resilience at high acceleration rates (rate 4:23% and rate 5:48%) over GRAPPA. The same trend of improved noise resilience is also observed in high-resolution brain imaging at high acceleration rates.
    Conclusion: The RAKI method offers a training database-free deep learning approach for MRI reconstruction, with the potential to improve many existing reconstruction approaches, and is compatible with conventional data acquisition protocols.
    MeSH term(s) Adult ; Algorithms ; Brain/diagnostic imaging ; Brain Mapping ; Databases, Factual ; Deep Learning ; Female ; Heart/diagnostic imaging ; Humans ; Image Enhancement/methods ; Image Interpretation, Computer-Assisted/methods ; Image Processing, Computer-Assisted/methods ; Magnetic Resonance Imaging ; Male ; Middle Aged ; Neural Networks, Computer ; Phantoms, Imaging ; Radionuclide Imaging ; Young Adult
    Language English
    Publishing date 2018-09-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 605774-3
    ISSN 1522-2594 ; 0740-3194
    ISSN (online) 1522-2594
    ISSN 0740-3194
    DOI 10.1002/mrm.27420
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: ULTRAHIGH FIELD and ULTRAHIGH RESOLUTION fMRI.

    Uğurbil, Kamil

    Current opinion in biomedical engineering

    2021  Volume 18

    Abstract: Functional magnetic resonance imaging (fMRI) has become one of the most powerful tools for investigating the human brain. Ultrahigh magnetic field (UHF) of 7 Tesla has played a critical role in enabling higher resolution and more accurate (relative to ... ...

    Abstract Functional magnetic resonance imaging (fMRI) has become one of the most powerful tools for investigating the human brain. Ultrahigh magnetic field (UHF) of 7 Tesla has played a critical role in enabling higher resolution and more accurate (relative to the neuronal activity) functional maps. However, even with these gains, the fMRI approach is challenged relative to the spatial scale over which brain function is organized. Therefore, going forward, significant advances in fMRI are still needed. Such advances will predominantly come from magnetic fields significantly higher than 7 Tesla, which is the most commonly used UHF platform today, and additional technologies that will include developments in pulse sequences, image reconstruction, noise suppression, and image analysis in order to further enhance and augment the gains than can be realized by going to higher magnetic fields.
    Language English
    Publishing date 2021-04-14
    Publishing country England
    Document type Journal Article
    ISSN 2468-4511
    ISSN 2468-4511
    DOI 10.1016/j.cobme.2021.100288
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  5. Article ; Online: Parallel excitation in the human brain at 9.4 T counteracting k-space errors with RF pulse design.

    Wu, Xiaoping / Vaughan, J Thomas / Uğurbil, Kâmil / Van de Moortele, Pierre-François

    Magnetic resonance in medicine

    2009  Volume 63, Issue 2, Page(s) 524–529

    Abstract: ... when measuring k-space trajectories prior to parallel transmit RF pulse design (acceleration x4). Excitation ...

    Abstract Multidimensional spatially selective radiofrequency (RF) pulses have been proposed as a method to mitigate transmit B1 inhomogeneity in MR experiments. These RF pulses, however, have been considered impractical for many years because they typically require very long RF pulse durations. The recent development of parallel excitation techniques makes it possible to design multidimensional RF pulses that are short enough for use in actual experiments. However, hardware and experimental imperfections can still severely alter the excitation patterns obtained with these accelerated pulses. In this note, we report at 9.4 T on a human eight-channel transmit system, substantial improvements in two-dimensional excitation pattern accuracy obtained when measuring k-space trajectories prior to parallel transmit RF pulse design (acceleration x4). Excitation patterns based on numerical simulations closely reproducing the experimental conditions were in good agreement with the experimental results.
    MeSH term(s) Algorithms ; Artifacts ; Brain/anatomy & histology ; Humans ; Image Enhancement/methods ; Image Interpretation, Computer-Assisted/methods ; Information Storage and Retrieval/methods ; Magnetic Resonance Imaging/methods ; Reproducibility of Results ; Sensitivity and Specificity ; Signal Processing, Computer-Assisted
    Language English
    Publishing date 2009-12-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 605774-3
    ISSN 1522-2594 ; 0740-3194
    ISSN (online) 1522-2594
    ISSN 0740-3194
    DOI 10.1002/mrm.22247
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Imaging at ultrahigh magnetic fields: History, challenges, and solutions.

    Uğurbil, Kamil

    NeuroImage

    2017  Volume 168, Page(s) 7–32

    Abstract: Following early efforts in applying nuclear magnetic resonance (NMR) spectroscopy to study biological processes in intact systems, and particularly since the introduction of 4 T human scanners circa 1990, rapid progress was made in imaging and ... ...

    Abstract Following early efforts in applying nuclear magnetic resonance (NMR) spectroscopy to study biological processes in intact systems, and particularly since the introduction of 4 T human scanners circa 1990, rapid progress was made in imaging and spectroscopy studies of humans at 4 T and animal models at 9.4 T, leading to the introduction of 7 T and higher magnetic fields for human investigation at about the turn of the century. Work conducted on these platforms has provided numerous technological solutions to challenges posed at these ultrahigh fields, and demonstrated the existence of significant advantages in signal-to-noise ratio and biological information content. Primary difference from lower fields is the deviation from the near field regime at the radiofrequencies (RF) corresponding to hydrogen resonance conditions. At such ultrahigh fields, the RF is characterized by attenuated traveling waves in the human body, which leads to image non-uniformities for a given sample-coil configuration because of destructive and constructive interferences. These non-uniformities were initially considered detrimental to progress of imaging at high field strengths. However, they are advantageous for parallel imaging in signal reception and transmission, two critical technologies that account, to a large extend, for the success of ultrahigh fields. With these technologies and improvements in instrumentation and imaging methods, today ultrahigh fields have provided unprecedented gains in imaging of brain function and anatomy, and started to make inroads into investigation of the human torso and extremities. As extensive as they are, these gains still constitute a prelude to what is to come given the increasingly larger effort committed to ultrahigh field research and development of ever better instrumentation and techniques.
    MeSH term(s) Animals ; Brain/diagnostic imaging ; History, 20th Century ; History, 21st Century ; Humans ; Magnetic Fields ; Magnetic Resonance Imaging/history ; Magnetic Resonance Imaging/instrumentation ; Magnetic Resonance Imaging/methods ; Neuroimaging/history ; Neuroimaging/instrumentation ; Neuroimaging/methods
    Language English
    Publishing date 2017-07-08
    Publishing country United States
    Document type Historical Article ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1147767-2
    ISSN 1095-9572 ; 1053-8119
    ISSN (online) 1095-9572
    ISSN 1053-8119
    DOI 10.1016/j.neuroimage.2017.07.007
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  7. Article ; Online: Heritability of brain neurovascular coupling.

    Christova, Peka / Uğurbil, Kâmil / Georgopoulos, Apostolos P

    Journal of neurophysiology

    2022  Volume 128, Issue 5, Page(s) 1307–1311

    Abstract: The moment-to-moment variation of neurovascular coupling in the brain was determined by computing the moment-to-moment turnover of the blood-oxygen-level-dependent signal (TBOLD) at resting state. Here we show ... ...

    Abstract The moment-to-moment variation of neurovascular coupling in the brain was determined by computing the moment-to-moment turnover of the blood-oxygen-level-dependent signal (TBOLD) at resting state. Here we show that
    MeSH term(s) Neurovascular Coupling ; Vesicular Acetylcholine Transport Proteins ; Brain ; Magnetic Resonance Imaging ; Brain Mapping ; Oxygen
    Chemical Substances Vesicular Acetylcholine Transport Proteins ; Oxygen (S88TT14065)
    Language English
    Publishing date 2022-10-19
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
    ZDB-ID 80161-6
    ISSN 1522-1598 ; 0022-3077
    ISSN (online) 1522-1598
    ISSN 0022-3077
    DOI 10.1152/jn.00402.2022
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Mitigating transmit-B

    Ma, Xiaodong / Uğurbil, Kâmil / Wu, Xiaoping

    Magnetic resonance in medicine

    2022  Volume 88, Issue 2, Page(s) 727–741

    Abstract: Purpose: To propose a novel deep learning (DL) approach to transmit-B: Methods: A deep encoder-decoder convolutional neural network was constructed and trained to learn the mapping from sTx to pTx images. The feasibility was demonstrated using 7 T ... ...

    Abstract Purpose: To propose a novel deep learning (DL) approach to transmit-B
    Methods: A deep encoder-decoder convolutional neural network was constructed and trained to learn the mapping from sTx to pTx images. The feasibility was demonstrated using 7 T Human-Connectome Project (HCP)-style diffusion MRI. The training dataset comprised images acquired on 5 healthy subjects using commercial Nova RF coils. Relevant hyperparameters were tuned with a nested cross-validation, and the generalization performance evaluated using a regular cross-validation.
    Results: Our DL method effectively improved the image quality for sTx images by restoring the signal dropout, with quality measures (including normalized root-mean-square error, peak SNR, and structural similarity index measure) improved in most brain regions. The improved image quality was translated into improved performances for diffusion tensor imaging analysis; our method improved accuracy for fractional anisotropy and mean diffusivity estimations, reduced the angular errors of principal eigenvectors, and improved the fiber orientation delineation relative to sTx images. Moreover, the final DL model trained on data of all 5 subjects was successfully used to predict pTx images for unseen new subjects (randomly selected from the 7 T HCP database), effectively recovering the signal dropout and improving color-coded fractional anisotropy maps with largely reduced noise levels.
    Conclusion: The proposed DL method has potential to provide images with reduced B1
    MeSH term(s) Artifacts ; Brain/diagnostic imaging ; Deep Learning ; Diffusion Tensor Imaging ; Feasibility Studies ; Humans ; Image Processing, Computer-Assisted/methods
    Language English
    Publishing date 2022-04-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 605774-3
    ISSN 1522-2594 ; 0740-3194
    ISSN (online) 1522-2594
    ISSN 0740-3194
    DOI 10.1002/mrm.29238
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  9. Article ; Online: Development of functional imaging in the human brain (fMRI); the University of Minnesota experience.

    Uğurbil, Kâmil

    NeuroImage

    2012  Volume 62, Issue 2, Page(s) 613–619

    Abstract: The human functional magnetic resonance imaging (fMRI) experiments performed in the Center for Magnetic Resonance Research (CMRR), University of Minnesota, were planned between two colleagues who had worked together previously in Bell Laboratories in the ...

    Abstract The human functional magnetic resonance imaging (fMRI) experiments performed in the Center for Magnetic Resonance Research (CMRR), University of Minnesota, were planned between two colleagues who had worked together previously in Bell Laboratories in the late nineteen seventies, namely myself and Seiji Ogawa. These experiments were motivated by the Blood Oxygenation Level Dependent (BOLD) contrast developed by Seiji. We discussed and planned human studies to explore imaging human brain activity using the BOLD mechanism on the 4 Tesla human system that I was expecting to receive for CMRR. We started these experiments as soon as this 4 Tesla instrument became marginally operational. These were the very first studies performed on the 4 Tesla scanner in CMRR; had the scanner become functional earlier, they would have been started earlier as well. We were aware of the competing effort at the Massachusetts General Hospital (MGH) and we knew that they had been informed of our initiative in Minneapolis to develop fMRI. We had positive results certainly by August 1991 annual meeting of the Society of Magnetic Resonance in Medicine (SMRM). I believe, however, that neither the MGH colleagues nor us, at the time, had enough data and/or conviction to publish these extraordinary observations; it took more or less another six months or so before the papers from these two groups were submitted for publication within five days of each other to the Proceedings of the National Academy of Sciences, USA, after rejection by Nature in our case. Thus, fMRI was achieved independently and at about the same time at MGH, in an effort credited largely to Ken Kwong, and in CMRR, University of Minnesota in an effort led by myself and Seiji Ogawa.
    MeSH term(s) Brain/blood supply ; Brain Mapping/history ; Brain Mapping/methods ; History, 20th Century ; History, 21st Century ; Humans ; Magnetic Resonance Imaging/history ; Magnetic Resonance Imaging/methods ; Minnesota ; Oxygen/blood
    Chemical Substances Oxygen (S88TT14065)
    Language English
    Publishing date 2012-02-08
    Publishing country United States
    Document type Historical Article ; Journal Article ; Review
    ZDB-ID 1147767-2
    ISSN 1095-9572 ; 1053-8119
    ISSN (online) 1095-9572
    ISSN 1053-8119
    DOI 10.1016/j.neuroimage.2012.01.135
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  10. Article ; Online: The road to functional imaging and ultrahigh fields.

    Uğurbil, Kâmil

    NeuroImage

    2012  Volume 62, Issue 2, Page(s) 726–735

    Abstract: The Center for Magnetic Resonance (CMRR) at the University of Minnesota was one of the laboratories where the work that simultaneously and independently introduced functional magnetic resonance imaging (fMRI) of human brain activity was carried out. ... ...

    Abstract The Center for Magnetic Resonance (CMRR) at the University of Minnesota was one of the laboratories where the work that simultaneously and independently introduced functional magnetic resonance imaging (fMRI) of human brain activity was carried out. However, unlike other laboratories pursuing fMRI at the time, our work was performed at 4T magnetic field and coincided with the effort to push human magnetic resonance imaging to field strength significantly beyond 1.5T which was the high-end standard of the time. The human fMRI experiments performed in CMRR were planned between two colleagues who had known each other and had worked together previously in Bell Laboratories, namely Seiji Ogawa and myself, immediately after the Blood Oxygenation Level Dependent (BOLD) contrast was developed by Seiji. We were waiting for our first human system, a 4T system, to arrive in order to attempt at imaging brain activity in the human brain and these were the first experiments we performed on the 4T instrument in CMRR when it became marginally operational. This was a prelude to a subsequent systematic push we initiated for exploiting higher magnetic fields to improve the accuracy and sensitivity of fMRI maps, first going to 9.4T for animal model studies and subsequently developing a 7T human system for the first time. Steady improvements in high field instrumentation and ever expanding armamentarium of image acquisition and engineering solutions to challenges posed by ultrahigh fields have brought fMRI to submillimeter resolution in the whole brain at 7T, the scale necessary to reach cortical columns and laminar differentiation in the whole brain. The solutions that emerged in response to technological challenges posed by 7T also propagated and continues to propagate to lower field clinical systems, a major advantage of the ultrahigh fields effort that is underappreciated. Further improvements at 7T are inevitable. Further translation of these improvements to lower field clinical systems to achieve new capabilities and to magnetic fields significantly higher than 7T to enable human imaging is inescapable.
    MeSH term(s) Brain/physiology ; Brain Mapping/history ; Brain Mapping/methods ; History, 20th Century ; History, 21st Century ; Humans ; Image Processing, Computer-Assisted/history ; Image Processing, Computer-Assisted/methods ; Magnetic Resonance Imaging/history ; Magnetic Resonance Imaging/methods
    Language English
    Publishing date 2012-02-08
    Publishing country United States
    Document type Historical Article ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1147767-2
    ISSN 1095-9572 ; 1053-8119
    ISSN (online) 1095-9572
    ISSN 1053-8119
    DOI 10.1016/j.neuroimage.2012.01.134
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