Matt started his MR journey as a Ph.D. student at UCLA under the tutelage of Dr. Ennis. There his research focused on the implementation of new pulse sequence techniques for 2D Phase Contrast MRI for faster and more accurate imaging. Following his PhD, he spent four years working at GE Healthcare as a scientist on the neuro applications and workflow team. Through collaboration with Stanford Psychology at the Center for Neurobiological Imaging, the team developed and commercialized a faster EPI imaging technique through the use of simultaneous multi-slice (HyperBand). Matt returns to Stanford as a research scientist looking to apply his experience as an MRI pulse sequence programmer, on both the Siemens and GE platforms, to bring the professional aspects of industry into the academic world of research.

Institute Affiliations

Honors & Awards

  • Leadership Training, GE Healthcare (2016)
  • Above & Beyond Award, GE Healthcare (2015 (3x), 2016 (2x) and 2017)
  • W.S. Moore Young Investigator Award, ISMRM (2012)
  • Biomedical Physics Travel Stipend, UCLA (2011-2012)
  • Student Travel Stipend, ISMRM (2011-2012)
  • Biomedical Physics Research Colloquium Top Speaker Prize, UCLA (2011)
  • Outstanding Undergraduate Physics Student, CSU Fresno (2008)
  • Ward & Oma T Miles Memorial Scholarship, CSU Fresno (2006-2008)
  • Dean's List, CSU Fresno (2005-2008)
  • Undergraduate Research Scholarship, CSU Fresno (2005-2008)

Education & Certifications

  • Ph.D., University of California, Los Angeles, Biomedical Physics (2013)
  • M.S., University of California, Los Angeles, Biomedical Physics (2010)
  • B.S., California State University, Fresno, Biomedical Physics (2008)

Service, Volunteer and Community Work

  • Board Member, Vista Charter School (5/1/2017 - Present)

    Vista Charter School is located in Ivins, UT and offers an educational environment where immersion in the arts and technology inspires student growth. I volunteer my time as a board member and also sit on the Academics Committee.


    585 E Center Street Ivins, Utah 84738

  • Volunteer, HOITT Group, LLC (6/1/2018 - Present)

    I volunteer my time and efforts with the HOITT Group, LLC with the goal of bringing a premier ice skating facility to St. George, UT.


    St. George, UT


  • Daniel B. Ennis, Matthew J. Middione, Julio A. Oscanoa Aida, Shreyas S. Vasanawala. "United States Patent 11550014 Artificial intelligence based reconstruction for phase contrast magnetic resonance imaging", The Board of Trustees of the Leland Stanford Junior University, The United States of America as represented by The Department Of Veterans Affairs, Jan 10, 2023

Work Experience

  • Scientist, MR Applications & Workflow, GE Healthcare (9/9/2013 - 9/22/2017)

    Managed collaborative relationships with key customers around the world. Provided technical support for scientists, clinicians,
    researchers and colleagues. Interfaced with the marketing team to develop marketing material for new product offerings. Researched technical and clinical trends in the industry to better inform the leadership of future product strategy. Engaged in product development with the engineering team to create product software packages. Assisted the service team to diagnose and debug software problems within the install base.


    333 Ravenswood Ave., Bldg 307, Menlo Park, CA 94025

All Publications

  • Multishot Diffusion-Weighted MRI of the Breasts in the Supine vs. Prone Position. Journal of magnetic resonance imaging : JMRI Moran, C. J., Middione, M. J., Mazzoli, V., McKay-Nault, J. A., Guidon, A., Waheed, U., Rosen, E. L., Poplack, S. P., Rosenberg, J., Ennis, D. B., Hargreaves, B. A., Daniel, B. L. 2022


    BACKGROUND: Diffusion-weighted imaging (DWI) may allow for breast cancer screening MRI without a contrast injection. Multishot methods improve prone DWI of the breasts but face different challenges in the supine position.PURPOSE: To establish a multishot DWI (msDWI) protocol for supine breast MRI and to evaluate the performance of supine vs. prone msDWI.STUDY TYPE: Prospective.POPULATION: Protocol optimization: 10 healthy women (ages 22-56), supine vs. prone: 24 healthy women (ages 22-62) and five women (ages 29-61) with breast tumors.FIELD STRENGTH/SEQUENCE: 3-T, protocol optimization msDWI: free-breathing (FB) 2-shots, FB 4-shots, respiratory-triggered (RT) 2-shots, RT 4-shots, supine vs. prone: RT 4-shot msDWI, T2-weighted fast-spin echo.ASSESSMENT: Protocol optimization and supine vs. prone: three observers performed an image quality assessment of sharpness, aliasing, distortion (vs. T2), perceived SNR, and overall image quality (scale of 1-5). Apparent diffusion coefficients (ADCs) in fibroglandular tissue (FGT) and breast tumors were measured.STATISTICAL TESTS: Effect of study variables on dichotomized ratings (4/5 vs. 1/2/3) and FGT ADCs were assessed with mixed-effects logistic regression. Interobserver agreement utilized Gwet's agreement coefficient (AC). Lesion ADCs were assessed by Bland-Altman analysis and concordance correlation (rhoc ). P value <0.05 was considered statistically significant.RESULTS: Protocol optimization: 4-shots significantly improved sharpness and distortion; RT significantly improved sharpness, aliasing, perceived SNR, and overall image quality. FGT ADCs were not significantly different between shots (P=0.812), FB vs. RT (P=0.591), or side (P=0.574). Supine vs. prone: supine images were rated significantly higher for sharpness, aliasing, and overall image quality. FGT ADCs were significantly higher supine; lesion ADCs were highly correlated (rhoc =0.92).DATA CONCLUSION: Based on image quality, supine msDWI outperformed prone msDWI. Lesion ADCs were highly correlated between the two positions, while FGT ADCs were higher in the supine position.EVIDENCE LEVEL: 2.TECHNICAL EFFICACY: Stage 1.

    View details for DOI 10.1002/jmri.28582

    View details for PubMedID 36583628

  • Accelerated two-dimensional phase-contrast for cardiovascular MRI using deep learning-based reconstruction with complex difference estimation. Magnetic resonance in medicine Oscanoa, J. A., Middione, M. J., Syed, A. B., Sandino, C. M., Vasanawala, S. S., Ennis, D. B. 2022


    PURPOSE: To develop and validate a deep learning-based reconstruction framework for highly accelerated two-dimensional (2D) phase contrast (PC-MRI) data with accurate and precise quantitative measurements.METHODS: We propose a modified DL-ESPIRiT reconstruction framework for 2D PC-MRI, comprised of an unrolled neural network architecture with a Complex Difference estimation (CD-DL). CD-DL was trained on 155 fully sampled 2D PC-MRI pediatric clinical datasets. The fully sampled data ( n = 29 $$ n=29 $$ ) was retrospectively undersampled (6-11 * $$ \times $$ ) and reconstructed using CD-DL and a parallel imaging and compressed sensing method (PICS). Measurements of peak velocity and total flow were compared to determine the highest acceleration rate that provided accuracy and precision within ± 5 % $$ \pm 5\% $$ . Feasibility of CD-DL was demonstrated on prospectively undersampled datasets acquired in pediatric clinical patients ( n = 5 $$ n=5 $$ ) and compared to traditional parallel imaging (PI) and PICS.RESULTS: The retrospective evaluation showed that 9 * $$ \times $$ accelerated 2D PC-MRI images reconstructed with CD-DL provided accuracy and precision (bias, [95 % $$ \% $$ confidence intervals]) within ± 5 % $$ \pm 5\% $$ . CD-DL showed higher accuracy and precision compared to PICS for measurements of peak velocity (2.8 % $$ \% $$ [ - 2 . 9 $$ -2.9 $$ , 4.5] vs. 3.9 % $$ \% $$ [ - 11 . 0 $$ -11.0 $$ , 4.9]) and total flow (1.8 % $$ \% $$ [ - 3 . 9 $$ -3.9 $$ , 3.4] vs. 2.9 % $$ \% $$ [ - 7 . 1 $$ -7.1 $$ , 6.9]). The prospective feasibility study showed that CD-DL provided higher accuracy and precision than PICS for measurements of peak velocity and total flow.CONCLUSION: In a retrospective evaluation, CD-DL produced quantitative measurements of 2D PC-MRI peak velocity and total flow with ≤ 5 % $$ \le 5\% $$ error in both accuracy and precision for up to 9 * $$ \times $$ acceleration. Clinical feasibility was demonstrated using a prospective clinical deployment of our 8 * $$ \times $$ undersampled acquisition and CD-DL reconstruction in a cohort of pediatric patients.

    View details for DOI 10.1002/mrm.29441

    View details for PubMedID 36093915

  • A gradient optimization toolbox for general purpose time-optimal MRI gradient waveform design. Magnetic resonance in medicine Loecher, M., Middione, M. J., Ennis, D. B. 2020; 84 (6): 3234-3245


    To introduce and demonstrate a software library for time-optimal gradient waveform optimization with a wide range of applications. The software enables direct on-the-fly gradient waveform design on the scanner hardware for multiple vendors.The open-source gradient optimization (GrOpt) toolbox was implemented in C with both Matlab and Python wrappers. The toolbox enables gradient waveforms to be generated based on a set of constraints that define the features and encodings for a given acquisition. The GrOpt optimization routine is based on the alternating direction method of multipliers (ADMM). Additional constraints enable error corrections to be added, or patient comfort and safety to be adressed. A range of applications and compute speed metrics are analyzed. Finally, the method is implemented and tested on scanners from different vendors.Time-optimal gradient waveforms for different pulse sequences and the constraints that define them are shown. Additionally, the ability to add, arbitrary motion (gradient moment) compensation or limit peripheral nerve stimulation is demonstrated. There exists a trade-off between computation time and gradient raster time, but it was observed that acceptable gradient waveforms could be generated in 1-40 ms. Gradient waveforms generated and run on the different scanners were functionally equivalent, and the images were comparable.GrOpt is an open source toolbox that enables on-the-fly optimization of gradient waveform design, subject to a set of defined constraints. GrOpt was presented for a range of imaging applications, analyzed in terms of computational complexity, and implemented to run on the scanner for a multi-vendor demonstration.

    View details for DOI 10.1002/mrm.28384

    View details for PubMedID 33463724

  • A gradient optimization toolbox for general purpose time-optimal MRI gradient waveform design MAGNETIC RESONANCE IN MEDICINE Loecher, M., Middione, M. J., Ennis, D. B. 2020

    View details for DOI 10.1002/mrm.28384

    View details for Web of Science ID 000545612400001

  • Optimization methods for magnetic resonance imaging gradient waveform design. NMR in biomedicine Middione, M. J., Loecher, M. n., Moulin, K. n., Ennis, D. B. 2020: e4308


    The development and implementation of novel MRI pulse sequences remains challenging and laborious. Gradient waveforms are typically designed using a combination of analytical and ad hoc methods to construct each gradient waveform axis independently. This strategy makes coding the pulse sequence complicated, in addition to being time inefficient. As a consequence, nearly all commercial MRI pulse sequences fail to maximize use of the available gradient hardware or efficiently mitigate physiological effects. This results in expensive MRI systems that underperform relative to their inherent hardware capabilities. To address this problem, a software solution is proposed that incorporates numerical optimization methods into MRI pulse sequence programming. Examples are shown for rotational variant vs. invariant waveform designs, acceleration nulled velocity encoding gradients, and mitigation of peripheral nerve stimulation for diffusion encoding. The application of optimization methods to MRI pulse sequence design incorporates gradient hardware limits and the prescribed MRI protocol parameters (e.g. field-of-view, resolution, gradient moments, and/or b-value) to simultaneously construct time-optimal gradient waveforms. In many cases, the resulting constrained gradient waveform design problem is convex and can be solved on-the-fly on the MRI scanner. The result is a set of multi-axis time-optimal gradient waveforms that satisfy the design constraints, thereby increasing SNR-efficiency. These optimization methods can also be used to mitigate imaging artifacts (e.g. eddy currents) or account for peripheral nerve stimulation. The result of the optimization method is to enable easier pulse sequence gradient waveform design and permit on-the-fly implementation for a range of MRI pulse sequences.

    View details for DOI 10.1002/nbm.4308

    View details for PubMedID 32342560

  • Advantages of Short Repetition Time Resting-State Functional MRI Enabled by Simultaneous Multi-slice Imaging. Journal of neuroscience methods Jahanian, H., Holdsworth, S., Christen, T., Wu, H., Zhu, K., Kerr, A. B., Middione, M. J., Dougherty, R. F., Moseley, M., Zaharchuk, G. 2018


    BACKGROUND: Recent advancements in simultaneous multi-slice (SMS) imaging techniques have enabled whole-brain resting-state fMRI (rs-fMRI) scanning at sub-second temporal resolution, providing spectral ranges much wider than the typically used range of 0.01-0.1Hz. However, the advantages of this accelerated acquisition for rs-fMRI have not been evaluated.NEW METHOD: In this study, we used SMS Echo Planar Imaging (EPI) to probe whole-brain functional connectivity with a short repetition time (TR=350ms) and compared it with standard EPI with a longer TR of 2000ms. We determined the effect of scan length and investigated the temporal filtration strategies that optimize results based on metrics of signal-noise separation and test-retest reliability using both seed-based and independent component analysis (ICA).RESULTS: We found that use of either the entire frequency range of 0.01-1.4Hz or the entire frequency range with the exclusion of typical cardiac and respiratory frequency values tended to provide the best functional connectivity maps.COMPARISON WITH EXISTING METHODS: We found that the SMS-acquired rs-fMRI scans had improved the signal-noise separation, while preserving the same level of test-retest reliability compared to conventional EPI, and enabled the detection of reliable functional connectivity networks with scan times as short as 3minutes.CONCLUSIONS: Our findings suggest that whole-brain rs-fMRI studies may benefit from the increased temporal resolution enabled by the SMS-EPI acquisition, leading to drastic scan time reductions, which in turn should enable the more widespread use of rs-fMRI in clinical research protocols.

    View details for PubMedID 30300699

  • Toward personalised diffusion MRI in psychiatry: improved delineation of fibre bundles with the highest-ever angular resolution in vivo tractography. Translational psychiatry Callaghan, F., Maller, J. J., Welton, T., Middione, M. J., Shankaranarayanan, A., Grieve, S. M. 2018; 8 (1): 91


    Diffusion MRI (dMRI) tractography is a uniquely powerful tool capable of demonstrating structural brain network abnormalities across a range of psychiatric disorders; however, it is not currently clinically useful. This is because limitations on sensitivity effectively restrict its application to scientific studies of cohorts, rather than individual patients. Recent improvements in dMRI hardware, acquisition, processing and analysis techniques may, however, overcome these measurement limitations. We therefore acquired the highest-ever angular resolution in vivo tractographic data set, and used these data to ask the question: 'is cutting-edge, optimised dMRI now sensitive enough to measure brain network abnormalities at a level that may enable personalised psychiatry?' The fibre tracking performance of this 'gold standard' data set of 1150 unique directions (11 shells) was compared to a conventional 64-direction protocol (single shell) and a clinically practical, highly optimised and accelerated 9-min protocol of 140 directions (3 shells). Three major tracts of relevance to psychiatry were evaluated: the cingulate bundle, the uncinate fasciculus and the corticospinal tract. We found up to a 34-fold improvement in tracking accuracy using the 1150-direction data set compared to the 64-direction data set, while 140-direction data offered a maximum 17-fold improvement. We also observed between 20 and 50% improvements in tracking efficiency for the 140-direction data set, a finding we then replicated in a normal cohort (n = 53). We found evidence that lower angular resolution data may introduce systematic anatomical biases. These data highlight the imminent potential of dMRI as a clinically meaningful technique at a personalised level, and should inform current practice in clinical studies.

    View details for DOI 10.1038/s41398-018-0140-8

    View details for PubMedID 29691374

    View details for PubMedCentralID PMC5915595

  • Hybrid-Space SENSE Reconstruction for Simultaneous Multi-Slice MRI IEEE TRANSACTIONS ON MEDICAL IMAGING Zhu, K., Dougherty, R. F., Wu, H., Middione, M. J., Takahashi, A. M., Zhang, T., Pauly, J. M., Kerr, A. B. 2016; 35 (8): 1824-1836


    Simultaneous Multi-Slice (SMS) magnetic resonance imaging (MRI) is a rapidly evolving technique for increasing imaging speed. Controlled aliasing techniques utilize periodic undersampling patterns to help mitigate the loss in signal-to-noise ratio (SNR) in SMS MRI. To evaluate the performance of different undersampling patterns, a quantitative description of the image SNR loss is needed. Additionally, eddy current effects in echo planar imaging (EPI) lead to slice-specific Nyquist ghosting artifacts. These artifacts cannot be accurately corrected for each individual slice before or after slice-unaliasing. In this work, we propose a hybrid-space sensitivity encoding (SENSE) reconstruction framework for SMS MRI by adopting a three-dimensional representation of the SMS acquisition. Analytical SNR loss maps are derived for SMS acquisitions with arbitrary phase encoding undersampling patterns. Moreover, we propose a matrix-decoding correction method that corrects the slice-specific Nyquist ghosting artifacts in SMS EPI acquisitions. Brain images demonstrate that the proposed hybrid-space SENSE reconstruction generates images with comparable quality to commonly used split-slice-generalized autocalibrating partially parallel acquisition reconstruction. The analytical SNR loss maps agree with those calculated by a Monte Carlo based method, but require less computation time for high quality maps. The analytical maps enable a fair comparison between the performances of coherent and incoherent SMS undersampling patterns. Phantom and brain SMS EPI images show that the matrix-decoding method performs better than the single-slice and slice-averaged Nyquist ghosting correction methods under the hybrid-space SENSE reconstruction framework.

    View details for DOI 10.1109/TMI.2016.2531635

    View details for Web of Science ID 000381436000004

    View details for PubMedID 26915118

    View details for PubMedCentralID PMC4988924

  • Phase Contrast MRI with Flow Compensation View Sharing MAGNETIC RESONANCE IN MEDICINE Wang, D., Shao, J., Rapacchi, S., Middione, M. J., Ennis, D. B., Hu, P. 2015; 73 (2): 505-513


    To develop and evaluate a technique for accelerating phase contrast MRI (PC-MRI) acquisitions without significant compromise in flow quantification accuracy.PC-MRI is commonly acquired using interleaved flow-compensated (FC) and flow-encoded (FE) echoes. We hypothesized that FC data, which represent background phase, do not change significantly over time. Therefore, we proposed to undersample the FC data and use an FC view sharing (FCVS) approach to synthesize a composite FC frame for each corresponding FE frame. FCVS was evaluated in a flow phantom and healthy volunteers and compared with a standard FC/FE PC-MRI.The FCVS sequence resulted in an error of 0.0% for forward flow and 2.0% for reverse flow volume when compared with FC/FE PC-MRI in a flow phantom. Measurements in the common carotid arteries showed that the FCVS method had -1.16 cm/s bias for maximum peak velocity and -0.019 mL bias in total flow, when compared with FC/FE with the same temporal resolution, but double the total acquisition time. These results represent ≤1.3% bias error in velocity and volumetric flow quantification.FCVS can accelerate PC-MRI acquisitions while maintaining flow and velocity measurement accuracy when there is limited temporal variation in the FC data.

    View details for DOI 10.1002/mrm.25133

    View details for Web of Science ID 000348139500008

    View details for PubMedID 24532480

    View details for PubMedCentralID PMC4459783

  • Convex Gradient Optimization for Increased Spatiotemporal Resolution and Improved Accuracy in Phase Contrast MRI MAGNETIC RESONANCE IN MEDICINE Middione, M. J., Wu, H. H., Ennis, D. B. 2014; 72 (6): 1552-1564


    To evaluate convex gradient optimization (CVX) for increased spatiotemporal resolution and improved accuracy for phase-contrast MRI (PC-MRI).A conventional flow-compensated and flow-encoded (FCFE) PC-MRI sequence was compared with a CVX PC-MRI sequence using numerical simulations, flow phantom experiments, and in vivo experiments. Flow measurements within the ascending aorta, main pulmonary artery, and right/left pulmonary arteries of normal volunteers (N = 10) were acquired at 3T and analyzed using a conventional FCFE sequence and a CVX sequence with either higher spatial resolution or higher temporal resolution. All sequences mitigated chemical shift-induced phase errors and used equivalent breath-hold durations.Chemical shift-optimized PC-MRI has increased sequence efficiency when using CVX, which can provide either higher spatial or higher temporal resolution compared with conventional FCFE PC-MRI. Numerical simulations, flow phantom experiments, and in vivo experiments indicate that CVX measurements of total flow and peak velocity are increased and more accurate when compared with FCFE.CVX PC-MRI increases sequence efficiency while reducing chemical shift-induced phase errors. This can be used to provide either higher spatial or higher temporal resolution than conventional chemical shift-mitigated PC-MRI methods to provide more accurate measurements of blood flow and peak velocity.

    View details for DOI 10.1002/mrm.25059

    View details for Web of Science ID 000344798300008

    View details for PubMedID 24347040

  • Velocity Encoding with the Slice Select Refocusing Gradient for Faster Imaging and Reduced Chemical Shift-Induced Phase Errors MAGNETIC RESONANCE IN MEDICINE Middione, M. J., Thompson, R. B., Ennis, D. B. 2014; 71 (6): 2014-2023


    To investigate a novel phase-contrast MRI velocity-encoding technique for faster imaging and reduced chemical shift-induced phase errors.Velocity encoding with the slice select refocusing gradient achieves the target gradient moment by time shifting the refocusing gradient, which enables the use of the minimum in-phase echo time (TE) for faster imaging and reduced chemical shift-induced phase errors. Net forward flow was compared in 10 healthy subjects (N = 10) within the ascending aorta (aAo), main pulmonary artery (PA), and right/left pulmonary arteries (RPA/LPA) using conventional flow compensated and flow encoded (401 Hz/px and TE = 3.08 ms) and slice select refocused gradient velocity encoding (814 Hz/px and TE = 2.46 ms) at 3 T.Improved net forward flow agreement was measured across all vessels for slice select refocused gradient compared to flow compensated and flow encoded: aAo vs. PA (1.7% ± 1.9% vs. 5.8% ± 2.8%, P = 0.002), aAo vs. RPA + LPA (2.1% ± 1.7% vs. 6.0% ± 4.3%, P = 0.03), and PA vs. RPA + LPA (2.9% ± 2.1% vs. 6.1% ± 6.3%, P = 0.04), while increasing temporal resolution (35%) and signal-to-noise ratio (33%).Slice select refocused gradient phase-contrast MRI with a high receiver bandwidth and minimum in-phase TE provides more accurate and less variable flow measurements through the reduction of chemical shift-induced phase errors and a reduced TE/repetition time, which can be used to increase the temporal/spatial resolution and/or reduce breath hold durations.

    View details for DOI 10.1002/mrm.24861

    View details for Web of Science ID 000336260900009

    View details for PubMedID 23836543

  • Chemical shift-induced phase errors in phase-contrast MRI MAGNETIC RESONANCE IN MEDICINE Middione, M. J., Ennis, D. B. 2013; 69 (2): 391–401


    Phase-contrast magnetic resonance imaging is subject to numerous sources of error, which decrease clinical confidence in the reported measures. This work outlines how stationary perivascular fat can impart a significant chemical shift induced phase-contrast magnetic resonance imaging measurement error using computational simulations, in vitro, and in vivo experiments. This chemical shift error does not subtract in phase difference processing, but can be minimized with proper parameter selection. The chemical shift induced phase errors largely depend on both the receiver bandwidth and the TE. Both theory and an in vivo comparison of the maximum difference in net forward flow between vessels with and without perivascular fat indicated that the effects of chemically shifted perivascular fat are minimized by the use of high bandwidth (814 Hz/px) and an in-phase TE (high BW-TE(IN)). In healthy volunteers (N = 10) high BW-TE(IN) significantly improves intrapatient net forward flow agreement compared with low bandwidth (401 Hz/px) and a mid-phase TE as indicated by significantly decreased measurement biases and limits of agreement for the ascending aorta (1.8 ± 0.5 mL vs. 6.4 ± 2.8 mL, P = 0.01), main pulmonary artery (2.0 ± 0.9 mL vs. 11.9 ± 5.8 mL, P = 0.04), the left pulmonary artery (1.3 ± 0.9 mL vs. 5.4 ± 2.5 mL, P = 0.003), and all vessels (1.7 ± 0.8 mL vs. 7.2 ± 4.4 mL, P = 0.001).

    View details for DOI 10.1002/mrm.24262

    View details for Web of Science ID 000314059500011

    View details for PubMedID 22488490

    View details for PubMedCentralID PMC3396715