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1. High-resolution single-shot spiral diffusion-weighted imaging at 7T using expanded encoding with compressed sensing

Author

Varela-Mattatall, Gabriel, Dubovan, Paul I., Santini, Tales, Gilbert, Kyle M., Menon, Ravi S., and Baron, Corey A.

Subjects
Physics - Medical Physics
Abstract

Purpose: The expanded encoding model incorporates spatially- and time-varying field perturbations for correction during reconstruction. So far, these reconstructions have used the conjugate gradient method with early stopping used as implicit regularization. However, this approach is likely suboptimal for low-SNR cases like diffusion or high-resolution MRI. Here, we investigate the extent that l1-wavelet regularization, or equivalently compressed sensing (CS), combined with expanded encoding improves trade-offs between spatial resolution, readout time and SNR for single-shot spiral diffusion-weighted imaging at 7T. The reconstructions were performed using our open-source GPU-enabled reconstruction toolbox, MatMRI, that allows inclusion of the different components of the expanded encoding model, with or without CS. Methods: In vivo accelerated single-shot spirals were acquired with five acceleration factors (2-6) and three in-plane spatial resolutions (1.5, 1.3, and 1.1 mm). From the in vivo reconstructions, we estimated diffusion tensors and computed fractional anisotropy maps. Then, simulations were used to quantitatively investigate and validate the impact of CS-based regularization on image quality when compared to a known ground truth. Results: In vivo reconstructions revealed improved image quality with retainment of small features when CS was used. Simulations showed that the joint use of the expanded encoding model and CS improves accuracy of image reconstructions (reduced mean-squared error) over the range of acceleration factors investigated. Conclusion: The expanded encoding model and CS regularization are complementary tools for single-shot spiral diffusion MRI, which enables both higher spatial resolutions and higher acceleration factors., Comment: 23 pages, 10 figures, GVM and PD are co-first authors

Published
2022

3. Minimal Specifications for Non-Human Primate MRI: Challenges in Standardizing and Harmonizing Data Collection

Author

Autio, Joonas A., Zhu, Qi, Li, Xiaolian, Glasser, Matthew F., Schwiedrzik, Caspar M., Fair, Damien A., Zimmermann, Jan, Yacoub, Essa, Menon, Ravi S., Van Essen, David C., Hayashi, Takuya, Russ, Brian, and Vanduffel, Wim

Subjects
Quantitative Biology - Neurons and Cognition
Abstract

Recent methodological advances in MRI have enabled substantial growth in neuroimaging studies of non-human primates (NHPs), while open data-sharing through the PRIME-DE initiative has increased the availability of NHP MRI data and the need for robust multi-subject multi-center analyses. Streamlined acquisition and analysis protocols would accelerate and improve these efforts. However, consensus on minimal standards for data acquisition protocols and analysis pipelines for NHP imaging remains to be established, particularly for multi-center studies. Here, we draw parallels between NHP and human neuroimaging and provide minimal guidelines for harmonizing and standardizing data acquisition. We advocate robust translation of widely used open-access toolkits that are well established for analyzing human data. We also encourage the use of validated, automated pre-processing tools for analyzing NHP data sets. These guidelines aim to refine methodological and analytical strategies for small and large-scale NHP neuroimaging data. This will improve reproducibility of results, and accelerate the convergence between NHP and human neuroimaging strategies which will ultimately benefit fundamental and translational brain science.

Published
2020

8. Imaging outcome measures of neuroprotection and repair in MS: A consensus statement from NAIMS.

Author

Oh, Jiwon, Ontaneda, Daniel, Azevedo, Christina, Klawiter, Eric C, Absinta, Martina, Arnold, Douglas L, Bakshi, Rohit, Calabresi, Peter A, Crainiceanu, Ciprian, Dewey, Blake, Freeman, Leorah, Gauthier, Susan, Henry, Roland, Inglese, Mathilde, Kolind, Shannon, Li, David KB, Mainero, Caterina, Menon, Ravi S, Nair, Govind, Narayanan, Sridar, Nelson, Flavia, Pelletier, Daniel, Rauscher, Alexander, Rooney, William, Sati, Pascal, Schwartz, Daniel, Shinohara, Russell T, Tagge, Ian, Traboulsee, Anthony, Wang, Yi, Yoo, Youngjin, Yousry, Tarek, Zhang, Yunyan, Sicotte, Nancy L, and Reich, Daniel S

Subjects
Brain Disorders, Neurodegenerative, Clinical Research, Biomedical Imaging, Multiple Sclerosis, Clinical Trials and Supportive Activities, Autoimmune Disease, Neurosciences, Neurological, Brain, Diffusion Tensor Imaging, Humans, Magnetic Resonance Imaging, Magnetic Resonance Spectroscopy, Multimodal Imaging, Nerve Regeneration, Neuroprotection, Outcome Assessment, Health Care, Positron-Emission Tomography, Spinal Cord, North American Imaging in Multiple Sclerosis Cooperative, Clinical Sciences, Cognitive Sciences, Neurology & Neurosurgery
Abstract

ObjectiveTo summarize current and emerging imaging techniques that can be used to assess neuroprotection and repair in multiple sclerosis (MS), and to provide a consensus opinion on the potential utility of each technique in clinical trial settings.MethodsClinicians and scientists with expertise in the use of MRI in MS convened in Toronto, Canada, in November 2016 at a North American Imaging in Multiple Sclerosis (NAIMS) Cooperative workshop meeting. The discussion was compiled into a manuscript and circulated to all NAIMS members in attendance. Edits and feedback were incorporated until all authors were in agreement.ResultsA wide spectrum of imaging techniques and analysis methods in the context of specific study designs were discussed, with a focus on the utility and limitations of applying each technique to assess neuroprotection and repair. Techniques were discussed under specific themes, and included conventional imaging, magnetization transfer ratio, diffusion tensor imaging, susceptibility-weighted imaging, imaging cortical lesions, magnetic resonance spectroscopy, PET, advanced diffusion imaging, sodium imaging, multimodal techniques, imaging of special regions, statistical considerations, and study design.ConclusionsImaging biomarkers of neuroprotection and repair are an unmet need in MS. There are a number of promising techniques with different strengths and limitations, and selection of a specific technique will depend on a number of factors, notably the question the trial seeks to answer. Ongoing collaborative efforts will enable further refinement and improved methods to image the effect of novel therapeutic agents that exert benefit in MS predominately through neuroprotective and reparative mechanisms.

Published
2019

10. An Open Resource for Non-human Primate Imaging

Author

Milham, Michael P, Ai, Lei, Koo, Bonhwang, Xu, Ting, Amiez, Céline, Balezeau, Fabien, Baxter, Mark G, Blezer, Erwin LA, Brochier, Thomas, Chen, Aihua, Croxson, Paula L, Damatac, Christienne G, Dehaene, Stanislas, Everling, Stefan, Fair, Damian A, Fleysher, Lazar, Freiwald, Winrich, Froudist-Walsh, Sean, Griffiths, Timothy D, Guedj, Carole, Hadj-Bouziane, Fadila, Hamed, Suliann Ben, Harel, Noam, Hiba, Bassem, Jarraya, Bechir, Jung, Benjamin, Kastner, Sabine, Klink, P Christiaan, Kwok, Sze Chai, Laland, Kevin N, Leopold, David A, Lindenfors, Patrik, Mars, Rogier B, Menon, Ravi S, Messinger, Adam, Meunier, Martine, Mok, Kelvin, Morrison, John H, Nacef, Jennifer, Nagy, Jamie, Rios, Michael Ortiz, Petkov, Christopher I, Pinsk, Mark, Poirier, Colline, Procyk, Emmanuel, Rajimehr, Reza, Reader, Simon M, Roelfsema, Pieter R, Rudko, David A, Rushworth, Matthew FS, Russ, Brian E, Sallet, Jerome, Schmid, Michael Christoph, Schwiedrzik, Caspar M, Seidlitz, Jakob, Sein, Julien, Shmuel, Amir, Sullivan, Elinor L, Ungerleider, Leslie, Thiele, Alexander, Todorov, Orlin S, Tsao, Doris, Wang, Zheng, Wilson, Charles RE, Yacoub, Essa, Ye, Frank Q, Zarco, Wilbert, Zhou, Yong-di, Margulies, Daniel S, and Schroeder, Charles E

Subjects
Biological Psychology, Psychology, Neurosciences, Biomedical Imaging, Animals, Brain, Connectome, Datasets as Topic, Information Dissemination, Magnetic Resonance Imaging, Neuroimaging, Primates, Cognitive Sciences, Neurology & Neurosurgery, Biological psychology
Abstract

Non-human primate neuroimaging is a rapidly growing area of research that promises to transform and scale translational and cross-species comparative neuroscience. Unfortunately, the technological and methodological advances of the past two decades have outpaced the accrual of data, which is particularly challenging given the relatively few centers that have the necessary facilities and capabilities. The PRIMatE Data Exchange (PRIME-DE) addresses this challenge by aggregating independently acquired non-human primate magnetic resonance imaging (MRI) datasets and openly sharing them via the International Neuroimaging Data-sharing Initiative (INDI). Here, we present the rationale, design, and procedures for the PRIME-DE consortium, as well as the initial release, consisting of 25 independent data collections aggregated across 22 sites (total = 217 non-human primates). We also outline the unique pitfalls and challenges that should be considered in the analysis of non-human primate MRI datasets, including providing automated quality assessment of the contributed datasets.

Published
2018

20. Uncovering the hidden effects of repetitive subconcussive head impact exposure: A mega‐analytic approach characterizing seasonal brain microstructural changes in contact and collision sports athletes.

Author

Kwiatkowski, Anna, Weidler, Carmen, Habel, Ute, Coverdale, Nicole S., Hirad, Adnan A., Manning, Kathryn Y., Rauscher, Alexander, Bazarian, Jeffrey J., Cook, Douglas J., Li, David K. B., Mahon, Bradford Z., Menon, Ravi S., Taunton, Jack, Reetz, Kathrin, Romanzetti, Sandro, and Huppertz, Charlotte

Subjects
DIFFUSION magnetic resonance imaging, DIFFUSION tensor imaging, HEAD injuries, WHITE matter (Nerve tissue), BRAIN injuries
Abstract

Repetitive subconcussive head impacts (RSHI) are believed to induce sub‐clinical brain injuries, potentially resulting in cumulative, long‐term brain alterations. This study explores patterns of longitudinal brain white matter changes across sports with RSHI‐exposure. A systematic literature search identified 22 datasets with longitudinal diffusion magnetic resonance imaging data. Four datasets were centrally pooled to perform uniform quality control and data preprocessing. A total of 131 non‐concussed active athletes (American football, rugby, ice hockey; mean age: 20.06 ± 2.06 years) with baseline and post‐season data were included. Nonparametric permutation inference (one‐sample t tests, one‐sided) was applied to analyze the difference maps of multiple diffusion parameters. The analyses revealed widespread lateralized patterns of sports‐season‐related increases and decreases in mean diffusivity (MD), radial diffusivity (RD), and axial diffusivity (AD) across spatially distinct white matter regions. Increases were shown across one MD‐cluster (3195 voxels; mean change: 2.34%), one AD‐cluster (5740 voxels; mean change: 1.75%), and three RD‐clusters (817 total voxels; mean change: 3.11 to 4.70%). Decreases were shown across two MD‐clusters (1637 total voxels; mean change: −1.43 to −1.48%), two RD‐clusters (1240 total voxels; mean change: −1.92 to −1.93%), and one AD‐cluster (724 voxels; mean change: −1.28%). The resulting pattern implies the presence of strain‐induced injuries in central and brainstem regions, with comparatively milder physical exercise‐induced effects across frontal and superior regions of the left hemisphere, which need further investigation. This article highlights key considerations that need to be addressed in future work to enhance our understanding of the nature of observed white matter changes, improve the comparability of findings across studies, and promote data pooling initiatives to allow more detailed investigations (e.g., exploring sex‐ and sport‐specific effects). [ABSTRACT FROM AUTHOR]

Published
2024
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33. Putative Concussion Biomarkers Identified in Adolescent Male Athletes Using Targeted Plasma Proteomics

Author

Miller, Michael R., primary, Robinson, Michael, additional, Fischer, Lisa, additional, DiBattista, Alicia, additional, Patel, Maitray A., additional, Daley, Mark, additional, Bartha, Robert, additional, Dekaban, Gregory A., additional, Menon, Ravi S., additional, Shoemaker, J. Kevin, additional, Diamandis, Eleftherios P., additional, Prassas, Ioannis, additional, and Fraser, Douglas D., additional

Published
2021
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41. Accelerating the Evolution of Nonhuman Primate Neuroimaging

Author

Milham, Michael, Petkov, Christopher I., Margulies, Daniel S., Schroeder, Charles E., Basso, Michele A., Belin, Pascal, Fair, Damien A., Fox, Andrew, Kastner, Sabine, Mars, Rogier B., Messinger, Adam, Poirier, Colline, Vanduffel, Wim, Van Essen, David C., Alvand, Ashkan, Becker, Yannick, Ben Hamed, Suliann, Benn, Austin, Bodin, Clementine, Boretius, Susann, Cagna, Bastien, Coulon, Olivier, El-Gohary, Sherif Hamdy, Evrard, Henry, Forkel, Stephanie J., Friedrich, Patrick, Froudist-Walsh, Sean, Garza-Villarreal, Eduardo A., Gao, Yang, Gozzi, Alessandro, Grigis, Antoine, Hartig, Renee, Hayashi, Takuya, Heuer, Katja, Howells, Henrietta, Ardesch, Dirk Jan, Jarrett, Wendy, Jedema, Hank P., Kagan, Igor, Kelly, Clare, Kennedy, Henry, Klink, P. Christiaan, Kwok, Sze Chai, Leech, Robert, Liu, Xiaojin, Madan, Christopher, Madushanka, Wasana, Majka, Piotr, Mallon, Ann-Marie, Marche, Kevin, Meguerditchian, Adrien, Menon, Ravi S., Merchant, Hugo, Mitchell, Anna, Nenning, Karl-Heinz, Nikolaidis, Aki, Ortiz-Rios, Michael, Pagani, Marco, Pareek, Vikas, Prescott, Mark, Procyk, Emmanuel, Rajimehr, Reza, Rautu, Ioana-Sabina, Raz, Amir, Roe, Anna Wang, Roumazeilles, Lea, Sakai, Tomoko, Sallet, Jerome, Sato, Chika, Sawiak, Stephen, Schiffer, Marike, Schwiedrzik, Caspar M., Seidlitz, Jakob, Sein, Julien, Shen, Zhi-ming, Shmuel, Amir, Silva, Afonso C., Simone, Luciano, Sirmpilatze, Nikoloz, Sliwa, Julia, Smallwood, Jonathan, Tasserie, Jordy, Thiebaut de Schotten, Michel, Toro, Roberto, Trapeau, Regis, Uhrig, Lynn, Vezoli, Julien, Wang, Zheng, Wells, Sara, Williams, Bella, Xu, Ting, Xu, Augix Guohua, Yacoub, Essa, Zhan, Ming, Ai, Lei, Balezeau, Fabien, Baxter, Mark G., Blezer, Erwin L.A., Brochier, Thomas, Chen, Aihua, Croxson, Paula L., Damatac, Christienne G., Dehaene, Stanislas, Everling, Stefan, Fleysher, Lazar, Freiwald, Winrich, Griffiths, Timothy D., Guedj, Carole, Hadj-Bouziane, Fadila, Harel, Noam, Hiba, Bassem, Jung, Benjamin, Koo, Bonhwang, Laland, Kevin N., Leopold, David A., Lindenfors, Patrik, Meunier, Martine, Mok, Kelvin, Morrison, John H., Nacef, Jennifer, Nagy, Jamie, Pinsk, Mark, Reader, Simon M., Roelfsema, Pieter R., Rudko, David A., Rushworth, Matthew F.S., Russ, Brian E., Schmid, Michael Christoph, Sullivan, Elinor L., Thiele, Alexander, Todorov, Orlin S., Tsao, Doris, Ungerleider, Leslie, Wilson, Charles R.E., Ye, Frank Q., Zarco, Wilbert, and Zhou, Yong-di

Subjects
General Neuroscience
Abstract

Nonhuman primate neuroimaging is on the cusp of a transformation, much in the same way its human counterpart was in 2010, when the Human Connectome Project was launched to accelerate progress. Inspired by an open data-sharing initiative, the global community recently met and, in this article, breaks through obstacles to define its ambitions.

Published
2020

45. Flexible retinotopy: motion-dependent position coding in the visual cortex

Author

Malick, Terrence, Goltz, Herbert C., Thomas, Christopher G., Gati, Joseph S., Menon, Ravi S., and Goodale, Melvyn A.

Subjects
Science and technology
Abstract

Although the visual cortex is organized retinotopically, it is not clear whether the cortical representation of position necessarily reflects perceived position. Using functional magnetic resonance imaging (fMRI), we show that the retinotopic representation of a stationary object in the cortex was systematically shifted when visual motion was present in the scene. Whereas the object could appear shifted in the direction of the visual motion, the representation of the object in the visual cortex was always shifted in the opposite direction. The results show that the representation of position in the primary visual cortex, as revealed by fMRI, can be dissociated from perceived location., When a stationary window or envelope is filled with a moving pattern, the position of the envelope can appear shifted in the direction of the internal motion (1, 2). The [...]

Published
2003

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