Showing papers by "Jamie Near published in 2021"
Montreal Neurological Institute and Hospital1, Douglas Mental Health University Institute2, University of Calgary3, Allen Institute for Brain Science4, Alberta Children's Hospital5, Columbia University6, University of Bern7, University of Minnesota8, University of Birmingham9, The Mind Research Network10
TL;DR: These three main steps in the post‐acquisition workflow of a single‐voxel MRS experiment (preprocessing, analysis and quantification) are reviewed and recommendations for best practices at each step are provided.
Abstract: Once an MRS dataset has been acquired, several important steps must be taken to obtain the desired metabolite concentration measures. First, the data must be preprocessed to prepare them for analysis. Next, the intensity of the metabolite signal(s) of interest must be estimated. Finally, the measured metabolite signal intensities must be converted into scaled concentration units employing a quantitative reference signal to allow meaningful interpretation. In this paper, we review these three main steps in the post-acquisition workflow of a single-voxel MRS experiment (preprocessing, analysis and quantification) and provide recommendations for best practices at each step.
156 citations
Brigham and Women's Hospital1, Harvard University2, Medical University of Vienna3, University of Kansas4, École Polytechnique Fédérale de Lausanne5, Columbia University6, University of Liverpool7, University of Bern8, University of Miami9, McGill University10, University of Minnesota11, University of Sydney12, King's College London13, Bangor University14
TL;DR: In this paper, a consensus group of MRS experts provides minimum guidelines for reporting MRS methods and results, including the standardized description of the MRS hardware, data acquisition, analysis, and quality assessment.
Abstract: The translation of MRS to clinical practice has been impeded by the lack of technical standardization. There are multiple methods of acquisition, post-processing, and analysis whose details greatly impact the interpretation of the results. These details are often not fully reported, making it difficult to assess MRS studies on a standardized basis. This hampers the reviewing of manuscripts, limits the reproducibility of study results, and complicates meta-analysis of the literature. In this paper a consensus group of MRS experts provides minimum guidelines for the reporting of MRS methods and results, including the standardized description of MRS hardware, data acquisition, analysis, and quality assessment. This consensus statement describes each of these requirements in detail and includes a checklist to assist authors and journal reviewers and to provide a practical way for journal editors to ensure that MRS studies are reported in full.
90 citations
University of Bern1, Copenhagen University Hospital2, University of Kansas3, École Polytechnique Fédérale de Lausanne4, Yale University5, The Mind Research Network6, Radboud University Nijmegen7, Medical University of Vienna8, University of Nottingham9, University of Miami10, Douglas Mental Health University Institute11, University of Minnesota12, University of New Mexico13, University of Birmingham14
TL;DR: This work covers terms used to describe all aspects of MRS, starting from the description of the MR signal and its theoretical basis to acquisition methods, processing and to quantification procedures, as well as terms involved in describing results, including those used with regard to aspects of quality, reproducibility or indications of error.
Abstract: With a 40-year history of use for in vivo studies, the terminology used to describe the methodology and results of magnetic resonance spectroscopy (MRS) has grown substantially and is not consistent in many aspects. Given the platform offered by this special issue on advanced MRS methodology, the authors decided to describe many of the implicated terms, to pinpoint differences in their meanings and to suggest specific uses or definitions. This work covers terms used to describe all aspects of MRS, starting from the description of the MR signal and its theoretical basis to acquisition methods, processing and to quantification procedures, as well as terms involved in describing results, for example, those used with regard to aspects of quality, reproducibility or indications of error. The descriptions of the meanings of such terms emerge from the descriptions of the basic concepts involved in MRS methods and examinations. This paper also includes specific suggestions for future use of terms where multiple conventions have emerged or coexisted in the past.
58 citations
Alexa Pichet Binette1, Alexa Pichet Binette2, Etienne Vachon-Presseau2, John C. Morris3 +216 more•Institutions (4)
TL;DR: In the preclinical phase of both sporadic and autosomal dominant AD, multiple behavioral features were associated with AD pathology, which may suggest potential pathways by which multidomain interventions might help delay AD onset or progression.
35 citations
Johns Hopkins University1, Kennedy Krieger Institute2, Georgia State University3, National Autonomous University of Mexico4, Stanford University5, University of Georgia6, University of British Columbia7, Heidelberg University8, University of Pennsylvania9, University of Nottingham10, Cleveland Clinic11, Aarhus University12, Medical University of Vienna13, Anschutz Medical Campus14, Neuroscience Research Australia15, Cincinnati Children's Hospital Medical Center16, Dartmouth College17, The Chinese University of Hong Kong18, University of Oxford19, University of Bergen20, University of Hasselt21, Katholieke Universiteit Leuven22, University of Freiburg23, University of Melbourne24, Jagiellonian University25, Lille University of Science and Technology26, Taipei Medical University27, Purdue University28, Cardiff University29, Hiroshima University30, University of Chieti-Pescara31, German National Metrology Institute32, Shandong University33, University of Oregon34, University of Calgary35, Ruhr University Bochum36, University of California, San Diego37, Maastricht University38, Swansea University39, Columbia University40, University of Kansas41, University of Washington42, University of Manchester43, King's College London44, Philips45, University of California, Davis46, Russian Academy of Sciences47, Bangor University48, McGill University49, GE Healthcare50, University of Oslo51, University of São Paulo52, University of Michigan53, Goethe University Frankfurt54, University of Florida55, Medical University of South Carolina56, University of Zurich57, University of Maryland, Baltimore58, Mater Dei Hospital59, University of Amsterdam60, Karolinska Institutet61, University of California, Irvine62, Royal Netherlands Academy of Arts and Sciences63, University of Düsseldorf64, University of Groningen65, University of Toronto66, Florey Institute of Neuroscience and Mental Health67, University of Ljubljana68, University of Alabama at Birmingham69, University of Birmingham70, Baylor College of Medicine71, Keio University72
TL;DR: In this paper, the authors compared the frequency drift data from 95 3T MRI scanners and found that the most extreme cases suffered from higher levels of drift, but the extent of drift varied across scanners which both linear and nonlinear drifts were observed.
18 citations
TL;DR: In this paper, the authors reported the simultaneous absolute quantification of brain metabolites and individual macromolecules in aging male and female Fischer 344 rats, measured longitudinally using proton magnetic resonance spectroscopy at 7 T.
9 citations
TL;DR: In this article, the authors investigated the impact of the MRI scanner upgrade on commonly used structural imaging measures and proton magnetic resonance spectroscopy indices, including frontal, temporal, and cingulate cortical thickness, along with decreases in parietal CT, amygdala, globus pallidus, hippocampus, and striatum volumes.
4 citations
TL;DR: In this article, a comprehensive longitudinal examination of morphometric change in 73 brain regions and at a voxel-wise level during normative aging in a mixed-sex cohort of Fischer 344 rats was performed.
Abstract: Animal models are widely used to study the pathophysiology of disease and to evaluate the efficacy of novel interventions, crucial steps towards improving disease outcomes in humans. The Fischer 344 (F344) wildtype rat is a common experimental background strain for transgenic models of disease and is also one of the most frequently used models in aging research. Despite frequency of use, characterization of neuroanatomical change with age has not been performed in the F344 rat. To this end, we present a comprehensive longitudinal examination of morphometric change in 73 brain regions and at a voxel-wise level during normative aging in a mixed-sex cohort of F344 rats. We identified age- and sex-related changes in regions such as the cortex, hippocampus, cingulum, caudoputamen, and nucleus accumbens, which are implicated in memory and motor control circuits frequently affected by aging and neurodegenerative disease. These findings provide a baseline for neuroanatomical changes associated with aging in male and female F344 rats, to which data from transgenic models or other background strains can be compared.
3 citations
TL;DR: In this article, the authors compared seven algorithms, including FSL-MRS, Gannet, AMARES, QUEST, LCModel, Osprey and Tarquin, using standardised vendor-specific basis sets (for GE, Philips and Siemens) where appropriate.
Abstract: Edited MRS sequences are widely used for studying GABA in the human brain. Several algorithms are available for modelling these data, deriving metabolite concentration estimates through peak fitting or a linear combination of basis spectra. The present study compares seven such algorithms, using data obtained in a large multi-site study. GABA-edited (GABA+, TE = 68 ms MEGA-PRESS) data from 222 subjects at 20 sites were processed via a standardised pipeline, before modelling with FSL-MRS, Gannet, AMARES, QUEST, LCModel, Osprey and Tarquin, using standardised vendor-specific basis sets (for GE, Philips and Siemens) where appropriate. After referencing metabolite estimates (to water or creatine), systematic differences in scale were observed between datasets acquired on different vendors' hardware, presenting across algorithms. Scale differences across algorithms were also observed. Using the correlation between metabolite estimates and voxel tissue fraction as a benchmark, most algorithms were found to be similarly effective in detecting differences in GABA+. An inter-class correlation across all algorithms showed single-rater consistency for GABA+ estimates of around 0.38, indicating moderate agreement. Upon inclusion of a basis set component explicitly modelling the macromolecule signal underlying the observed 3.0 ppm GABA peaks, single-rater consistency improved to 0.44. Correlation between discrete pairs of algorithms varied, and was concerningly weak in some cases. Our findings highlight the need for consensus on appropriate modelling parameters across different algorithms, and for detailed reporting of the parameters adopted in individual studies to ensure reproducibility and meaningful comparison of outcomes between different studies.
1 citations
TL;DR: The findings suggest that degeneration of microstructural organization in GM, as determined on the basis of cortical MD measured by DTI, is accompanied by the decline of Glx metabolism within the same GM region.
Abstract: Background: Diffusion tensor imaging (DTI), which is a technique for measuring the degree and direction of movement of water molecules in tissue, has been widely used to noninvasively assess white matter (WM) or gray matter (GM) microstructures in vivo. Mean diffusivity (MD), which is the average diffusion across all directions, has been considered as a marker of WM tract degeneration or extracellular space enlargement in GM. Recent lines of evidence suggest that cortical MD can better identify early-stage Alzheimer’s disease than structural morphometric parameters in magnetic resonance imaging. However, knowledge of the relationships between cortical MD and other biological factors in the same cortical region, e.g. metabolites, is still limited. Methods:
Thirty-three healthy elderly individuals [aged 50–77 years (mean, 63.8±7.4 years); 11 males and 22 females] were enrolled. We estimated the associations between cortical MD and neurotransmitter levels. Specifically, we measured levels of γ-aminobutyric acid (GABA) and glutamate + glutamine (Glx), which are inhibitory and excitatory neurotransmitters, respectively, in medial prefrontal cortex (mPFC) and posterior cingulate cortex (PCC) using MEGA-PRESS magnetic resonance spectroscopy, and we measured regional cortical MD using DTI. Results:
Cortical MD was significantly negatively associated with Glx levels in both mPFC and PCC. No significant association was observed between cortical MD and GABA levels in either GM region. Conclusion:
Our findings suggest that degeneration of microstructural organization in GM, as determined on the basis of cortical MD measured by DTI, is accompanied by the decline of Glx metabolism within the same GM region.
1 citations
TL;DR: In this paper, magnetic resonance spectroscopy (MRS) measurements along with two-photon mesoscopic imaging of calcium signals in excitatory and inhibitory neurons of living, unanesthetized mice were used to assess if MRS-measured Glutamate (Glu) and GABA reflect activations of brain regions.
Abstract: To assess if magnetic resonance spectroscopy (MRS)-measured Glutamate (Glu) and GABA reflect excitatory and inhibitory neural activities, respectively, we conducted MRS measurements along with two-photon mesoscopic imaging of calcium signals in excitatory and inhibitory neurons of living, unanesthetized mice. For monitoring stimulus-driven activations of a brain region, MRS signals and mesoscopic neural activities were measured during two consecutive sessions of 15-min prolonged sensory stimulations. In the first session, putative excitatory neuronal activities were increased, while inhibitory neuronal activities remained at the baseline level. In the second half, while excitatory neuronal activities remained elevated, inhibitory neuronal activities were significantly enhanced. We assessed regional neurochemical statuses by measuring MRS signals, which were overall in accordance with the neural activities, and neuronal activities and neurochemical statuses in a mouse model of Dravet syndrome under resting condition. Mesoscopic assessments showed that activities of inhibitory neurons in the cortex were diminished relative to wild-type mice in contrast to spared activities of excitatory neurons. Consistent with these observations, the Dravet model exhibited lower concentrations of GABA than wild-type controls. Collectively, the current investigations demonstrate that MRS-measured Glu and GABA can reflect spontaneous and stimulated activities of neurons producing and releasing these neurotransmitters in an awake condition.