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Removal of nuisance signals from limited and sparse1H MRSI data using a union-of-subspaces model

Chao Ma, Fan Lam, Curtis L. Johnson, Zhi-Pei Liang
2015 Magnetic Resonance in Medicine  
Results-The proposed method has been evaluated using in vivo MRSI data.  ...  Conclusions-Nuisance signals in 1 H MRSI data reside in low-dimensional subspaces.  ...  One approach is to use prior knowledge of the lipid and metabolite signals, such as the spatial support of the lipid signal (14) (15) (16) (17) , the spectral support of the metabolite signal (18, 19  ... 
doi:10.1002/mrm.25635 pmid:25762370 pmcid:PMC4567537 fatcat:sgsl3sdbyzad5cm67igdmn73ya

Blind recovery of biochemical markers of brain cancer in MRSI

Shuyan Du, Xiangling Mao, Dikoma Shungu, Paul Sajda, J. Michael Fitzpatrick, Milan Sonka
2004 Medical Imaging 2004: Image Processing  
This positivity constraint enables recovery of physically meaningful spectra even in the presence of noise that causes a significant number of the observation amplitudes to be negative.  ...  We therefore use = 2.2204 × 10 −16 (the value of floating point relative accuracy used by MATLAB 6.5)  ...  ACKNOWLEDGMENTS This research was supported by an NSF CAREER Award (BES-0133804) to P.S. and the DoD Multidisciplinary University Research Initiative (MURI) program administered by the Office of Naval  ... 
doi:10.1117/12.534652 dblp:conf/miip/DuMSS04 fatcat:q3owuqkmova57atzrqn7nsfy5i

Whole‐brain high‐resolution metabolite mapping with 3D compressed‐sensing SENSE low‐rank 1 H FID‐MRSI

Antoine Klauser, Paul Klauser, Frédéric Grouiller, Sébastien Courvoisier, François Lazeyras
2021 NMR in Biomedicine  
There is a growing interest in the neuroscience community to map the distribution of brain metabolites in vivo.  ...  We first evaluated the acceleration performance using retrospective undersampling of a fully sampled dataset.  ...  | MRSI data preprocessing and reconstruction model | Remaining water and lipid signal removal Residual water was removed using the Hankel singular value decomposition (HSVD) method. 50 HSVD was applied  ... 
doi:10.1002/nbm.4615 pmid:34595791 pmcid:PMC9285075 fatcat:rbs2v64elvgrdfrphi4sjfvx4e

Whole-Brain High-Resolution Metabolite Mapping with 3D Compressed-Sensing-SENSE-LowRank 1H FID-MRSI [article]

Antoine Klauser, Paul Klauser, Frederic Grouiller, Sebastien Courvoisier, Francois Lazeyras
2020 bioRxiv   pre-print
The successful combination of the 3D 1H-FID-MRSI with a constrained reconstruction enables the detailed mapping of metabolite concentrations at high-resolution in the whole brain and with an acquisition  ...  There is a growing interest of the neuroscience community to map the distribution of brain metabolites in vivo.  ...  MRSI data preprocessing and reconstruction model Remaining water and lipid signal removal Residual water was removed using Hankel singular value decomposition (HSVD) method [45] .  ... 
doi:10.1101/2020.05.18.101618 fatcat:seaz2xdjnvgphfukoclgc5ojo4

Compartmentalized low-rank recovery for high-resolution lipid unsuppressed MRSI

Ipshita Bhattacharya, Mathews Jacob
2016 Magnetic Resonance in Medicine  
THEORY We denote the underlying spatiospectral function in MRSI by x(r, f), where r is the spatial index and f is the spectral index.  ...  The MRSI dataset is modeled as the sum of metabolite and lipid signals, each of which is support limited to the brain and extracranial regions, respectively, in addition to being orthogonal to each other  ...  This work is inspired by use of orthogonality constraints in (40) , where lipid and metabolite signals are shown to have strikingly different spectral signatures (e.g., metabolite are highly localized  ... 
doi:10.1002/mrm.26537 pmid:27851875 pmcid:PMC5427002 fatcat:sqsaazi5vfcpffqumkcpmsuygq

Automated tissue segmentation and blind recovery of1H MRS imaging spectral patterns of normal and diseased human brain

Shuyan Du, Xiangling Mao, Paul Sajda, Dikoma C. Shungu
2007 NMR in Biomedicine  
to enhance the clinical utility of in vivo 1 H MRSI.  ...  Central to the proposed approach is automatic iterative data selection which uses prior knowledge about the spatial distribution of the spectra to remove voxels that are due to artifacts and undesired  ...  In (b), after removal of the strong lipid contribution by active data selection, cNMF can be applied again to recover the 'tumor' and 'normal brain' spectral patterns with greater specificity (the red  ... 
doi:10.1002/nbm.1151 pmid:17347991 fatcat:a34emdbmxncqtj3s54oajr4dvu

Accelerated MR spectroscopic imaging—a review of current and emerging techniques

Wolfgang Bogner, Ricardo Otazo, Anke Henning
2020 NMR in Biomedicine  
These include shortening of repetition times, spatial-spectral encoding, undersampling of k-space and time domain, and use of spatial-spectral prior knowledge in the reconstruction.  ...  In this way in vivo MRSI has considerably advanced in terms of spatial coverage, spatial resolution, acquisition speed, artifact suppression, number of detectable metabolites and quantification precision  ...  Moser, Lukas Hingerl and Gilbert Hangel for their support with the preparation of Figures 1, 4, 6 , and 8 as well as Zhi-Pei Liang and Fan Lam for providing Figure 15 . ORCID  ... 
doi:10.1002/nbm.4314 pmid:32399974 pmcid:PMC8244067 fatcat:kx2yyrjp7vbhvks5j723s5prre

Ultra-high resolution brain metabolite mapping at 7 T by short-TR Hadamard-encoded FID-MRSI

Gilbert Hangel, Bernhard Strasser, Michal Považan, Eva Heckova, Lukas Hingerl, Roland Boubela, Stephan Gruber, Siegfried Trattnig, Wolfgang Bogner
2018 NeuroImage  
Lipid contamination was removed during postprocessing using L2-regularisation. Simulations, phantom and volunteer measurements were performed.  ...  This facilitates the use of UHR-MRSI for clinical applications, such as measurements of the small structures and metabolic pathologic deviations found in small Multiple Sclerosis lesions.  ...  Lipid artefact removal Lipid removal during data processing using L2-regularisation (Bilgic et al., 2013) , as in our study, can reduce lipid signals by a lipid suppression factor (LSF) of 9-10.  ... 
doi:10.1016/j.neuroimage.2016.10.043 pmid:27825954 fatcat:jltpe5k7azgcta447oyogn5w6a

Automated Analysis of 1H Magnetic Resonance Metabolic Imaging Data as an Aid to Clinical Decision-Making in the Evaluation of Intracranial Lesions

Dikoma C. Shungu, Shuyan Du, Xiangling Mao, Linda A. Heier, Susan C. Pannullo, Paul Sajda
2007 IEEE Engineering in Medicine and Biology Society. Conference Proceedings  
This paper discusses this impediment to widespread clinical use of 1 H MRSI and then describes an automated data analysis approach that promises to facilitate use of the technique in the evaluation of  ...  imaging (MRI) in the clinical evaluation of neurological disorders and diagnostic decisionmaking.  ...  From the spatial distribution of the recovered spectral patterns, it can be seen that the lipids are concentrated near the skull, while the spectral pattern for the brain is internal 1 Set ˆ= X X (use  ... 
doi:10.1109/iembs.2007.4353294 pmid:18002960 fatcat:mf4tzzeh3bbutghkgr7dukdil4

A Subspace Approach to Spectral Quantification for MR Spectroscopic Imaging

Yudu Li, Fan Lam, Bryan Clifford, Zhi-Pei Liang
2017 IEEE Transactions on Biomedical Engineering  
Based on this model, the spectral quantification can be solved in two steps: a) subspace estimation based on the empirical distributions of the spectral parameters estimated using spectral priors, and  ...  Objective-To provide a new approach to spectral quantification for magnetic resonance spectroscopic imaging (MRSI), incorporating both spatial and spectral priors.  ...  Acknowledgments This work was supported in part by the National Institutes of Health (NIH-R21-EB021013-01, NIH-P41-EB002034) and in part by Beckman Postdoctoral Fellowship.  ... 
doi:10.1109/tbme.2017.2741922 pmid:28829303 pmcid:PMC5646283 fatcat:rb3swxg7orfihgoew2cl3bxql4

Achieving High-Resolution 1H-MRSI of the Human Brain with Compressed-Sensing and Low-Rank Reconstruction at 7 Tesla

Antoine Klauser, Bernhard Strasser, Bijaya Thapa, Francois Lazeyras, Ovidiu Andronesi
2021 Journal of magnetic resonance (San Diego, Calif. 1997 : Print)  
High-resolution and whole-slab brain MRSI remains however very challenging due to lengthy acquisition, low signal, lipid contamination and field inhomogeneity.  ...  This new application of compressed sensing acceleration paves the way for high-resolution MRSI in clinical setting with acquisition times of 5 min for 2D MRSI at 2.5 mm and of 20 min for 3D MRSI at 3.3  ...  .: IZSEZ0_188859, and the National Institutes of Health through National Cancer Institute grant 1R01CA211080.  ... 
doi:10.1016/j.jmr.2021.107048 pmid:34438355 pmcid:PMC8717865 fatcat:pfidjvdn4rcklaqnsgcgz2gfea

Simultaneous mapping of metabolites and individual macromolecular components via ultra-short acquisition delay 1 H MRSI in the brain at 7T

Michal Považan, Bernhard Strasser, Gilbert Hangel, Eva Heckova, Stephan Gruber, Siegfried Trattnig, Wolfgang Bogner
2017 Magnetic Resonance in Medicine  
In this study, we aimed to create an improved MM model by parameterization of the in vivo MM spectrum into individual components, and to use this new model to quantify free induction decay MR spectroscopic  ...  Purpose: Short-echo-time proton MR spectra at 7T feature nine to 10 distinct macromolecule (MM) resonances that overlap with the signals of metabolites.  ...  Malgorzata Marjanska for valuable advice on the handling of lipid signals in LCModel, and Dr. Michael Weber for a thoughtful statistical analysis of the data.  ... 
doi:10.1002/mrm.26778 pmid:28643447 pmcid:PMC5811892 fatcat:el27sts2fbbjtp6d2amthkcegu

Achieving High-Resolution Whole-Brain Slab 1H-MRSI with Compressed-Sensing and Low-Rank Reconstruction at 7 Tesla [article]

Antoine Klauser, Bernhard Strasser, Bijaya Thapa, Francois Lazeyras, Ovidiu Andronesi
2020 bioRxiv   pre-print
High-resolution and whole-brain slab MRSI remains however very challenging due to lengthy acquisition, low signal, lipid contamination and field inhomogeneity.  ...  This new application of compressed sensing acceleration paves the way for high-resolution MRSI in clinical setting with acquisition times of 5 min for 2D MRSI at 2.5~mm and of 20 min for 3D MRSI at 3.3  ...  This research was supported by the Swiss National Science Foundation grant number: IZSEZ0 188859, and the National Institutes of Health through National Cancer Institute grant 1R01CA211080.  ... 
doi:10.1101/2020.05.13.092668 fatcat:wi755wcl7zglzau2sxky2ec5nq

Lipid suppressed and tissue-fraction corrected metabolic distributions in human central brain structures using 2D 1H Magnetic Resonance Spectroscopic Imaging at 7 tesla [article]

Alex A Bhogal, Tommy A Broeders, Lisan Morsinkhof, Mirte Edens, Sahar Nassirpour, Paul Chang, Dennis W.J. Klomp, Christiaan Vinkers, Jannie P Wijnen
2020 bioRxiv   pre-print
scan-time constraints, are among the factors that hinder the widespread implementation of in vivo MRSI.  ...  FID-MRSI) measurements made using a 7 tesla MR scanner.  ...  The authors would like to acknowledge Philippe Cornelisse for his assistance in data acquisition.  ... 
doi:10.1101/2020.06.09.142646 fatcat:7qinicvwrjglnagqrbqf3ufuvy

High-resolution1H-MRSI of the brain using short-TE SPICE

Chao Ma, Fan Lam, Qiang Ning, Curtis L. Johnson, Zhi-Pei Liang
2016 Magnetic Resonance in Medicine  
Results-In vivo 1 H-MRSI results show that the proposed method can effectively remove the remaining water and lipid signals from sparse MRSI data acquired at 20 ms TE.  ...  A set of signal processing algorithms are developed to remove the water and lipid signals and jointly reconstruct the metabolite and baseline signals.  ...  Alternative constraints include the spatial and spectral sparsity constraints on the metabolite signals.  ... 
doi:10.1002/mrm.26130 pmid:26841000 pmcid:PMC5493212 fatcat:5hivyqf7czbp7d2iycw4u46tym
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