Manifold Learning in MR spectroscopy using nonlinear dimensionality reduction and unsupervised clustering.

Abstract:

PURPOSE:To investigate whether nonlinear dimensionality reduction improves unsupervised classification of (1) H MRS brain tumor data compared with a linear method. METHODS:In vivo single-voxel (1) H magnetic resonance spectroscopy (55 patients) and (1) H magnetic resonance spectroscopy imaging (MRSI) (29 patients) data were acquired from histopathologically diagnosed gliomas. Data reduction using Laplacian eigenmaps (LE) or independent component analysis (ICA) was followed by k-means clustering or agglomerative hierarchical clustering (AHC) for unsupervised learning to assess tumor grade and for tissue type segmentation of MRSI data. RESULTS:An accuracy of 93% in classification of glioma grade II and grade IV, with 100% accuracy in distinguishing tumor and normal spectra, was obtained by LE with unsupervised clustering, but not with the combination of k-means and ICA. With (1) H MRSI data, LE provided a more linear distribution of data for cluster analysis and better cluster stability than ICA. LE combined with k-means or AHC provided 91% accuracy for classifying tumor grade and 100% accuracy for identifying normal tissue voxels. Color-coded visualization of normal brain, tumor core, and infiltration regions was achieved with LE combined with AHC. CONCLUSION:The LE method is promising for unsupervised clustering to separate brain and tumor tissue with automated color-coding for visualization of (1) H MRSI data after cluster analysis.

journal_name

Magn Reson Med

authors

Yang G,Raschke F,Barrick TR,Howe FA

doi

10.1002/mrm.25447

subject

Has Abstract

pub_date

2015-09-01 00:00:00

pages

868-78

issue

3

eissn

0740-3194

issn

1522-2594

journal_volume

74

pub_type

杂志文章
  • An optimized center-out k-space trajectory for multishot MRI: comparison with spiral and projection reconstruction.

    abstract::A method for collecting MRI data on a set of rotated trajectories that begin at the center of k-space is outlined. It is theoretically slightly faster, slightly less susceptible to off-resonance and motion-induced phase, and produces images with slightly better signal-to-noise ratio than methods using Archimedean spir...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/(sici)1522-2594(199910)42:4<714::aid-mrm13

    authors: Pipe JG

    更新日期:1999-10-01 00:00:00

  • Nonbalanced SSFP-based quantitative magnetization transfer imaging.

    abstract::The previously reported concept for quantitative magnetization transfer (MT) imaging using balanced steady-state free precession (SSFP) is applied to nonbalanced SSFP sequences. This offers the possibility to derive quantitative MT parameters of targets with high-susceptibility variations such as the musculoskeletal s...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.22331

    authors: Gloor M,Scheffler K,Bieri O

    更新日期:2010-07-01 00:00:00

  • 2D multislice and 3D MRI sequences are often equally sensitive.

    abstract::A simple theoretical model was developed to compare the sensitivities (i.e., signal-to-noise ratios per unit imaging time) of two-dimensional (2D) multislice and 3D imaging sequences. The model shows that the sensitivities of 3D and 2D multislice MRI sequences are usually similar. Sensitivities are identical in T2-wei...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/(sici)1522-2594(199904)41:4<824::aid-mrm23

    authors: Johnson G,Wadghiri YZ,Turnbull DH

    更新日期:1999-04-01 00:00:00

  • Convex gradient optimization for increased spatiotemporal resolution and improved accuracy in phase contrast MRI.

    abstract:PURPOSE:To evaluate convex gradient optimization (CVX) for increased spatiotemporal resolution and improved accuracy for phase-contrast MRI (PC-MRI). METHODS:A conventional flow-compensated and flow-encoded (FCFE) PC-MRI sequence was compared with a CVX PC-MRI sequence using numerical simulations, flow phantom experim...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.25059

    authors: Middione MJ,Wu HH,Ennis DB

    更新日期:2014-12-01 00:00:00

  • Contrast-enhanced MRI of brown adipose tissue after pharmacological stimulation.

    abstract::A non-invasive method for studying the modifications induced in lipid depots by hormonal stimulation could extend knowledge of adipose tissues. We studied the effect of adrenergic stimulation on interscapular brown adipose tissue (IBAT) of rats using contrast-enhanced MRI. Controls and rats pre-treated with adrenaline...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.20851

    authors: Sbarbati A,Cavallini I,Marzola P,Nicolato E,Osculati F

    更新日期:2006-04-01 00:00:00

  • Present clinical status of magnetic resonance imaging.

    abstract::Magnetic resonance imaging has achieved clinical importance and has become the primary tool in the investigation of head, spinal cord, pelvis, cancellous bone, pericardium (with gating), gallbladder, lymph node masses, and very soon, in the evaluation of joints. In many areas, particularly with respiratory and ECG gat...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章,评审

    doi:10.1002/mrm.1910020402

    authors: Margulis AR,Fisher MR

    更新日期:1985-08-01 00:00:00

  • MRI-based transfer function determination through the transfer matrix by jointly fitting the incident and scattered B 1 + field.

    abstract:PURPOSE:A purely experimental method for MRI-based transfer function (TF) determination is presented. A TF characterizes the potential for radiofrequency heating of a linear implant by relating the incident tangential electric field to a scattered electric field at its tip. We utilize the previously introduced transfer...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.27974

    authors: Tokaya JP,Raaijmakers AJE,Luijten PR,Sbrizzi A,van den Berg CAT

    更新日期:2020-03-01 00:00:00

  • Multiecho segmented EPI with z-shimmed background gradient compensation (MESBAC) pulse sequence for fMRI.

    abstract::A MultiEcho Segmented EPI with z-shimmed BAckground gradient Compensation (MESBAC) pulse sequence is proposed and validated for functional MRI (fMRI) study in regions suffering from severe susceptibility artifacts. This sequence provides an effective tradeoff between spatial and temporal resolution and reduces image d...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.10219

    authors: Li Z,Wu G,Zhao X,Luo F,Li SJ

    更新日期:2002-08-01 00:00:00

  • Parallel reconstruction using null operations.

    abstract::A novel iterative k-space data-driven technique, namely parallel reconstruction using null operations (PRUNO), is presented for parallel imaging reconstruction. In PRUNO, both data calibration and image reconstruction are formulated into linear algebra problems based on a generalized system model. An optimal data cali...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.22899

    authors: Zhang J,Liu C,Moseley ME

    更新日期:2011-11-01 00:00:00

  • Regional and temporal variations in tissue sodium concentration during the acute stroke phase.

    abstract::A technique for noninvasively quantifying the concentration of sodium ((23) Na) ions was applied to the study of ischemic stroke. (23) Na-magnetic resonance imaging techniques have shown considerable potential for measuring subtle changes in ischemic tissue, although studies to date have suffered primarily from poor s...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.23031

    authors: Wetterling F,Gallagher L,Macrae IM,Junge S,Fagan AJ

    更新日期:2012-03-01 00:00:00

  • Assessment and correction of macroscopic field variations in 2D spoiled gradient-echo sequences.

    abstract:PURPOSE:To model and correct the dephasing effects in the gradient-echo signal for arbitrary RF excitation pulses with large flip angles in the presence of macroscopic field variations. METHODS:The dephasing of the spoiled 2D gradient-echo signal was modeled using a numerical solution of the Bloch equations to calcula...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.28139

    authors: Soellradl M,Lesch A,Strasser J,Pirpamer L,Stollberger R,Ropele S,Langkammer C

    更新日期:2020-08-01 00:00:00

  • Quantitation of absolute 2H enrichment of plasma glucose by 2H NMR analysis of its monoacetone derivative.

    abstract::A simple (2)H NMR method for quantifying absolute (2)H-enrichments in all seven aliphatic positions of glucose following its derivatization to monoacetone glucose is presented. The method is based on the addition of a small quantity of (2)H-enriched formate to the NMR sample. When the method was applied to [2-(2)H]mon...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.10234

    authors: Jones JG,Perdigoto R,Rodrigues TB,Geraldes CF

    更新日期:2002-09-01 00:00:00

  • T2 relaxation-time mapping in healthy and diseased skeletal muscle using extended phase graph algorithms.

    abstract:PURPOSE:Multi-echo spin-echo (MSE) transverse relaxometry mapping using multi-component models is used to study disease activity in neuromuscular disease by assessing the T2 of the myocytic component (T2water ). Current extended phase graph algorithms are not optimized for fat fractions above 50% and the effects of ina...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.28290

    authors: Keene KR,Beenakker JM,Hooijmans MT,Naarding KJ,Niks EH,Otto LAM,van der Pol WL,Tannemaat MR,Kan HE,Froeling M

    更新日期:2020-11-01 00:00:00

  • The effect of reducing repetition time TR on the measurement of liver R2 for the purpose of measuring liver iron concentration.

    abstract::The effects of reducing the pulse repetition time from 2500 ms to 1000 ms when using spin-density-projection-assisted R2-magnetic resonance imaging for the purpose of measuring liver iron concentration were evaluated. Repeated liver R2 measurements were made using both protocols on 60 subjects with liver iron concentr...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.22712

    authors: Pavitt HL,Aydinok Y,El-Beshlawy A,Bayraktaroglu S,Ibrahim AS,Hamdy MM,Pang W,Sharples C,St Pierre TG

    更新日期:2011-05-01 00:00:00

  • Common k-space acquisition: a method to improve myocardial grid-tag contrast.

    abstract::A current limitation of many myocardial tag acquisitions employing SPAMM encoding is the relatively rapid loss of tag contrast over the cardiac cycle. Acquisition schemes that apply line tags produce prolonged tag contrast compared with directly excited grid tags. However, a grid-tag series can be generated by combini...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.1910370519

    authors: Doyle M,Walsh EG,Foster RE,Pohost GM

    更新日期:1997-05-01 00:00:00

  • Diffusion-prepared 3D gradient spin-echo sequence for improved oscillating gradient diffusion MRI.

    abstract:PURPOSE:Oscillating gradient (OG) enables the access of short diffusion times for time-dependent diffusion MRI (dMRI); however, it poses several technical challenges for clinical use. This study proposes a 3D oscillating gradient-prepared gradient spin-echo (OGprep-GRASE) sequence to improve SNR and shorten acquisition...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.28401

    authors: Wu D,Liu D,Hsu YC,Li H,Sun Y,Qin Q,Zhang Y

    更新日期:2021-01-01 00:00:00

  • Perfusion-based event-related functional MRI.

    abstract::Perfusion-based event-related functional MRI was performed by measuring flow-sensitive alternating inversion recovery (FAIR) signal changes during repeated single-trial, short visual stimulation (250 msec). In the visual cortex activation area, the blood flow increases immediately after the stimulus, reaches the maxim...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/(sici)1522-2594(199912)42:6<1011::aid-mrm3

    authors: Liu HL,Gao JH

    更新日期:1999-12-01 00:00:00

  • Feasibility of multiple-mouse dynamic contrast-enhanced MRI.

    abstract::Dynamic contrast-enhanced (DCE-) MRI is often used to evaluate the response to experimental antiangiogenic therapies in small animal models of cancer. Unfortunately, DCE-MRI studies often require a substantial investment of both time and money to achieve the desired level of statistical significance. Multiple-mouse MR...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.21348

    authors: Ramirez MS,Ragan DK,Kundra V,Bankson JA

    更新日期:2007-09-01 00:00:00

  • Numerical simulations of carotid MRI quantify the accuracy in measuring atherosclerotic plaque components in vivo.

    abstract:PURPOSE:Atherosclerotic carotid plaques can be quantified in vivo by MRI. However, the accuracy in segmentation and quantification of components such as the thin fibrous cap (FC) and lipid-rich necrotic core (LRNC) remains unknown due to the lack of a submillimeter scale ground truth. METHODS:A novel approach was take...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.24905

    authors: Nieuwstadt HA,Geraedts TR,Truijman MT,Kooi ME,van der Lugt A,van der Steen AF,Wentzel JJ,Breeuwer M,Gijsen FJ

    更新日期:2014-07-01 00:00:00

  • Generalization of intravoxel incoherent motion model by introducing the notion of continuous pseudodiffusion variable.

    abstract:PURPOSE:A generalized intravoxel incoherent motion (IVIM) model, called the GIVIM, was proposed to better account for complex perfusion present in the tissues having various vessels and flow regimes, such as the liver. THEORY AND METHODS:The notions of continuous pseudodiffusion variable as well as perfusion fraction ...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.26064

    authors: Kuai ZX,Liu WY,Zhang YL,Zhu YM

    更新日期:2016-11-01 00:00:00

  • System identification theory in pharmacokinetic modeling of dynamic contrast-enhanced MRI: influence of contrast injection.

    abstract::Optimization of experimental settings of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), like the contrast administration protocol, is of great importance for reliable quantification of the microcirculatory properties, such as the volume transfer-constant K(trans). Using system identification theory an...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.21575

    authors: Aerts HJ,van Riel NA,Backes WH

    更新日期:2008-05-01 00:00:00

  • Local planar gradients with order-of-magnitude strength and speed advantage.

    abstract::A three-axis uniplanar gradient coil was designed and built to provide order-of-magnitude increases in gradient strength of up to 500 mT/m on the x- and y-axes, and 1000 mT/m for the z-axis at 640 A input over a limited FOV ( approximately 16 cm) for superficial regions, compared to conventional gradient coils, with s...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.21263

    authors: Aksel B,Marinelli L,Collick BD,Von Morze C,Bottomley PA,Hardy CJ

    更新日期:2007-07-01 00:00:00

  • Advantage of sampling density weighted apodization over postacquisition filtering apodization for sodium MRI of the human brain.

    abstract::For sodium imaging of the human brain, Gibbs' ringing can degrade image appearance and confound image analysis; k-space filtering is generally required. In this work, the signal to noise ratio (SNR) advantage of sampling density weighted apodization (SDWA) over uniform k-space sampling with postacquisition filtering a...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.21738

    authors: Stobbe R,Beaulieu C

    更新日期:2008-10-01 00:00:00

  • Constrained estimation of the arterial input function for myocardial perfusion cardiovascular magnetic resonance.

    abstract::Accurate quantification of myocardial perfusion remains challenging due to saturation of the arterial input function at high contrast concentrations. A method for estimating the arterial input function directly from tissue curves in the myocardium that avoids these difficulties is presented. In this constrained altern...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.22809

    authors: Fluckiger JU,Schabel MC,DiBella EV

    更新日期:2011-08-01 00:00:00

  • Cerebrospinal fluid-suppressed high-resolution diffusion imaging of human brain.

    abstract::A cerebrospinal fluid (CSF)-suppressed flow-attenuated inversion recovery (FLAIR) double-shot diffusion echo-planar imaging (EPI) sequence was developed and used, along with a non-CSF-suppressed version of the sequence, to determine the extent of the contribution of CSF partial-volume averaging to the apparent diffusi...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.1910370117

    authors: Falconer JC,Narayana PA

    更新日期:1997-01-01 00:00:00

  • Quantifying the intra- and extravascular contributions to spin-echo fMRI at 3 T.

    abstract::Functional MRI (fMRI) by means of spin-echo (SE) techniques provides an interesting alternative to gradient-echo methods because the contrast is based primarily on dynamic averaging associated with the blood oxygenation level-dependent (BOLD) effect. In this article the contributions from different brain compartments ...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.20221

    authors: Jochimsen TH,Norris DG,Mildner T,Möller HE

    更新日期:2004-10-01 00:00:00

  • Chemically induced analgesic nephropathy in the rat monitored by proton-electron double-resonance imaging (PEDRI).

    abstract::Proton-electron double-resonance imaging (PEDRI) was used to assess renal function by monitoring the flow of the exogenous nitroxide free radical proxyl carboxylic acid (PCA) through normal and injured kidneys in the living rat. Kidney damage was induced by treatment with 2-bromoethylamine (BEA), which provides a well...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.1910400214

    authors: Seimenis I,Foster MA,Lurie DJ,Hutchison JM,Whiting PH,Payne S

    更新日期:1998-08-01 00:00:00

  • MRI evaluation of myocardial perfusion without a contrast agent using magnetization transfer.

    abstract::We propose a new magnetic resonance imaging (MRI) technique that is sensitive to myocardial tissue perfusion that obviates the use of an extrinsic contrast agent. Significant advantages of such a technique are that it avoids accumulation of contrast agent when repeated studies are performed on the same subject and tha...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.1910300219

    authors: Prasad PV,Burstein D,Edelman RR

    更新日期:1993-08-01 00:00:00

  • Design and evaluation of quantitative MRI phantoms to mimic the simultaneous presence of fat, iron, and fibrosis in the liver.

    abstract:PURPOSE:To design, construct, and evaluate quantitative MR phantoms that mimic MRI signals from the liver with simultaneous control of three parameters: proton-density fat fraction (PDFF), R 2 ∗ ...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.28452

    authors: Zhao R,Hamilton G,Brittain JH,Reeder SB,Hernando D

    更新日期:2021-02-01 00:00:00

  • Sensitivity regularization of the Cramér-Rao lower bound to minimize B1 nonuniformity effects in quantitative magnetization transfer imaging.

    abstract:PURPOSE:To develop and validate a regularization approach of optimizing B1 insensitivity of the quantitative magnetization transfer (qMT) pool-size ratio (F). METHODS:An expression describing the impact of B1 inaccuracies on qMT fitting parameters was derived using a sensitivity analysis. To simultaneously optimize fo...

    journal_title:Magnetic resonance in medicine

    pub_type: 杂志文章

    doi:10.1002/mrm.27337

    authors: Boudreau M,Pike GB

    更新日期:2018-12-01 00:00:00