A deep learning approach to estimation of subject-level bias and variance in high angular resolution diffusion imaging.

Abstract:

:The ability to evaluate empirical diffusion MRI acquisitions for quality and to correct the resulting imaging metrics allows for improved inference and increased replicability. Previous work has shown promise for estimation of bias and variance of generalized fractional anisotropy (GFA) but comes at the price of computational complexity. This paper aims to provide methods for estimating GFA, bias of GFA and standard deviation of GFA quickly and accurately. In order to provide a method for bias and variance estimation that can return results faster than the previously studied statistical techniques, three deep, fully-connected neural networks are developed for GFA, bias of GFA, and standard deviation of GFA. The results of these networks are compared to the observed values of the metrics as well as those fit from the statistical techniques (i.e. Simulation Extrapolation (SIMEX) for bias estimation and wild bootstrap for variance estimation). Our GFA network provides predictions that are closer to the true GFA values than a Q-ball fit of the observed data (root-mean-square error (RMSE) 0.0077 vs 0.0082, p < .001). The bias network also shows statistically significant improvement in comparison to the SIMEX-estimated error of GFA (RMSE 0.0071 vs. 0.01, p < .001).

journal_name

Magn Reson Imaging

authors

Hainline AE,Nath V,Parvathaneni P,Schilling KG,Blaber JA,Anderson AW,Kang H,Landman BA

doi

10.1016/j.mri.2019.03.021

subject

Has Abstract

pub_date

2019-06-01 00:00:00

pages

130-136

eissn

0730-725X

issn

1873-5894

pii

S0730-725X(18)30436-3

journal_volume

59

pub_type

杂志文章
  • Alterations in diffusion properties of white matter in Williams syndrome.

    abstract::Diffusion tensor imaging (DTI) was used to investigate the involvement of brain white matter in Williams syndrome (WS), a genetic neurodevelopmental disorder. Whole-brain DTIs were obtained from 16 young adults with WS and 16 normal controls. A voxel-based analysis was performed to compare fractional anisotropy (FA) v...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2011.07.012

    authors: Arlinghaus LR,Thornton-Wells TA,Dykens EM,Anderson AW

    更新日期:2011-11-01 00:00:00

  • Spectral pattern of total creatine and trimethyl ammonium in multiple sclerosis.

    abstract::Fatigue and impairment mobility are frequent problems in multiple sclerosis (MS). Despite its enormous potential, in vivo (1)H MRS of skeletal muscles for MS patients is a largely unexplored field. One fundamental question remains unanswered: whether MS can cause observable proton metabolite changes. High quality two-...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2004.01.005

    authors: Hu J,Xu Y,Jiang Q,Sehgal V,Shen Y,Xuan Y,Xia Y

    更新日期:2004-04-01 00:00:00

  • In vivo nuclear magnetic resonance imaging and spectroscopy of aquatic organisms.

    abstract::NMR imaging and localized 1H spectroscopy of a variety of aquatic organisms in vivo is described for the first time. The practical consideration of life support, water volume, salinity, and anesthesia are discussed and solutions presented. Such animal studies shape our understanding of physiology, biochemistry, and bi...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/0730-725x(90)90253-x

    authors: Blackband SJ,Stoskopf MK

    更新日期:1990-01-01 00:00:00

  • Structural changes in glutamate cell swelling followed by multiparametric q-space diffusion MR of excised rat spinal cord.

    abstract::Diffusion in the extracellular and intracellular spaces (ECS and ICS, respectively) was evaluated in excised spinal cords, before and after cell swelling induced by glutamate, by high b-value q-space diffusion MR of specific markers and water. The signal decays of deuterated tetramethylammonium (TMA-d(12)) chloride, a...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2004.01.029

    authors: Biton IE,Mayk A,Assaf Y,Cohen Y

    更新日期:2004-06-01 00:00:00

  • 3D Slicer as an image computing platform for the Quantitative Imaging Network.

    abstract::Quantitative analysis has tremendous but mostly unrealized potential in healthcare to support objective and accurate interpretation of the clinical imaging. In 2008, the National Cancer Institute began building the Quantitative Imaging Network (QIN) initiative with the goal of advancing quantitative imaging in the con...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2012.05.001

    authors: Fedorov A,Beichel R,Kalpathy-Cramer J,Finet J,Fillion-Robin JC,Pujol S,Bauer C,Jennings D,Fennessy F,Sonka M,Buatti J,Aylward S,Miller JV,Pieper S,Kikinis R

    更新日期:2012-11-01 00:00:00

  • Noise estimation in single- and multiple-coil magnetic resonance data based on statistical models.

    abstract::Noise estimation is a challenging task in magnetic resonance imaging (MRI), with applications in quality assessment, filtering or diffusion tensor estimation. Main noise estimators based on the Rician model are revisited and classified in this article, and new useful methods are proposed. Additionally, all the surveye...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2009.05.025

    authors: Aja-Fernández S,Tristán-Vega A,Alberola-López C

    更新日期:2009-12-01 00:00:00

  • Glutamate quantification by PRESS or MEGA-PRESS: Validation, repeatability, and concordance.

    abstract:PURPOSE:While PRESS is often employed to measure glutamate concentrations, MEGA-PRESS enables simultaneous Glx (glutamate and glutamine) and GABA measurements. This study aimed to compare validation, repeatability, and concordance of different approaches for glutamate quantification at 3T to aid future studies in their...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2017.12.029

    authors: van Veenendaal TM,Backes WH,van Bussel FCG,Edden RAE,Puts NAJ,Aldenkamp AP,Jansen JFA

    更新日期:2018-05-01 00:00:00

  • In vitro experiments on ICOSA6 4D flow MRI measurement for the quantification of velocity and turbulence parameters.

    abstract:PURPOSE:To perform comprehensive in vitro experiments using six-directional icosahedral flow encoding (ICOSA6) 4D flow magnetic resonance imaging (MRI) under various scan conditions to analyze the robustness of velocity and turbulence quantification. MATERIALS AND METHODS:In vitro flow phantoms with steady flow rates ...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2020.06.020

    authors: Ha H,Park KJ,Dyverfeldt P,Ebbers T,Yang DH

    更新日期:2020-10-01 00:00:00

  • Evaluation of EPI distortion correction methods for quantitative MRI of the brain at high magnetic field.

    abstract::High field MRI has been applied to high-resolution structural and functional imaging of the brain. Echo planar imaging (EPI) is an ultrafast acquisition technique widely used in diffusion imaging, functional MRI and perfusion imaging. However, it suffers from geometric and intensity distortions caused by static magnet...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2015.06.010

    authors: Hong X,To XV,Teh I,Soh JR,Chuang KH

    更新日期:2015-11-01 00:00:00

  • Double-spin-echo diffusion weighting with a modified eddy current adjustment.

    abstract::Magnetic field inhomogeneities like eddy current-related gradient fields cause geometric distortions in echo-planar imaging (EPI). This in particular affects diffusion-weighted imaging where these distortions vary with the direction of the diffusion weighting and hamper the accurate determination of diffusion paramete...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2009.12.004

    authors: Finsterbusch J

    更新日期:2010-04-01 00:00:00

  • MRI appearance of disseminated osseous tuberculosis.

    abstract::Disseminated osseous tuberculosis is a rare disease. This is a report of two cases of disseminated osseous tuberculosis imaged with MRI at 1.5-T, CT, plain radiography and bone scintigraphy. CT and plain radiography demonstrated either highly destructive or cystic lesions with sclerotic margins. Bone scintigraphy and ...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/0730-725x(87)90384-5

    authors: Quinn SF,Murray W,Prochaska J,Cochran C,Clark R

    更新日期:1987-01-01 00:00:00

  • 1H magnetic resonance imaging and 31P magnetic resonance spectroscopy in experimental filariasis.

    abstract::1H Magnetic resonance imaging and 31P magnetic resonance spectroscopy (MRS) have been carried out in experimental rodent filariasis, i.e., Acanthocheilonema viteae infection in the rodent host, Mastomys coucha. The T2-weighted image of the infected host shows fine hyperintense thread like structures of adult filariid ...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/s0730-725x(97)00180-x

    authors: Shukla-Dave A,Fatma N,Roy R,Srivastava S,Chatterjee RK,Govindaraju V,Viswanathan AK,Raghunathan P

    更新日期:1997-01-01 00:00:00

  • Assessment of cardiac iron by MRI susceptometry and R2* in patients with thalassemia.

    abstract::A magnetic resonance imaging cardiac magnetic susceptometry (MRI-CS) technique for assessing cardiac tissue iron concentration based on phase mapping was developed. Normal control subjects (n=9) and thalassemia patients (n=13) receiving long-term blood transfusion therapy underwent MRI-CS and MRI measurements of the c...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2009.12.001

    authors: Wang ZJ,Fischer R,Chu Z,Mahoney DH Jr,Mueller BU,Muthupillai R,James EB,Krishnamurthy R,Chung T,Padua E,Vichinsky E,Harmatz P

    更新日期:2010-04-01 00:00:00

  • Quantitative magnetic resonance imaging of 'Fuyu' persimmon fruit during development and ripening.

    abstract::Qualitative and quantitative proton magnetic resonance imaging techniques were applied to persimmon (Diospyros kaki cv 'Fuyu') fruit during development and post-harvest ripening. Spin-lattice (T(1)) relaxation times in mesocarp parenchyma and vascular tissue exhibited a sigmoidal pattern of increase leading to commerc...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/s0730-725x(03)00082-1

    authors: Clark CJ,MacFall JS

    更新日期:2003-07-01 00:00:00

  • GPU-accelerated nonparametric kinetic analysis of DCE-MRI data from glioblastoma patients treated with bevacizumab.

    abstract::Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is often used to examine vascular function in malignant tumors and noninvasively monitor drug efficacy of antivascular therapies in clinical studies. However, complex numerical methods used to derive tumor physiological properties from DCE-MRI images can b...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2012.09.007

    authors: Hsu YH,Ferl GZ,Ng CM

    更新日期:2013-05-01 00:00:00

  • Whole-brain, ultra-high spatial resolution ex vivo MRI with off-the-shelf components.

    abstract:BACKGROUND:Ultra-high spatial resolution imaging of whole, ex vivo brains provides new opportunities to understand neurological disease. Recent work has demonstrated that 100 μm isotropic resolution can reveal anatomical details that are otherwise difficult to appreciate, but relied on fabrication facilities, fabricati...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2020.11.002

    authors: Kim S,Sakaie K,Blümcke I,Jones S,Lowe MJ

    更新日期:2021-02-01 00:00:00

  • NMR imaging, NMR diffraction and applications of pulsed gradient spin echoes in porous media.

    abstract::Diffraction ideas were first introduced to NMR by Mansfield and Grannell. Here we compare "Mansfield (k-space) diffraction" with the "diffusive (q-space) diffraction," noting their similarities and differences. The diffusive-diffraction concept is extremely helpful in elucidating the Pulsed Gradient Spin Echo NMR expe...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/s0730-725x(96)00152-x

    authors: Callaghan PT

    更新日期:1996-01-01 00:00:00

  • Ultrashort echo (UTE) versus pointwise encoding time reduction with radial acquisition (PETRA) sequences at 3 Tesla for knee meniscus: A comparative study.

    abstract:PURPOSE:The purposes of this study were to (1) correlate the ultrashort echo time (TE) signal intensity of the pointwise encoding time reduction with radial acquisition (PETRA) sequence with that of the ultrashort echo (UTE) sequence using in vivo meniscal ultrashort TE imaging of the knee with a 3-Tesla (3T) clinical ...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2015.09.003

    authors: Lee YH,Suh JS,Grodzki D

    更新日期:2016-02-01 00:00:00

  • Influence of cholecystectomy on the flow dynamic pattern of bile in the extrahepatic bile duct: Assessment by cine-dynamic MRCP with spatially-selective IR pulse.

    abstract:PURPOSE:To evaluate the influence of cholecystectomy on the flow dynamic pattern of bile in the extrahepatic bile duct by using cine-dynamic MRCP with spatially-selective inversion-recovery (IR) pulse non-invasively. MATERIALS AND METHODS:56 patients with cholecystectomy and 48 control subjects without cholecystectomy...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2020.08.016

    authors: Sotozono H,Tamada T,Kanki A,Yasokawa K,Fukunaga T,Yamamoto A,Ito K

    更新日期:2020-12-01 00:00:00

  • Diffusion-weighted MRI and MR- volumetry--in the evaluation of tumor response after preoperative chemoradiotherapy in patients with locally advanced rectal cancer.

    abstract:PURPOSE:To determine the diagnostic performance of diffusion-weighted MRI and MR volumetry for the assessment of tumor response after preoperative chemoradiotherapy (CRT) in patients with locally advanced rectal cancer. MATERIALS AND METHODS:Forty-three patients with rectal cancer who underwent preoperative CRT were p...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2014.08.041

    authors: Birlik B,Obuz F,Elibol FD,Celik AO,Sokmen S,Terzi C,Sagol O,Sarioglu S,Gorken I,Oztop I

    更新日期:2015-02-01 00:00:00

  • Simultaneous imaging of locus coeruleus and substantia nigra with a quantitative neuromelanin MRI approach.

    abstract::Quantitative MRI of neuromelanin (NM) containing structures (referred to as NM-MRI) in the brainstem, namely the locus coeruleus (LC) and substantia nigra (SN), may assist with the early detection of Parkinson's disease (PD) and Alzheimer's disease (AD) as well as differential diagnosis in the early disease stages. In...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2014.07.003

    authors: Chen X,Huddleston DE,Langley J,Ahn S,Barnum CJ,Factor SA,Levey AI,Hu X

    更新日期:2014-12-01 00:00:00

  • Changes in the liver parenchyma after proton beam radiotherapy: evaluation with MR imaging.

    abstract::The objective of this study was to describe magnetic resonance (MR) findings with a 1.5T imager for hepatic parenchymal changes after proton beam radiotherapy. Thirty-two patients who received proton radiotherapy with doses of 50-87 Gy underwent MR imaging 1-75 months (mean 22 months) after the start of irradiation. A...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/s0730-725x(00)00152-1

    authors: Onaya H,Itai Y,Yoshioka H,Ahmadi T,Niitsu M,Okumura T,Akine Y,Matsuzaki Y,Doi M,Tsuji H,Tsujii H

    更新日期:2000-07-01 00:00:00

  • Spiral demystified.

    abstract::Spiral acquisition schemes offer unique advantages such as flow compensation, efficient k-space sampling and robustness against motion that make this option a viable choice among other non-Cartesian sampling schemes. For this reason, the main applications of spiral imaging lie in dynamic magnetic resonance imaging suc...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章,评审

    doi:10.1016/j.mri.2010.03.036

    authors: Delattre BM,Heidemann RM,Crowe LA,Vallée JP,Hyacinthe JN

    更新日期:2010-07-01 00:00:00

  • Peripheral nerve diffusion tensor imaging.

    abstract::We examined if MR diffusion tensor imaging with fiber tracking could be performed on the sciatic nerve. In 3 healthy volunteers the proximal thigh was examined on a 1.5-Tesla MR-scanner with a 2-channel phased-array coil. Though inherently susceptible to motion, field inhomogeneities, and fast T(2)-relaxation of the d...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2004.01.073

    authors: Skorpil M,Karlsson M,Nordell A

    更新日期:2004-06-01 00:00:00

  • A proposal for a semiquantitative scoring system for lymphedema using Non-contrast Magnetic Resonance Lymphography (NMRL): Reproducibility among readers and correlation with clinical grading.

    abstract:PURPOSE:To assess the ability and reproducibility of Non-contrast Magnetic Resonance Lymphography (NMRL) in detecting and quantify lymphedema, using a semiquantitative scoring system. METHODS AND MATERIAL:This is a monocentric retrospective study of 134 consecutive patients with a clinical diagnosis of limb lymphedema...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2020.02.004

    authors: Franconeri A,Ballati F,Panzuto F,Raciti MV,Smedile A,Maggi A,Asteggiano C,Esposito M,Stoppa D,Lungarotti L,Bortolotto C,Giardini D,De Silvestri A,Calliada F

    更新日期:2020-05-01 00:00:00

  • Semi-automatic lung segmentation of DCE-MRI data sets of 2-year old children after congenital diaphragmatic hernia repair: Initial results.

    abstract::In congenital diaphragmatic hernia (CDH), lung hypoplasia and secondary pulmonary hypertension are the major causes of death and severe disability. Based on new therapeutic strategies survival rates could be improved to up to 80%. However, after surgical repair of CDH, long-term follow-up of these pediatric patients i...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2015.08.003

    authors: Zöllner FG,Daab M,Weidner M,Sommer V,Zahn K,Schaible T,Weisser G,Schoenberg SO,Neff KW,Schad LR

    更新日期:2015-12-01 00:00:00

  • Noncontrast MRI with diffusion-weighted imaging as the sole imaging modality for detecting liver malignancy in patients with high risk for hepatocellular carcinoma.

    abstract:PURPOSE:To compare the diagnostic performance of the noncontrast MRI including DWI to the standard MRI for detecting hepatic malignancies in patients with chronic liver disease. MATERIALS AND METHODS:We included 135 patients with 136 histologically-confirmed hepatocellular carcinomas (HCCs), 12 cholangiocarcinomas, an...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2013.12.021

    authors: Kim YK,Kim YK,Park HJ,Park MJ,Lee WJ,Choi D

    更新日期:2014-07-01 00:00:00

  • Deep neural network inspired by iterative shrinkage-thresholding algorithm with data consistency (NISTAD) for fast Undersampled MRI reconstruction.

    abstract::With the aim of developing a fast algorithm for high-quality MRI reconstruction from undersampled k-space data, we propose a novel deep neural Network, which is inspired by Iterative Shrinkage Thresholding Algorithm with Data consistency (NISTAD). NISTAD consists of three consecutive blocks: an encoding block, which m...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2020.04.016

    authors: Qiu W,Li D,Jin X,Liu F,Sun B

    更新日期:2020-07-01 00:00:00

  • Parallel imaging for first-pass myocardial perfusion.

    abstract::Two parallel imaging methods used for first-pass myocardial perfusion imaging were compared in terms of signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) and image artifacts. One used adaptive Time-adaptive SENSitivity Encoding (TSENSE) and the other used GeneRalized Autocalibrating Partially Parallel Acquisi...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/j.mri.2006.10.012

    authors: Irwan R,Lubbers DD,van der Vleuten PA,Kappert P,Götte MJ,Sijens PE

    更新日期:2007-06-01 00:00:00

  • Application of magnetic resonance imaging to the measurement of neurodegeneration in rat brain: MRI data correlate strongly with histology and enzymatic analysis.

    abstract::Focal brain ischemia was induced by middle cerebral artery occlusion in the rat. The volume of cerebral damage was determined 2 days later by MRI in vivo and in the same animals histologically. The edema volume as measured by MRI and the histologically determined infarction was highly correlated. As a consequence, the...

    journal_title:Magnetic resonance imaging

    pub_type: 杂志文章

    doi:10.1016/0730-725x(92)90411-r

    authors: Allegrini PR,Sauer D

    更新日期:1992-01-01 00:00:00