A computational diffusion MRI and parametric dictionary learning framework for modeling the diffusion signal and its features.

Abstract:

:In this work, we first propose an original and efficient computational framework to model continuous diffusion MRI (dMRI) signals and analytically recover important diffusion features such as the Ensemble Average Propagator (EAP) and the Orientation Distribution Function (ODF). Then, we develop an efficient parametric dictionary learning algorithm and exploit the sparse property of a well-designed dictionary to recover the diffusion signal and its features with a reduced number of measurements. The properties and potentials of the technique are demonstrated using various simulations on synthetic data and on human brain data acquired from 7T and 3T scanners. It is shown that the technique can clearly recover the dMRI signal and its features with a much better accuracy compared to state-of-the-art approaches, even with a small and reduced number of measurements. In particular, we can accurately recover the ODF in regions of multiple fiber crossing, which could open new perspectives for some dMRI applications such as fiber tractography.

journal_name

Med Image Anal

journal_title

Medical image analysis

authors

Merlet S,Caruyer E,Ghosh A,Deriche R

doi

10.1016/j.media.2013.04.011

subject

Has Abstract

pub_date

2013-10-01 00:00:00

pages

830-43

issue

7

eissn

1361-8415

issn

1361-8423

pii

S1361-8415(13)00064-9

journal_volume

17

pub_type

杂志文章
  • Analytical and fast Fiber Orientation Distribution reconstruction in 3D-Polarized Light Imaging.

    abstract::Three dimensional Polarized Light Imaging (3D-PLI) is an optical technique which allows mapping the spatial fiber architecture of fibrous postmortem tissues, at sub-millimeter resolutions. Here, we propose an analytical and fast approach to compute the fiber orientation distribution (FOD) from high-resolution vector d...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2020.101760

    authors: Alimi A,Deslauriers-Gauthier S,Matuschke F,Müller A,Muenzing SEA,Axer M,Deriche R

    更新日期:2020-10-01 00:00:00

  • RMDL: Recalibrated multi-instance deep learning for whole slide gastric image classification.

    abstract::The whole slide histopathology images (WSIs) play a critical role in gastric cancer diagnosis. However, due to the large scale of WSIs and various sizes of the abnormal area, how to select informative regions and analyze them are quite challenging during the automatic diagnosis process. The multi-instance learning bas...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2019.101549

    authors: Wang S,Zhu Y,Yu L,Chen H,Lin H,Wan X,Fan X,Heng PA

    更新日期:2019-12-01 00:00:00

  • HookNet: Multi-resolution convolutional neural networks for semantic segmentation in histopathology whole-slide images.

    abstract::We propose HookNet, a semantic segmentation model for histopathology whole-slide images, which combines context and details via multiple branches of encoder-decoder convolutional neural networks. Concentric patches at multiple resolutions with different fields of view, feed different branches of HookNet, and intermedi...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2020.101890

    authors: van Rijthoven M,Balkenhol M,Siliņa K,van der Laak J,Ciompi F

    更新日期:2021-02-01 00:00:00

  • Towards cross-modal organ translation and segmentation: A cycle- and shape-consistent generative adversarial network.

    abstract::Synthesized medical images have several important applications. For instance, they can be used as an intermedium in cross-modality image registration or used as augmented training samples to boost the generalization capability of a classifier. In this work, we propose a generic cross-modality synthesis approach with t...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2018.12.002

    authors: Cai J,Zhang Z,Cui L,Zheng Y,Yang L

    更新日期:2019-02-01 00:00:00

  • Rubik's Cube+: A self-supervised feature learning framework for 3D medical image analysis.

    abstract::Due to the development of deep learning, an increasing number of research works have been proposed to establish automated analysis systems for 3D volumetric medical data to improve the quality of patient care. However, it is challenging to obtain a large number of annotated 3D medical data needed to train a neural net...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2020.101746

    authors: Zhu J,Li Y,Hu Y,Ma K,Zhou SK,Zheng Y

    更新日期:2020-08-01 00:00:00

  • Tongue contour tracking in dynamic ultrasound via higher-order MRFs and efficient fusion moves.

    abstract::Analyses of the human tongue motion as captured from 2D dynamic ultrasound data often requires segmentation of the mid-sagittal tongue contours. However, semi-automatic extraction of the tongue shape presents practical challenges. We approach this segmentation problem by proposing a novel higher-order Markov random fi...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2012.07.001

    authors: Tang L,Bressmann T,Hamarneh G

    更新日期:2012-12-01 00:00:00

  • Multi-task exclusive relationship learning for alzheimer's disease progression prediction with longitudinal data.

    abstract::Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive impairment of memory and other cognitive functions. Currently, many multi-task learning approaches have been proposed to predict the disease progression at the early stage using longitudinal data, with each task corresponding to a pa...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2019.01.007

    authors: Wang M,Zhang D,Shen D,Liu M

    更新日期:2019-04-01 00:00:00

  • Piecewise-diffeomorphic image registration: application to the motion estimation between 3D CT lung images with sliding conditions.

    abstract::In this paper, we propose a new strategy for modelling sliding conditions when registering 3D images in a piecewise-diffeomorphic framework. More specifically, our main contribution is the development of a mathematical formalism to perform Large Deformation Diffeomorphic Metric Mapping registration with sliding condit...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2012.10.001

    authors: Risser L,Vialard FX,Baluwala HY,Schnabel JA

    更新日期:2013-02-01 00:00:00

  • Spine detection in CT and MR using iterated marginal space learning.

    abstract::Examinations of the spinal column with both, Magnetic Resonance (MR) imaging and Computed Tomography (CT), often require a precise three-dimensional positioning, angulation and labeling of the spinal disks and the vertebrae. A fully automatic and robust approach is a prerequisite for an automated scan alignment as wel...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2012.09.007

    authors: Michael Kelm B,Wels M,Kevin Zhou S,Seifert S,Suehling M,Zheng Y,Comaniciu D

    更新日期:2013-12-01 00:00:00

  • Dynamically constructed network with error correction for accurate ventricle volume estimation.

    abstract::Automated ventricle volume estimation (AVVE) on cardiac magnetic resonance (CMR) images is very important for clinical cardiac disease diagnosis. However, current AVVE methods ignore the error correction for the estimated volume. This results in clinically intolerable ventricle volume estimation error and further lead...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2020.101723

    authors: Luo G,Wang W,Tam C,Wang K,Cao S,Zhang H,Chen B,Li S

    更新日期:2020-08-01 00:00:00

  • Respiratory motion models: a review.

    abstract::The problem of respiratory motion has proved a serious obstacle in developing techniques to acquire images or guide interventions in abdominal and thoracic organs. Motion models offer a possible solution to these problems, and as a result the field of respiratory motion modelling has become an active one over the past...

    journal_title:Medical image analysis

    pub_type: 杂志文章,评审

    doi:10.1016/j.media.2012.09.005

    authors: McClelland JR,Hawkes DJ,Schaeffter T,King AP

    更新日期:2013-01-01 00:00:00

  • Explainable cardiac pathology classification on cine MRI with motion characterization by semi-supervised learning of apparent flow.

    abstract::We propose a method to classify cardiac pathology based on a novel approach to extract image derived features to characterize the shape and motion of the heart. An original semi-supervised learning procedure, which makes efficient use of a large amount of non-segmented images and a small amount of images segmented man...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2019.06.001

    authors: Zheng Q,Delingette H,Ayache N

    更新日期:2019-08-01 00:00:00

  • MR to ultrasound registration for image-guided prostate interventions.

    abstract::A deformable registration method is described that enables automatic alignment of magnetic resonance (MR) and 3D transrectal ultrasound (TRUS) images of the prostate gland. The method employs a novel "model-to-image" registration approach in which a deformable model of the gland surface, derived from an MR image, is r...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2010.11.003

    authors: Hu Y,Ahmed HU,Taylor Z,Allen C,Emberton M,Hawkes D,Barratt D

    更新日期:2012-04-01 00:00:00

  • Self-similarity weighted mutual information: a new nonrigid image registration metric.

    abstract::Mutual information (MI) has been widely used as a similarity measure for rigid registration of multi-modal and uni-modal medical images. However, robust application of MI to deformable registration is challenging mainly because rich structural information, which are critical cues for successful deformable registration...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2013.12.003

    authors: Rivaz H,Karimaghaloo Z,Collins DL

    更新日期:2014-02-01 00:00:00

  • Neighborhood resolved fiber orientation distributions (NRFOD) in automatic labeling of white matter fiber pathways.

    abstract::Accurate digital representation of major white matter bundles in the brain is an important goal in neuroscience image computing since the representations can be used for surgical planning, intra-patient longitudinal analysis and inter-subject population connectivity studies. Reconstructing desired fiber bundles genera...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2018.02.008

    authors: Ugurlu D,Firat Z,Türe U,Unal G

    更新日期:2018-05-01 00:00:00

  • Automated classification of lung bronchovascular anatomy in CT using AdaBoost.

    abstract::Lung CAD systems require the ability to classify a variety of pulmonary structures as part of the diagnostic process. The purpose of this work was to develop a methodology for fully automated voxel-by-voxel classification of airways, fissures, nodules, and vessels from chest CT images using a single feature set and cl...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2007.03.004

    authors: Ochs RA,Goldin JG,Abtin F,Kim HJ,Brown K,Batra P,Roback D,McNitt-Gray MF,Brown MS

    更新日期:2007-06-01 00:00:00

  • Continuous diffusion signal, EAP and ODF estimation via Compressive Sensing in diffusion MRI.

    abstract::In this paper, we exploit the ability of Compressed Sensing (CS) to recover the whole 3D Diffusion MRI (dMRI) signal from a limited number of samples while efficiently recovering important diffusion features such as the Ensemble Average Propagator (EAP) and the Orientation Distribution Function (ODF). Some attempts to...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2013.02.010

    authors: Merlet SL,Deriche R

    更新日期:2013-07-01 00:00:00

  • A work flow to build and validate patient specific left atrium electrophysiology models from catheter measurements.

    abstract::Biophysical models of the atrium provide a physically constrained framework for describing the current state of an atrium and allow predictions of how that atrium will respond to therapy. We propose a work flow to simulate patient specific electrophysiological heterogeneity from clinical data and validate the resultin...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2018.04.005

    authors: Corrado C,Williams S,Karim R,Plank G,O'Neill M,Niederer S

    更新日期:2018-07-01 00:00:00

  • CHAOS Challenge - combined (CT-MR) healthy abdominal organ segmentation.

    abstract::Segmentation of abdominal organs has been a comprehensive, yet unresolved, research field for many years. In the last decade, intensive developments in deep learning (DL) introduced new state-of-the-art segmentation systems. Despite outperforming the overall accuracy of existing systems, the effects of DL model proper...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2020.101950

    authors: Kavur AE,Gezer NS,Barış M,Aslan S,Conze PH,Groza V,Pham DD,Chatterjee S,Ernst P,Özkan S,Baydar B,Lachinov D,Han S,Pauli J,Isensee F,Perkonigg M,Sathish R,Rajan R,Sheet D,Dovletov G,Speck O,Nürnberger A,Maier-H

    更新日期:2020-12-25 00:00:00

  • Adaptive local window for level set segmentation of CT and MRI liver lesions.

    abstract::We propose a novel method, the adaptive local window, for improving level set segmentation technique. The window is estimated separately for each contour point, over iterations of the segmentation process, and for each individual object. Our method considers the object scale, the spatial texture, and the changes of th...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2017.01.002

    authors: Hoogi A,Beaulieu CF,Cunha GM,Heba E,Sirlin CB,Napel S,Rubin DL

    更新日期:2017-04-01 00:00:00

  • Automated localization of breast cancer in DCE-MRI.

    abstract::Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is increasingly being used for the detection and diagnosis of breast cancer. Compared to mammography, DCE-MRI provides higher sensitivity, however its specificity is variable. Moreover, DCE-MRI data analysis is time consuming and depends on reader expertis...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2014.12.001

    authors: Gubern-Mérida A,Martí R,Melendez J,Hauth JL,Mann RM,Karssemeijer N,Platel B

    更新日期:2015-02-01 00:00:00

  • Segmentation of lumen and outer wall of abdominal aortic aneurysms from 3D black-blood MRI with a registration based geodesic active contour model.

    abstract::Segmentation of the geometric morphology of abdominal aortic aneurysm is important for interventional planning. However, the segmentation of both the lumen and the outer wall of aneurysm in magnetic resonance (MR) image remains challenging. This study proposes a registration based segmentation methodology for efficien...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2017.05.005

    authors: Wang Y,Seguro F,Kao E,Zhang Y,Faraji F,Zhu C,Haraldsson H,Hope M,Saloner D,Liu J

    更新日期:2017-08-01 00:00:00

  • Vessel extraction from non-fluorescein fundus images using orientation-aware detector.

    abstract::The automatic extraction of blood vessels in non-fluorescein eye fundus images is a tough task in applications such as diabetic retinopathy screening. However, vessel shapes have complex variations, and accurate modeling of retinal vascular structures is challenging. We have therefore developed a new approach to accur...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2015.09.002

    authors: Yin B,Li H,Sheng B,Hou X,Chen Y,Wu W,Li P,Shen R,Bao Y,Jia W

    更新日期:2015-12-01 00:00:00

  • Segmentation of the skull in MRI volumes using deformable model and taking the partial volume effect into account.

    abstract::Segmentation of the skull in medical imagery is an important stage in applications that require the construction of realistic models of the head. Such models are used, for example, to simulate the behavior of electro-magnetic fields in the head and to model the electrical activity of the cortex in EEG and MEG data. In...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/s1361-8415(00)00016-5

    authors: Rifa H,Bloch I,Hutchinson S,Wiart J,Garnero L

    更新日期:2000-09-01 00:00:00

  • Multimodal image registration using floating regressors in the joint intensity scatter plot.

    abstract::This paper presents a new approach for multimodal medical image registration and compares it to normalized mutual information (NMI) and the correlation ratio (CR). Like NMI and CR, the new method's measure of registration quality is based on the distribution of points in the joint intensity scatter plot (JISP); compac...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2007.12.002

    authors: Orchard J

    更新日期:2008-08-01 00:00:00

  • Super-Resolved q-Space deep learning with uncertainty quantification.

    abstract::Diffusion magnetic resonance imaging (dMRI) provides a noninvasive method for measuring brain tissue microstructure. q-Space deep learning(q-DL) methods have been developed to accurately estimate tissue microstructure from dMRI scans acquired with a reduced number of diffusion gradients. In these methods, deep network...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2020.101885

    authors: Qin Y,Liu Z,Liu C,Li Y,Zeng X,Ye C

    更新日期:2021-01-01 00:00:00

  • Multi-modal volume registration by maximization of mutual information.

    abstract::A new information-theoretic approach is presented for finding the registration of volumetric medical images of differing modalities. Registration is achieved by adjustment of the relative position and orientation until the mutual information between the images is maximized. In our derivation of the registration proced...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/s1361-8415(01)80004-9

    authors: Wells WM 3rd,Viola P,Atsumi H,Nakajima S,Kikinis R

    更新日期:1996-03-01 00:00:00

  • Capturing intraoperative deformations: research experience at Brigham and Women's Hospital.

    abstract::During neurosurgical procedures the objective of the neurosurgeon is to achieve the resection of as much diseased tissue as possible while achieving the preservation of healthy brain tissue. The restricted capacity of the conventional operating room to enable the surgeon to visualize critical healthy brain structures ...

    journal_title:Medical image analysis

    pub_type: 杂志文章,评审

    doi:10.1016/j.media.2004.11.005

    authors: Warfield SK,Haker SJ,Talos IF,Kemper CA,Weisenfeld N,Mewes AU,Goldberg-Zimring D,Zou KH,Westin CF,Wells WM,Tempany CM,Golby A,Black PM,Jolesz FA,Kikinis R

    更新日期:2005-04-01 00:00:00

  • Sequential conditional reinforcement learning for simultaneous vertebral body detection and segmentation with modeling the spine anatomy.

    abstract::Accurate vertebral body (VB) detection and segmentation are critical for spine disease identification and diagnosis. Existing automatic VB detection and segmentation methods may cause false-positive results to the background tissue or inaccurate results to the desirable VB. Because they usually cannot take both the gl...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2020.101861

    authors: Zhang D,Chen B,Li S

    更新日期:2021-01-01 00:00:00

  • Quantitative analysis of multi-spectral fundus images.

    abstract::We have developed a new technique for extracting histological parameters from multi-spectral images of the ocular fundus. The new method uses a Monte Carlo simulation of the reflectance of the fundus to model how the spectral reflectance of the tissue varies with differing tissue histology. The model is parameterised ...

    journal_title:Medical image analysis

    pub_type: 杂志文章

    doi:10.1016/j.media.2006.05.007

    authors: Styles IB,Calcagni A,Claridge E,Orihuela-Espina F,Gibson JM

    更新日期:2006-08-01 00:00:00