Double diffusion encoding and applications for biomedical imaging.

Abstract:

:Diffusion Magnetic Resonance Imaging (dMRI) is one of the most important contemporary non-invasive modalities for probing tissue structure at the microscopic scale. The majority of dMRI techniques employ standard single diffusion encoding (SDE) measurements, covering different sequence parameter ranges depending on the complexity of the method. Although many signal representations and biophysical models have been proposed for SDE data, they are intrinsically limited by a lack of specificity. Advanced dMRI methods have been proposed to provide additional microstructural information beyond what can be inferred from SDE. These enhanced contrasts can play important roles in characterizing biological tissues, for instance upon diseases (e.g. neurodegenerative, cancer, stroke), aging, learning, and development. In this review we focus on double diffusion encoding (DDE), which stands out among other advanced acquisitions for its versatility, ability to probe more specific diffusion correlations, and feasibility for preclinical and clinical applications. Various DDE methodologies have been employed to probe compartment sizes (Section 3), decouple the effects of microscopic diffusion anisotropy from orientation dispersion (Section 4), probe displacement correlations, study exchange, or suppress fast diffusing compartments (Section 6). DDE measurements can also be used to improve the robustness of biophysical models (Section 5) and study intra-cellular diffusion via magnetic resonance spectroscopy of metabolites (Section 7). This review discusses all these topics as well as important practical aspects related to the implementation and contrast in preclinical and clinical settings (Section 9) and aims to provide the readers a guide for deciding on the right DDE acquisition for their specific application.

journal_name

J Neurosci Methods

authors

Henriques RN,Palombo M,Jespersen SN,Shemesh N,Lundell H,Ianuş A

doi

10.1016/j.jneumeth.2020.108989

subject

Has Abstract

pub_date

2021-01-15 00:00:00

pages

108989

eissn

0165-0270

issn

1872-678X

pii

S0165-0270(20)30412-X

journal_volume

348

pub_type

杂志文章
  • A minimally invasive approach to long-term head fixation in behaving nonhuman primates.

    abstract::We have designed a device for long-term head fixation for use in behaving nonhuman primates that is robust yet minimally invasive and simple to use. This device is a modified version of the halo system that is used in humans for cervical traction and stabilization after spinal column injuries. This device consists of ...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2009.04.012

    authors: Davis TS,Torab K,House P,Greger B

    更新日期:2009-06-30 00:00:00

  • MR-guided stereotactic navigation.

    abstract::Functional magnetic resonance imaging allows precise localization of brain regions specialized for different perceptual and higher cognitive functions. However, targeting these deep brain structures for electrophysiology still remains a challenging task. Here, we propose a novel framework for MRI-stereotactic registra...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2011.11.031

    authors: Ohayon S,Tsao DY

    更新日期:2012-03-15 00:00:00

  • A double-labeled preparation for simultaneous measurement of [3H]-noradrenaline and [14C]-glutamic acid exocytosis from streptolysin-O (SLO)-perforated synaptosomes.

    abstract::We have developed a novel method to examine [3H]-noradrenaline and [14C]-glutamate release from the same sample of streptolysin-O (SLO) perforated rat cortical synaptosomes. Ca2+ -dependent [3H]-noradrenaline and [14C]-glutamate release was examined at different temperatures and was found to be greater at 30 degrees C...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(01)00350-8

    authors: McFadden SC,Bobich JA,Zheng Q

    更新日期:2001-05-30 00:00:00

  • Evoking defined gaze directions in untrained awake monkeys.

    abstract::Monkeys were partially surrounded by opaque screens except for some distant small holes through which they observed various stimuli or actions, or well-defined background patterns. Gaze direction was measured by an infrared cornea reflection method. Without training or reward, the animal's gaze was directed through on...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2004.02.024

    authors: Krüger J,Hauser J

    更新日期:2004-08-30 00:00:00

  • A visual aid for computer-based analysis of sleep-wake state in rats.

    abstract::Computer-based sleep scoring systems are often calibrated by reference to a conventional visual analysis of electroencephalographic (EEG) and electromyographic (EMG) traces. However, these types of data place high demands on digital storage capacity which may limit the duration or feasibility of some studies. The pres...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2005.04.004

    authors: Mileva-Seitz VR,Louis RP,Stephenson R

    更新日期:2005-10-15 00:00:00

  • Quantitation of multiple gene expression by in situ hybridization autoradiography: accurate normalization using Bayes classifier.

    abstract::In the method of in situ hybridization autoradiography, quantitative comparisons among multiple mRNA signals have proven difficult for many reasons, attributable both to technical factors (e.g. different probe specific activities) as well as to large differences in the patterns and levels of expression of different ge...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(99)00015-1

    authors: Zhao W,Truettner J,Schmidt-Kastner R,Belayev L,Ginsberg MD

    更新日期:1999-04-01 00:00:00

  • Fiber optic sensor embedded smart helmet for real-time impact sensing and analysis through machine learning.

    abstract:BACKGROUND:Mild traumatic brain injury (mTBI) strongly associates with chronic neurodegenerative impairments such as post-traumatic stress disorder (PTSD) and mild cognitive impairment. Early detection of concussive events would significantly enhance the understanding of head injuries and provide better guidance for ur...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2021.109073

    authors: Zhuang Y,Yang Q,Han T,O'Malley R,Kumar A,Gerald RE 2nd,Huang J

    更新日期:2021-01-10 00:00:00

  • Use of a capillary alginate gel (Capgel™) to study the three-dimensional development of sensory nerves reveals the formation of a rudimentary perineurium.

    abstract:BACKGROUND:Peripheral neuropathies affect approximately 20 million people in the United States and often stem from other chronic conditions, such as diabetes. In vitro methodologies to facilitate the understanding and treatment of these disorders often lack the cellular and functional complexity required to accurately ...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2018.05.003

    authors: Anderson WA,Willenberg AR,Bosak AJ,Willenberg BJ,Lambert S

    更新日期:2018-07-15 00:00:00

  • A new reproducible focal cerebral ischemia model by introduction of polyvinylsiloxane into the middle cerebral artery: a comparison study.

    abstract::A reliable focal cerebral ischemia model is essential in evaluating the efficacy and safety of neuroprotective therapy for stroke. We present a focal embolic ischemic model of rat with reproducible and predictable brain infarction by comparing it with two other most commonly used focal cerebral ischemia models. To pro...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(02)00142-5

    authors: Yang Y,Yang T,Li Q,Wang CX,Shuaib A

    更新日期:2002-08-30 00:00:00

  • Replating improves whole cell voltage clamp recording of human fetal dorsal root ganglion neurons.

    abstract::The whole cell patch clamp technique allows recording of membrane currents in an entire cell under voltage clamp conditions. However, technical difficulties arise in large cells bearing extensive processes, such as human fetal dorsal root ganglion (DRG) neurons in culture. In order to improve space clamp conditions, h...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(90)90094-v

    authors: Caviedes P,Ault B,Rapoport SI

    更新日期:1990-10-01 00:00:00

  • Application of scanning electron microscopy in an analysis of the retina of lower vertebrates.

    abstract::The scanning electron microscope (SEM) is a useful tool in the study of the retina of lower vertebrates. SEM analysis (preparation over the critical point) offers a useful addition to the existing histological preparations. It is suitable for a comparative analysis, in which the arrangement of different cellular eleme...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(84)90049-9

    authors: Breidbach O

    更新日期:1984-11-01 00:00:00

  • Resolution-based spectral clustering for brain parcellation using functional MRI.

    abstract:BACKGROUND:Brain parcellation is important for exploiting neuroimaging data. Variability in physiology between individuals has led to the need for data-driven approaches to parcellation, with recent research focusing on simultaneously estimating and partitioning the network structure of the brain. NEW METHOD:We view d...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2020.108628

    authors: Dillon K,Wang YP

    更新日期:2020-04-01 00:00:00

  • Antinociceptive potency of intrathecal morphine in the rat tail flick test: a comparative study using acute lumbar catheter in rats with or without a chronic atlanto-occipital catheter.

    abstract::Chronic spinal catheterization via an atlanto-occipital puncture (CAO) has been widely used to study the effects of drugs on spinal nociceptive mechanisms, but this method is associated with spinal cord damage that may change the efficacy of spinally injected analgesics. Using a slight modification of the method of St...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(03)00197-3

    authors: Prado WA

    更新日期:2003-10-15 00:00:00

  • Long-term cortical CBF recording by laser-Doppler flowmetry in awake freely moving rats subjected to reversible photothrombotic stroke.

    abstract::This study aimed at developing a laser-Doppler flowmetry (LDF) device suitable for long-term cortical cerebral blood flow (cCBF) measurement in awake, freely moving rats. The device included a flow probe adapter for permanent fixation to the skull bone and a connector that held the flow probe in the adapter in exactly...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(99)00041-2

    authors: Gu WG,Jiang W,Brännström T,Wester P

    更新日期:1999-08-01 00:00:00

  • A simple electronic unit allowing extracellular recording and stimulation through the same wire hook or suction electrode.

    abstract::A simple and easily constructed unit was designed using a buffer amplifier, a programmable transconductance amplifier and an active filter. The unit allows extracellular recording and stimulation through the same electrode. Thus in experiments where it is required to stimulate a nerve and record the effects of the sti...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(84)90034-7

    authors: Hatzopoulos A,Theophilidis G

    更新日期:1984-08-01 00:00:00

  • Immunoperoxidase staining of cerebrospinal fluid IgG in isoelectric focusing gels: a sensitive new technique.

    abstract::An isoelectric focusing (IEF) technique using direct peroxidase or peroxidase-antiperoxidase (PAP) overlay staining for detection of cerebrospinal fluid (CSF) oligoclonal IgG is described. The method involves chemical fixation of all proteins in the gel followed by application of peroxidase coupled antiserum as a spec...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(80)90035-7

    authors: Mattson DH,Roos RP,Arnason BG

    更新日期:1980-10-01 00:00:00

  • The interpretation of significance tests for independent and dependent samples.

    abstract::The assumptions upon which a correct interpretation of the t-test depends are rarely fulfilled by data from the neurosciences. This applies to both independent and correlated samples. The Mann-Whitney U-test is suggested as an alternative for the t-test for independent samples. The way in which significant results fro...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章,评审

    doi:10.1016/0165-0270(83)90058-4

    authors: Krauth J

    更新日期:1983-12-01 00:00:00

  • Rapid quantification of ischaemic injury and cerebroprotection in brain slices using densitometric assessment of 2,3,5-triphenyltetrazolium chloride staining.

    abstract::2,3,5-Triphenyltetrazolium chloride (TTC), a marker of mitochondrial enzyme activity, is widely used to assess the effects of cerebral ischaemia in vivo. In the present study, we characterised its utility as a simple rapid macrohistological measure of ischaemic damage in brain slices. Coronal rat corticostriatal slice...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(00)00277-6

    authors: Mathews KS,McLaughlin DP,Ziabari LH,Toner CC,Street PC,Hisgrove E,Bezzina EL,Stamford JA

    更新日期:2000-10-15 00:00:00

  • Studies on long term behavioural changes in group-housed rat models of brain and spinal cord injury using an automated home cage recording system.

    abstract:BACKGROUND:Neurotrauma patients face major neurological sequelae. The failure in the preclinical-to-clinical translation of candidate therapies could be due to poor evaluation of rodent behaviours after neurotrauma. NEW METHOD:A home cage automated system was used to study the long term behaviour of individual rats wi...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2019.04.005

    authors: Yip PK,Chapman GE,Sillito RR,Ip THR,Akhigbe G,Becker SC,Price AW,Michael-Titus AT,Armstrong JD,Tremoleda JL

    更新日期:2019-06-01 00:00:00

  • Response of zebrafish larvae to mild electrical stimuli: A 96-well setup for behavioural screening.

    abstract:BACKGROUND:Zebrafish larvae have a high potential as model system to replace rodents, especially in screening and drug discovery applications. However, an experimental setup to deliver mild electrical stimuli with simultaneous high throughput behavioural tracking has not yet been described. NEW METHOD:A new tool was d...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2018.03.002

    authors: Steenbergen PJ

    更新日期:2018-05-01 00:00:00

  • A simple method for reconditioning epoxy-coated microelectrodes for extracellular single neuron recording.

    abstract::Epoxy-insulated tungsten microelectrodes can be used once or twice in our lab before the impedance becomes too low. Dipping the electrodes in epoxy followed by curing restores their initial high impedance which is associated with good isolation of single neurons. It is a cost effective and simple procedure. ...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(02)00365-5

    authors: Verhagen JV,Gabbott PL,Rolls ET

    更新日期:2003-03-15 00:00:00

  • Patch-clamp studies in the CNS illustrate a simple new method for obtaining viable neurons in rat brain slices: glycerol replacement of NaCl protects CNS neurons.

    abstract::Viable neurons in brain slices are crucial for electrophysiological studies. The present study describes a new method for obtaining viable cells in several regions of the central nervous system including the ventral tegmental area, the hypothalamus, the periaqueductal grey matter and the spinal cord. The essence of th...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2006.06.006

    authors: Ye JH,Zhang J,Xiao C,Kong JQ

    更新日期:2006-12-15 00:00:00

  • Linear inverse filtering improves spatial separation of nonlinear brain dynamics: a simulation study.

    abstract::We examined topographic variations in nonlinear measures based on scalp voltages, which were generated by two simulated current dipoles each placed in a different hemisphere of a spherical volume conductor (three-shell model). Dipole dynamics were that of a three-torus and the x-component of the Lorenz-system and scal...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/s0165-0270(00)00188-6

    authors: Fell J,Hauk O,Hinrichs H

    更新日期:2000-05-15 00:00:00

  • The strength and spread of the electric field induced by transcranial rotating permanent magnet stimulation in comparison with conventional transcranial magnetic stimulation.

    abstract:BACKGROUND:Weak or low intensity transcranial stimulation of the brain, such as low field magnetic stimulation and electrical stimulation, can produce significant functional and therapeutic neuromodulatory effects. NEW METHOD:We have recently developed a portable wearable multifocal brain stimulator called transcrania...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2018.09.002

    authors: Helekar SA,Convento S,Nguyen L,John BS,Patel A,Yau JM,Voss HU

    更新日期:2018-11-01 00:00:00

  • Physiological monitoring of small animals during magnetic resonance imaging.

    abstract::Maintaining a stable physiologic state is essential when studying animal models of epilepsy with simultaneous electroencephalograph (EEG) and functional magnetic resonance imaging (fMRI) or EEG and magnetic resonance spectroscopy (MRS). To achieve and maintain such stability in rats in the MRI environment, a minimally...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2004.11.019

    authors: Mirsattari SM,Bihari F,Leung LS,Menon RS,Wang Z,Ives JR,Bartha R

    更新日期:2005-06-15 00:00:00

  • A transgenic rat expressing green fluorescent protein (GFP) in peripheral nerves provides a new hindlimb model for the study of nerve injury and regeneration.

    abstract:BACKGROUND:In order to evaluate nerve regeneration in clinically relevant hindlimb surgical paradigms not feasible in fluorescent mice models, we developed a rat that expresses green fluorescent protein (GFP) in neural tissue. METHODS:Transgenic Sprague-Dawley rat lines were created using pronuclear injection of a tra...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2011.10.011

    authors: Moore AM,Borschel GH,Santosa KB,Flagg ER,Tong AY,Kasukurthi R,Newton P,Yan Y,Hunter DA,Johnson PJ,Mackinnon SE

    更新日期:2012-02-15 00:00:00

  • Rapid annotation of seizures and interictal-ictal-injury continuum EEG patterns.

    abstract:BACKGROUND:Manual annotation of seizures and interictal-ictal-injury continuum (IIIC) patterns in continuous EEG (cEEG) recorded from critically ill patients is a time-intensive process for clinicians and researchers. In this study, we evaluated the accuracy and efficiency of an automated clustering method to accelerat...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2020.108966

    authors: Jing J,d'Angremont E,Ebrahim S,Tabaeizadeh M,Ng M,Herlopian A,Dauwels J,Westover MB

    更新日期:2020-10-22 00:00:00

  • ATP-competitive LRRK2 inhibitors interfere with monoclonal antibody binding to the kinase domain of LRRK2 under native conditions. A method to directly monitor the active conformation of LRRK2?

    abstract::Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common genetic cause of Parkinson's disease. LRRK2 kinase activity is required for toxicity in neuronal cell cultures suggesting that selective kinase inhibitors may prevent neurodegeneration in patients. Directly monitoring LRRK2 activity in cells would b...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2012.12.015

    authors: Gillardon F,Kremmer E,Froehlich T,Ueffing M,Hengerer B,Gloeckner CJ

    更新日期:2013-03-30 00:00:00

  • Geometric classification of brain network dynamics via conic derivative discriminants.

    abstract:BACKGROUND:Over the past decade, pattern decoding techniques have granted neuroscientists improved anatomical specificity in mapping neural representations associated with function and cognition. Dynamical patterns are of particular interest, as evidenced by the proliferation and success of frequency domain methods tha...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/j.jneumeth.2018.06.019

    authors: Singh MF,Braver TS,Ching S

    更新日期:2018-10-01 00:00:00

  • A weighted index of bilateral brain lesions.

    abstract::Attempts to correlate the amount of bilateral brain injury with behavioral changes can be complicated if the lesions are bilaterally unsymmetrical in volume. Further complications are introduced if unilateral lesions are ineffective in producing behavioral changes. An index, W%, is proposed which is based on the produ...

    journal_title:Journal of neuroscience methods

    pub_type: 杂志文章

    doi:10.1016/0165-0270(84)90046-3

    authors: Hodos W,Bobko P

    更新日期:1984-11-01 00:00:00