Journal of Neuroscience Methods

Article	Citations
Data augmentation for deep-learning-based electroencephalography	235
NODDI in clinical research	157
Grad-CAM helps interpret the deep learning models trained to classify multiple sclerosis types using clinical brain magnetic resonance imaging	77
High-pass filtering artifacts in multivariate classification of neural time series data	76
A major depressive disorder classification framework based on EEG signals using statistical, spectral, wavelet, functional connectivity, and nonlinear analysis	71
A comprehensive assessment of Brain Computer Interfaces: Recent trends and challenges	65
Animal models of pain: Diversity and benefits	63
The rt-TEP tool: real-time visualization of TMS-Evoked Potentials to maximize cortical activation and minimize artifacts	62
TMS-induced silent periods: A review of methods and call for consistency	61
TAAC - TMS Adaptable Auditory Control: A universal tool to mask TMS clicks	59
MI-EEGNET: A novel convolutional neural network for motor imagery classification	58
The sensitivity of diffusion MRI to microstructural properties and experimental factors	58
A convolutional-recurrent neural network approach to resting-state EEG classification in Parkinson’s disease	56
CWT Based Transfer Learning for Motor Imagery Classification for Brain computer Interfaces	55
Efficient whole brain transduction by systemic infusion of minimally purified AAV-PHP.eB	53
Through the looking glass: A review of cranial window technology for optical access to the brain	53
Towards in vivo g-ratio mapping using MRI: Unifying myelin and diffusion imaging	48
Non-invasive brain stimulation for Parkinson’s disease: Clinical evidence, latest concepts and future goals: A systematic review	46
Neural anatomy and optical microscopy (NAOMi) simulation for evaluating calcium imaging methods	46
Model-based geometrical optimisation and in vivo validation of a spatially selective multielectrode cuff array for vagus nerve neuromodulation	46
Automatic classification methods for detecting drowsiness using wavelet packet transform extracted time-domain features from single-channel EEG signal	45
The role of electroencephalography electrical reference in the assessment of functional brain–heart interplay: From methodology to user guidelines	45
Gradient waveform design for tensor-valued encoding in diffusion MRI	44
A novel approach for automated alcoholism detection using Fourier decomposition method	42
EEG Integrated Platform Lossless (EEG-IP-L) pre-processing pipeline for objective signal quality assessment incorporating data annotation and blind source separation	41

Classification of Parkinson's disease based on multi-modal features and stacking ensemble learning	41
Single-trial EEG emotion recognition using Granger Causality/Transfer Entropy analysis	41
A novel approach to correlate the salivary exosomes and their protein cargo in the progression of cognitive impairment into Alzheimer’s disease	39
Reproducibility of power spectrum, functional connectivity and network construction in resting-state EEG	39
Use of common average reference and large-Laplacian spatial-filters enhances EEG signal-to-noise ratios in intrinsic sensorimotor activity	36
A review of critical challenges in MI-BCI: From conventional to deep learning methods	36
Neural tissue-microelectrode interaction: Brain micromotion, electrical impedance, and flexible microelectrode insertion	35
A drug-vs-food “choice” self-administration procedure in rats to investigate pharmacological and environmental mechanisms of substance use disorders	35
Diagnostic classification of autism using resting-state fMRI data improves with full correlation functional brain connectivity compared to partial correlation	34
Machine learning applications on neuroimaging for diagnosis and prognosis of epilepsy: A review	34
Use of the CatWalk gait analysis system to assess functional recovery in rodent models of peripheral nerve injury – a systematic review	34
Brain imaging-based machine learning in autism spectrum disorder: methods and applications	33
A data-driven method to identify frequency boundaries in multichannel electrophysiology data	33
VEP atlas: An anatomic and functional human brain atlas dedicated to epilepsy patients	32
Can transsynaptic viral strategies be used to reveal functional aspects of neural circuitry?	32
Diagnosis of Alzheimer's disease based on regional attention with sMRI gray matter slices	31
Dynamics of isoflurane-induced vasodilation and blood flow of cerebral vasculature revealed by multi-exposure speckle imaging	31
Double diffusion encoding and applications for biomedical imaging	30
Theoretical and methodological analysis of EEG based seizure detection and prediction: An exhaustive review	30
Adaptive spike detection and hardware optimization towards autonomous, high-channel-count BMIs	29
The present and the future of microstructure MRI: From a paradigm shift to normal science	29
GRP-DNet: A gray recurrence plot-based densely connected convolutional network for classification of epileptiform EEG	28
Using rAAV2-retro in rhesus macaques: Promise and caveats for circuit manipulation	27
Genetically encoded sensors towards imaging cAMP and PKA activity in vivo	27
Motor imagery EEG decoding using manifold embedded transfer learning	27
Designing and comparing cleaning pipelines for TMS-EEG data: A theoretical overview and practical example	26
Identification and verification of a 'true' TMS evoked potential in TMS-EEG	25
Removing artifacts from TMS-evoked EEG: A methods review and a unifying theoretical framework	25
Correcting physiological noise in whole-head functional near-infrared spectroscopy	25
A simple Ca2+-imaging approach to neural network analyses in cultured neurons	24
Automated sleep state classification of wide-field calcium imaging data via multiplex visibility graphs and deep learning	24
A method for quantification of vesicular compartments within cells using 3D reconstructed confocal z-stacks: Comparison of ImageJ and Imaris to count early endosomes within basal forebrain cholinergic	24
Convolutional neural networks ensemble model for neonatal seizure detection	24
Retrograde gene transfer into neural pathways mediated by adeno-associated virus (AAV)-AAV receptor interaction	23
The role of neuronavigation in TMS–EEG studies: Current applications and future perspectives	23
Fiber optic sensor embedded smart helmet for real-time impact sensing and analysis through machine learning	23
A review on Alzheimer’s disease classification from normal controls and mild cognitive impairment using structural MR images	23
Realistic Microstructure Simulator (RMS): Monte Carlo simulations of diffusion in three-dimensional cell segmentations of microscopy images	22
Long-term culture of SH-SY5Y neuroblastoma cells in the absence of neurotrophins: A novel model of neuronal ageing	22
Automatic sleep scoring: A deep learning architecture for multi-modality time series	22
Identifying novel biomarkers with TMS-EEG – Methodological possibilities and challenges	22
A hybrid high-resolution anatomical MRI atlas with sub-parcellation of cortical gyri using resting fMRI	22
Comparative analysis of spectral and temporal combinations in CSP-based methods for decoding hand motor imagery tasks	21
Differences in cerebral blood vasculature and flow in awake and anesthetized mouse cortex revealed by quantitative optical coherence tomography angiography	21
Bridging the gap: TMS-EEG from lab to clinic	21
Probing neural tissues at small scales: Recent progress of oscillating gradient spin echo (OGSE) neuroimaging in humans	20
Aging effect on head motion: A Machine Learning study on resting state fMRI data	20
Eavesdropping wires: Recording activity in axons using genetically encoded calcium indicators	20
Validation of DREADD agonists and administration route in a murine model of sleep enhancement	19
Increased maturation of iPSC-derived neurons in a hydrogel-based 3D culture	19

EEG artifact rejection by extracting spatial and spatio-spectral common components	19
Detecting acute pain signals from human EEG	19
Virtual histology of an entire mouse brain from formalin fixation to paraffin embedding. Part 1: Data acquisition, anatomical feature segmentation, tracking global volume and density changes	19
Near-infrared and far-red genetically encoded indicators of neuronal activity	19
Morphological active contour model for automatic brain tumor extraction from multimodal magnetic resonance images	18
A classification algorithm of an SSVEP brain-Computer interface based on CCA fusion wavelet coefficients	18
TMS-EEG responses across the lifespan: Measurement, methods for characterisation and identified responses	18
The blood biomarkers puzzle – A review of protein biomarkers in neurodegenerative diseases	18
Effects of the concentration level, eye fatigue and coffee consumption on the performance of a BCI system based on visual ERP-P300	18
NeuroGPU: Accelerating multi-compartment, biophysically detailed neuron simulations on GPUs	17
Development of deep learning models for microglia analyses in brain tissue using DeePathology™ STUDIO	17
A radiofrequency coil to facilitate task-based fMRI of awake marmosets	17
Detection and analysis of MEG signals in occipital region with double-channel OPM sensors	17
Multiparametric EEG analysis of brain network dynamics during neonatal seizures	16
Spatial extent of cortical motor hotspot in navigated transcranial magnetic stimulation	16
A novel deep learning model based on the ICA and Riemannian manifold for EEG-based emotion recognition	16
The reliability of two prospective cortical biomarkers for pain: EEG peak alpha frequency and TMS corticomotor excitability	16
Array processing of neural signals recorded from the peripheral nervous system for the classification of action potentials	16
A vapor exposure method for delivering heroin alters nociception, body temperature and spontaneous activity in female and male rats	16
Genetically encoded sensors for Chloride concentration	16
High-resolution magnetic resonance imaging-based atlases for the young and adolescent domesticated pig (Sus scrofa)	16
FB-EEGNet: A fusion neural network across multi-stimulus for SSVEP target detection	16
Development and validation of chemical kindling in adult zebrafish: A simple and improved chronic model for screening of antiepileptic agents	16
Probability mapping based artifact detection and removal from single-channel EEG signals for brain–computer interface applications	16
Mu rhythm separation from the mix with alpha rhythm: Principal component analyses and factor topography	16
A review of methods for classification and recognition of ASD using fMRI data	16
µ-rhythm phase from somatosensory but not motor cortex correlates with corticospinal excitability in EEG-triggered TMS	16
A hybrid method for muscle artifact removal from EEG signals	15
Virtual EEG-electrodes: Convolutional neural networks as a method for upsampling or restoring channels	15
Feature Selection Using Extreme Gradient Boosting Bayesian Optimization to upgrade the Classification Performance of Motor Imagery signals for BCI	15
The diagnosis of amnestic mild cognitive impairment by combining the characteristics of brain functional network and support vector machine classifier	14
Quality assessment of anatomical MRI images from generative adversarial networks: Human assessment and image quality metrics	14
Application of rapid invisible frequency tagging for brain computer interfaces	14
A fisher linear discriminant analysis classifier fused with naïve Bayes for simultaneous detection in an asynchronous brain-computer interface	14
OpenSync: An open-source platform for synchronizing multiple measures in neuroscience experiments	14
Decoding Imagined Speech and Computer Control using Brain Waves	14
An LC-APCI+-MS/MS-based method for determining the concentration of neurosteroids in the brain of male mice with different gut microbiota	14
Measuring metabolic rate in single flies during sleep and waking states via indirect calorimetry	14
Protein-retention expansion microscopy for visualizing subcellular organelles in fixed brain tissue	14
Multi-view optimization of time-frequency common spatial patterns for brain-computer interfaces	13
Fascicle localisation within peripheral nerves through evoked activity recordings: A comparison between electrical impedance tomography and multi-electrode arrays	13
Recording EEG in cochlear implant users: Guidelines for experimental design and data analysis for optimizing signal quality and minimizing artifacts	13
A multi-metric approach to characterizing mouse peripheral auditory nerve function using the auditory brainstem response	13
Identification of brain structures and blood vessels by conventional ultrasound in rats	13
Estimation of laminar BOLD activation profiles using deconvolution with a physiological point spread function	13
Light-field microscopy for fast volumetric brain imaging	13
Modified middle cerebral artery occlusion model provides detailed intraoperative cerebral blood flow registration and improves neurobehavioral evaluation	13
An efficient approach for wholemount preparation of the myenteric plexus of rat colon	13
Quantifying mitochondrial volume density in phrenic motor neurons	13
Microstructure with diffusion MRI: what scale we are sensitive to?	13
Automatic coregistration of MRI and on-scalp MEG	13
Decoding olfactory EEG signals for different odor stimuli identification using wavelet-spatial domain feature	13
CluSem: Accurate clustering-based ensemble method to predict motor imagery tasks from multi-channel EEG data	13
Viruses in connectomics: Viral transneuronal tracers and genetically modified recombinants as neuroscience research tools	12
Locomotion is impacted differently according to the perinatal brain injury model: Meta-analysis of preclinical studies with implications for cerebral palsy	12
Functional connectivity using high density EEG shows competitive reliability and agreement across test/retest sessions	12
EEG rhythm based emotion recognition using multivariate decomposition and ensemble machine learning classifier	12
Source-based artifact-rejection techniques for TMS–EEG	12
Validation of an EEG seizure detection paradigm optimized for clinical use in a chronically implanted subcutaneous device	12
Spatial-frequency-temporal convolutional recurrent network for olfactory-enhanced EEG emotion recognition	12
Use of transcranial magnetic stimulation for studying the neural basis of numerical cognition: A systematic review	12
An efficient new assay for measuring zebrafish anxiety: Tall tanks that better characterize between-individual differences	12
Quantification of tissue sodium concentration in the ischemic stroke: A comparison between external and internal references for 23Na MRI	12
All-optical electrophysiology in behaving animals	11
Let's get wild: A review of free-ranging rat assays as context-enriched supplements to traditional laboratory models	11
Integrated 3D motion analysis with functional magnetic resonance neuroimaging to identify neural correlates of lower extremity movement	11
DRGquant: A new modular AI-based pipeline for 3D analysis of the DRG	11
Addressing the missing data challenge in multi-modal datasets for the diagnosis of Alzheimer’s disease	11
The impact of water changes on stress and subject variation in a zebrafish (Danio rerio) anxiety-related task	11
A novel ex vivo, in situ method to study the human brain through MRI and histology	11
Imaging the endocannabinoid signaling system	11
Spatio-Spectral CCA (SS-CCA): A novel approach for frequency recognition in SSVEP-based BCI	11
Aptamer-modified biosensors to visualize neurotransmitter flux	11
An MRI protocol for anatomical and functional evaluation of the California sea lion brain	11
A standardized head-fixation system for performing large-scale, in vivo physiological recordings in mice	11
Analytic consistency and neural correlates of peak alpha frequency in the study of pain	11
Age and sex differences in primary microglia culture: A comparative study	11
Virtual histology of an entire mouse brain from formalin fixation to paraffin embedding. Part 2: Volumetric strain fields and local contrast changes	11
Novel method to produce a layered 3D scaffold for human pluripotent stem cell-derived neuronal cells	11
Functional interrogation of neural circuits with virally transmitted optogenetic tools	11

A 120-target brain-computer interface based on code-modulated visual evoked potentials	11
Tangential high-density electrode insertions allow to simultaneously measure neuronal activity across an extended region of the visual field in mouse superior colliculus	11
Moving back in the brain to drive the field forward: Targeting neurostimulation to different brain regions in animal models of depression and neurodegeneration	11
A scalable, fully automated approach for regional quantification of immunohistochemical staining of astrocytes in the rat brain	11
Ballistocardiogram artifact removal in simultaneous EEG-fMRI using generative adversarial network	10
Perfusion pressure determines vascular integrity and histomorphological quality following perfusion fixation of the brain	10
Deep active learning for interictal ictal injury continuum EEG patterns	10
Crispr/Cas-based modeling of NF2 loss in meningioma cells	10
Exploring the light/dark box test: Protocols and implications for neuroscience research	10
Spectral Independent Component Analysis with noise modeling for M/EEG source separation	10
Application of a convolutional neural network for fully-automated detection of spike ripples in the scalp electroencephalogram	10
Toolkit for Oscillatory Real-time Tracking and Estimation (TORTE)	10
A novel 5D brain parcellation approach based on spatio-temporal encoding of resting fMRI data from deep residual learning	10
Effects of inter-stimulus intervals on concurrent P300 and SSVEP features for hybrid brain-computer interfaces	10
Fluorescence microendoscopy for in vivo deep-brain imaging of neuronal circuits	10
Translating morphology from bench side to bed side via neurophysiology: 8-min protocol for peripheral neuropathy research	10
Unlocking the brain: A new method for Western blot protein detection from fixed brain tissue	10
Classification of EEG signals: An interpretable approach using functional data analysis	10
Topology-guided cyclic brain connectivity generation using geometric deep learning	10
Use of metal-based contrast agents for in vivo MR and CT imaging of phagocytic cells in neurological pathologies	9
A multiscale siamese convolutional neural network with cross-channel fusion for motor imagery decoding	9
Mining naturalistic human behaviors in long-term video and neural recordings	9
Modular and state-relevant functional network connectivity in high-frequency eyes open vs eyes closed resting fMRI data	9
Improved AAV vector system for cell-type-specific RNA interference	9
Seeing glutamate at central synapses	9
The larval diving response (LDR): Validation of an automated, high-throughput, ecologically relevant measure of anxiety-related behavior in larval zebrafish (Danio rerio)	9
Real-Time Point Process Filter for Multidimensional Decoding Problems Using Mixture Models	9
Integration of human whole-brain transcriptome and neuroimaging data: Practical considerations of current available methods	9
Refinements to rodent head fixation and fluid/food control for neuroscience	9
A bioassay for neuromuscular junction-restricted complement activation by myasthenia gravis acetylcholine receptor antibodies	9
Narrowband multivariate source separation for semi-blind discovery of experiment contrasts	9
Identifying autism spectrum disorder in resting-state fNIRS signals based on multiscale entropy and a two-branch deep learning network	9
An optimized and validated protocol for inducing chronic experimental autoimmune encephalomyelitis in C57BL/6J mice	9
A review of objective assessments for hyperactivity in attention deficit hyperactivity disorder	9
In vivo demonstration of Congo Red labeled amyloid plaques via perfusion in the Alzheimer disease rat model	9
A 3D cell culture approach for studying neuroinflammation	9
ERP-WGAN: A data augmentation method for EEG single-trial detection	9
Optimizing multivariate pattern classification in rapid event-related designs	9
A visual-degradation-inspired model with HSV color-encoding for contour detection	9
Nonhuman primate models of ischemic stroke and neurological evaluation after stroke	9
Probing machine-learning classifiers using noise, bubbles, and reverse correlation	9
SPiDbox: design and validation of an open-source “Skinner-box” system for the study of jumping spiders	8
Classification of patients with AD from healthy controls using entropy-based measures of causality brain networks	8
Identification of the gliogenic state of human neural stem cells to optimize in vitro astrocyte differentiation	8
Convolutional neural networks for decoding electroencephalography responses and visualizing trial by trial changes in discriminant features	8
A method for estimating and characterizing explicitly nonlinear dynamic functional network connectivity in resting-state fMRI data	8
Label-free assessment of myelin status using birefringence microscopy	8
Denoising Algorithm for Event-Related Desynchronization-Based Motor Intention Recognition in Robot-assisted Stroke Rehabilitation Training with Brain-Machine Interaction	8
The Dome: A virtual reality apparatus for freely locomoting rodents	8
Classification of autism based on short-term spontaneous hemodynamic fluctuations using an adaptive graph neural network	8
SimMEEG software for simulating event-related MEG and EEG data with underlying functional connectivity	8
Emotion-movement relationship: A study using functional brain network and cortico-muscular coupling	8
Molecular fMRI of neurochemical signaling	8
Evaluation of motor cortical excitability using evoked torque responses: A new tool with high reliability	8
Sequential semi-supervised segmentation for serial electron microscopy image with small number of labels	8
Methodological and analytical issues of progressive ratio schedules: Definition and scaling of breakpoint	8
CUBIC-f: An optimized clearing method for cell tracing and evaluation of neurite density in the salamander brain	8
Tracking the fate and migration of cells in live animals with cell-cycle indicators and photoconvertible proteins	8
Characterization of the GfaABC1D promoter to selectively target astrocytes in the rhesus macaque brain	8
LIONirs: flexible Matlab toolbox for fNIRS data analysis	8
A comparison of the Avisoft (v.5.2) and MATLAB Mouse Song Analyzer (v.1.3) vocalization analysis systems in C57BL/6, Fmr1-FVB.129, NS-Pten-FVB, and 129 mice	8
Head mounted telemetry system for seizures monitoring and sleep scoring on non-human primate	8
A conditional GABAergic synaptic vesicle marker for Drosophila	8
MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo	7
Interrogating autonomic peripheral nervous system neurons with viruses – A literature review	7
Enhancing transient protein expression in HEK-293 cells by briefly exposing the culture to DMSO	7
‘High-Density-SleepCleaner’: An open-source, semi-automatic artifact removal routine tailored to high-density sleep EEG	7
The fully automated bat (FAB) flight room: A human-free environment for studying navigation in flying bats and its initial application to the retrosplenial cortex	7
Texture analysis in brain T2 and diffusion MRI differentiates histology-verified grey and white matter pathology types in multiple sclerosis	7
Different ischemic duration and frequency of ischemic postconditioning affect neuroprotection in focal ischemic stroke	7
Robotic stereotaxic system based on 3D skull reconstruction to improve surgical accuracy and speed	7
Disjoint subspaces for common and distinct component analysis: Application to the fusion of multi-task FMRI data	7
Recognizing the individualized sensorimotor loop of stroke patients during BMI-supported rehabilitation training based on brain functional connectivity analysis	7
Graph-theoretical analysis identifies transient spatial states of resting-state dynamic functional network connectivity and reveals dysconnectivity in schizophrenia	7
Novel proton exchange rate MRI presents unique contrast in brains of ischemic stroke patients	7
Modeling the mature CNS: A predictive screening platform for neurodegenerative disease drug discovery	7
Optical recording of neural responses to gold-nanorod mediated photothermal neural inhibition	7
A diagnostic unified classification model for classifying multi-sized and multi-modal brain graphs using graph alignment	7
A L1 normalization enhanced dynamic window method for SSVEP-based BCIs	7
A level set method based on domain transformation and bias correction for MRI brain tumor segmentation	7
A novel tool for the removal of muscle artefacts from EEG: Improving data quality in the gamma frequency range	7
Regional segmentation strategy for DTI analysis of human corpus callosum indicates motor function deficit in mild cognitive impairment	7
A step-by-step guide for microsurgical collection of uncontaminated cerebrospinal fluid from rat cisterna magna	7
Phenomenological model of auditory nerve population responses to cochlear implant stimulation	7
Simultaneous flow cytometric characterization of multiple cell types and metabolic states in the rat brain after repeated mild traumatic brain injury	7
Microelectrode clusters enable therapeutic deep brain stimulation without noticeable side-effects in a rodent model of Parkinson’s disease	7
Defining the filter parameters for phase-amplitude coupling from a bispectral point of view	7
A modified four vessel occlusion model of global cerebral ischemia in rats	7
fMRI-Informed EEG for brain mapping of imagined lower limb movement: Feasibility of a brain computer interface	7
Construction of a computerized adaptive test (CAT-CCNB) for efficient neurocognitive and clinical psychopathology assessment	7
Rethinking data treatment: The sucrose preference threshold for anhedonia in stress-induced rat models of depression	7
Practical solutions for including sex as a biological variable (SABV) in preclinical neuropsychopharmacological research	7
An optimized animal model of lysolecithin induced demyelination in optic nerve; more feasible, more reproducible, promising for studying the progressive forms of multiple sclerosis	7
Visualizing the cerebral distribution of chemical elements: A challenge met with LIBS elemental imaging	7
Animal studies in clinical MRI scanners: A custom setup for combined fMRI and deep-brain stimulation in awake rats	7