Journal of Neuroscience Methods最新文献

{"title":"Magnetic resonance imaging cerebral blood perfusion measurement in awake mice","authors":"Ahmed A. Bahrani ,&nbsp;Stephen R. Dundon ,&nbsp;TianYu Gao ,&nbsp;Christopher J. Gant ,&nbsp;Rungruedee Kimseng ,&nbsp;Jenna L. Gollihue ,&nbsp;Colin B. Rogers ,&nbsp;Blaine E. Weiss ,&nbsp;Pradoldej Sompol ,&nbsp;David K. Powel ,&nbsp;Christopher M. Norris","doi":"10.1016/j.jneumeth.2025.110525","DOIUrl":"10.1016/j.jneumeth.2025.110525","url":null,"abstract":"<div><h3>Background</h3><div>Cerebral blood perfusion (CBP) plays a vital role in delivering oxygen and essential nutrients to support neuronal activity. Researchers commonly use mouse models with magnetic resonance imaging (MRI) to study CBP and brain function. However, a major challenge in these studies is the use of anesthesia, which significantly alters cerebrovascular dynamics and metabolic activity.</div></div><div><h3>New method</h3><div>A 3D-printed, custom-designed frame and head mounting plate were used with an existing Bruker mouse cradle. To evaluate the repeatability of CBP measurements in awake versus anesthetized conditions, we used a flow-sensitive alternating inversion recovery (FAIR) sequence on a wild-type mouse that underwent a three-day training before scanning to acclimate it to the MRI environment.</div></div><div><h3>Results</h3><div>CBP was significantly higher under anesthesia than in the awake condition for both the whole brain and cortex (P &lt; 0.001). Under anesthesia, the mean perfusion for was 70.9 ± 5.6 ml/min/100 g for the whole brain and 67.8 ± 8.5 ml/min/100 g for just the cortex. Under awake conditions, the whole brain perfusion was 51.1 ± 3.3 ml/min/100 g and 46.7 ± 3.4 ml/min/100 g for the cortex. Perfusion variability, measured by variance and standard deviation, was consistently higher under anesthesia.</div></div><div><h3>Comparison with existing methods</h3><div>We built a unique mouse head stabilizing system for MRI and are the first to have specifically focused on CBP during awake conditions.</div></div><div><h3>Conclusions</h3><div>Our findings confirm that anesthesia significantly increases CBP, affecting the accuracy, reproducibility and relevance of perfusion-related studies. Accordingly, we developed a practical, MRI-compatible setup for imaging awake mice and used it to measure perfusion for more reliable neuroimaging research.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"422 ","pages":"Article 110525"},"PeriodicalIF":2.7,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144534180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel adaptive time-window method for detecting slow wave–spindle coupling: Comparison of temporal co-occurrence and phase-amplitude coupling approaches","authors":"D. Baena ,&nbsp;L.B. Ray ,&nbsp;S.M. Fogel","doi":"10.1016/j.jneumeth.2025.110526","DOIUrl":"10.1016/j.jneumeth.2025.110526","url":null,"abstract":"<div><h3>Background</h3><div>Slow wave–spindle (SW-SP) coupling is critical to the role of sleep in cognition. However, the reliability and validity of available detection methods remain lacking, employ varying approaches, and have yet to be directly compared and rigorously validated. This study aimed to: (1) compare phase amplitude coupling (PAC)-based methods (PACTools and YASA) with the “temporal co-occurrence”, Fixed Time Window approach for detecting SW-SP coupling, and, (2) introduce a refined adaptive SW-SP coupling method to improve precision and accuracy, by precisely aligning spindle detection with slow wave half-wave durations.</div></div><div><h3>New method</h3><div>A novel SW-SP coupling detection method was developed, incorporating dynamic time windows based on slow wave half-wave durations. This method adjusts to the morphology of individual slow waves offering precise alignment of spindle events with slow wave peaks and troughs.</div></div><div><h3>Results</h3><div>PAC-based methods showed high sensitivity but low specificity, resulting in excessive false positives. Across PAC indices (MVLMI, KLMI, PLV, GLMMI), the average F1-score was ∼0.45 ± 0.01. YASA, which detects coupling events based on sigma-band oscillations, exhibited moderate accuracy (0.46 ± 0.007), with an F1-score of 0.446 ± 0.011, reflecting its tendency to over-detect events due to reliance on sigma power fluctuations rather than discrete spindles. The Fixed Time Window method demonstrated higher specificity, identifying 533 ± 28 coupled spindles per participant, but relied on static temporal boundaries, leading to an average lag of 1.04 ± 0.01 s relative to slow wave peaks. The Adaptive Half-Wave method improved upon this by dynamically adjusting detection windows to slow wave morphology, reducing the average lag to 0.15 ± 0.007 s while maintaining high specificity (accuracy = 0.83 ± 0.01, precision = 0.96 ± 0.01).</div></div><div><h3>Comparison with existing methods</h3><div>The adaptive method provides a significant improvement in temporal precision and specificity by dynamically aligning detection windows with slow wave morphology. Fully integrated into the Counting Sheep PSG EEG toolbox, it streamlines workflows for spindle detection, slow wave characterization, and coupling analysis within an easy to use, EEGLAB-compatible environment.</div></div><div><h3>Conclusions</h3><div>As SW-SP coupling gains recognition as an important measure of sleep’s role in cognition, the need for a standardized detection method has become clear. The adaptive method provides a robust, open-source solution, addressing the need for standardized SW-SP coupling detection.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"422 ","pages":"Article 110526"},"PeriodicalIF":2.7,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of MRS acquisition methods for separation of overlapping signals at 3 T","authors":"Tiffany K. Bell ,&nbsp;Dana Goerzen ,&nbsp;Jamie Near ,&nbsp;Ashley D. Harris","doi":"10.1016/j.jneumeth.2025.110523","DOIUrl":"10.1016/j.jneumeth.2025.110523","url":null,"abstract":"<div><h3>Background</h3><div>Proton magnetic resonance spectroscopy (MRS) can be used to quantify multiple neurometabolites. However, due to the difficulty of separating overlapping signals at the commonly used field strength of 3 T, the quantified values are often composites of metabolically related chemicals. This can complicate interpretation and mask effects of interest. Therefore, it is important to determine the ability to accurately separate these signals at 3 T. Data acquired at 7 T can provide a benchmark, as higher field strength facilitates spectral resolution and reduces the signal overlap.</div></div><div><h3>New Methods</h3><div>This study assessed the ability of multiple 3 T MRS sequences to separate the commonly acquired neurochemicals (Glutamate (Glu) and Glutamine (Gln); N-Acetyl aspartate (NAA) and N-acetylaspartylglutamate (NAAG); Creatine (Cr) and Phosphocreatine (PCr); Choline (Cho), Phosphocholine (PC) and Glycerophosphocholine (GPC)). We compared metabolites quantified at 3 T from 6 acquisitions (PRESS, TE= 20, 30, 40, 80 ms, semi-LASER, TE=28 ms and STEAM TE=6 ms) with those quantified at 7 T using STEAM (TE=8 ms).</div></div><div><h3>Results</h3><div>Sequences with short echo times (STEAM-6, PRESS-20) generally performed better at separating most metabolites when using correlative and difference analyses with 7 T reference data. The exceptions were NAAG, which was best quantified with PRESS-80, and Cr and PCr, which were not well separated by any sequence.</div></div><div><h3>Comparison with existing methods and conclusion</h3><div>When wanting to specifically separate composite metabolite signals using single voxel MRS, shorter echo times generally perform better. Researchers should be mindful of the effects of acquisition parameters on the metabolite measures.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"423 ","pages":"Article 110523"},"PeriodicalIF":2.7,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Longitudinal EEG-based assessment of neuroplasticity and adaptive responses to transcranial focused ultrasound stimulation","authors":"Jamal Alsamri ,&nbsp;Mohammad Alamgeer ,&nbsp;Malak Zayed Alamri ,&nbsp;Mukhtar Ghaleb ,&nbsp;Somia A. Asklany ,&nbsp;Hamad Almansour ,&nbsp;Safa Alsafari ,&nbsp;Elham Abdullah Alghamdi","doi":"10.1016/j.jneumeth.2025.110521","DOIUrl":"10.1016/j.jneumeth.2025.110521","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Background&lt;/h3&gt;&lt;div&gt;An emerging non-invasive neuromodulation technique named Transcranial-focused ultrasound stimulation (tFUS) offered several advantages than the conventional methods in terms of high spatial precision and penetration depth. In neurological disorders, this emerging method have gained a lot of attention, because of has the potential for therapeutic modulation of brain activity. Then, lack of standardized, Real-Time (RT) assessment protocols will result in unclear comprehension regarding the way the repeated tFUS applications may impacts the neuroplasticity and adaptive brain responses in a long-term. Here, the short-term and long-term neuroplastic modifications were effectively identified by the the longitudinal integration of EEG biomarkers with tFUS stimulation sessions. An adaptive modulation strategies customized for individual neural responses are also facilitated by this hypothesis.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;New methods&lt;/h3&gt;&lt;div&gt;To integrate the tFUS with high-resolution electroencephalogram (EEG) monitoring in many sessions, Integrated Longitudinal Evaluation Protocol (ILEP) model was suggested in this study&lt;strong&gt;.&lt;/strong&gt; To extract amplitude, latency, spectral dynamics, and connectivity features from evoked potentials, pre-, during-, and post-stimulation EEG signals were identified by the protocol. Then, for monitoring neuroadaptive trajectories over time, the intrgration of the statistical modeling and neural network (NN)-based pattern recognition was employed, and it will assist in analysing those features. For the purpose of differentiating the short-term oscillatory effects from long-term neuroplastic shifts, the following ways will helps in processing the EEG signals: time-frequency decomposition, event-related potential (ERP) analysis, and machine learning (ML) classifiers. Here, the subject-specific response patterns and temporal evolution of brain dynamics were effectively detected by the application of the Deep learning (DL) models.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Results analysis&lt;/h3&gt;&lt;div&gt;After the tFUS, both the short-term and long-term modifications in brain activity were effectively detected by the application of ILEP, and it was demonstrated by the outcomes of the simulation and empirical data. Here, the location-specific, session-dependent EEG modifications are consistent with the adaptive neuroplastic processes, and it was revealed by the outcomes of the simulation. Then, accurate neuroadaptive signals were separated from noise and temporary conditions, and it was facilitated by the potential of the model.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Comparison with existing methods&lt;/h3&gt;&lt;div&gt;A dynamic, session-over-session monitoring of brain responses was facilitated by the ILEP model. But static images was offered by those conventional methods. With an integration of closed-loop feedback and advanced neural modelling, the suggested model executes better than the conventional methods. This suggested model also facilitates in offering ","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"422 ","pages":"Article 110521"},"PeriodicalIF":2.7,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144517087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative analysis of tissue-clearing methods for whole brain imaging of adult zebrafish using BABB, iDISCO, and ECi","authors":"Naemah Md Hamzah ,&nbsp;Siong Meng Lim ,&nbsp;Fei Tieng Lim ,&nbsp;Mitra Amiri Khabooshan ,&nbsp;Jan Kaslin ,&nbsp;Abu Bakar Abdul Majeed ,&nbsp;Kalavathy Ramasamy","doi":"10.1016/j.jneumeth.2025.110520","DOIUrl":"10.1016/j.jneumeth.2025.110520","url":null,"abstract":"<div><h3>Background</h3><div>Recent advancement in macro-imaging that enables 3D visualisation of intact brain tissues overcomes the limitations of conventional 2D visualisation. To this end, various tissue-clearing techniques have been developed to make tissues transparent for 3D imaging. Although the established benzyl alcohol and benzyl benzoate (BABB) method reduces opacity and preserves fluorescence of biomarkers, its carcinogenicity and incompatibility with sensitive microscopes limit its applicability.</div></div><div><h3>New methods</h3><div>This study developed an alternative tissue-clearing technique suited for the adult zebrafish brains by adopting the iDISCO protocol plus the use of ethanol with ethyl cinnamate (ECi) for evaluation of fluorescence preservation following whole brain staining of the mature dopaminergic neuron (DpN) marker [i.e., tyrosine hydroxylase (TH)], for downstream imaging.</div></div><div><h3>Results</h3><div>The ethanol with ECi method showed enhanced signal stability and excellent fluorescence retention over time. This tissue-clearing method resulted in high-resolution and consistent clarity of the complex adult zebrafish brains, hence suitable for future 3D imaging with minimal photodamage and enhanced long-term fluorescence preservation.</div></div><div><h3>Comparison with existing methods</h3><div>When compared to the BABB tissue-clearing method, ECi demonstrated more superior tissue clearing for whole-brain imaging, preserving fluorescence signals, neuronal projections and structural integrity while minimising tissue shrinkage. Unlike BABB which quenched fluorescence and caused significant sample shrinkage, ECi maintained TH-immunoreactive cell counts and fluorescence stability up to 30 days. Its compatibility with the UltraMicroscope II allows advanced neuroimaging applications.</div></div><div><h3>Conclusion</h3><div>This ethanol with ECi method offers a safe, fast and simple alternative tissue-clearing techniques suited for high-resolution and long-term imaging of the adult zebrafish brains.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"422 ","pages":"Article 110520"},"PeriodicalIF":2.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144489955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correlating brain arteriovenous malformations location with clinical and angio-architectural characteristics: A voxel-based lesion symptom mapping approach","authors":"Haroun Ghannouchi ,&nbsp;Jie Wang ,&nbsp;Tom Boeken ,&nbsp;Emily Rius ,&nbsp;Xavier Guerra ,&nbsp;Kevin Premat ,&nbsp;Julien Allard ,&nbsp;Pierre-Marie Chiaroni ,&nbsp;Stéphanie Lenck ,&nbsp;Mahmoud Elhorany ,&nbsp;Atika Talbi ,&nbsp;Bertrand Mathon ,&nbsp;Aurélien Nouet ,&nbsp;Alice Jacquens ,&nbsp;Mehdi Drir ,&nbsp;Nader-Antoine Sourour ,&nbsp;Frédéric Clarençon ,&nbsp;Eimad Shotar","doi":"10.1016/j.jneumeth.2025.110519","DOIUrl":"10.1016/j.jneumeth.2025.110519","url":null,"abstract":"<div><h3>Background</h3><div>Brain arteriovenous malformations (bAVMs) are potentially aggressive neurological diseases.</div></div><div><h3>New method</h3><div>Our aim was to assess the applicability of voxel-based lesion symptom mapping (VLSM) to bAVMs and extend the approach to correlate bAVM location with hitherto unknown aspects of the disease.</div><div>This single-center retrospective study of all adult patients managed between 1998 and 2022 with an available pretreatment MRI scan 3D contrast-enhanced T1-weighted fast spoiled gradient-recalled acquisition, a nidus size&gt; 5 mm and no recent hemorrhage. Spatial normalization and semiautomated nidus segmentation were performed. Validatory tests correlating location with epilepsy and headache were conducted with univariate analyses and the VLSM pipeline. Exploratory VLSM analyses were performed.</div></div><div><h3>Results</h3><div>One hundred and sixty-four patients with 168 bAVMs were included (mean age 38, 29–52[IQR]; 85 men). Statistical analyses on categorical location variables confirmed bAVMs revealed by seizure were positively correlated with temporal lobe location (p = 0.028) while headache was correlated with occipital lobe location (p = 0.027). VLSM analyses failed to reproduce these results as positive controls. Exploratory analyses demonstrated a significant correlation between proximal flow-related aneurysms (13/155 bAVMs, 8.39 %) and central gyri location (z &gt; 4.03, p &lt; 0.05). This result was confirmed by univariate and multivariate analyses.</div></div><div><h3>Comparison with existing methods</h3><div>In comparison to statistical analyses based on bAVM location as a categorical variable, VLSM offers high spatial resolution at the cost of decreased sensitivity.</div></div><div><h3>Conclusion</h3><div>Employing VLSM to correlate location and clinical and angioarchitectural characteristics requires large datasets to achieve sufficient statistical power. Proximal flow-related aneurysms might be correlated with bAVM central gyri location.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"422 ","pages":"Article 110519"},"PeriodicalIF":2.7,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144489954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electroencephalography: A valuable tool for assessing motor impairment and recovery post-stroke","authors":"Jinru Feng ,&nbsp;Weili Jia ,&nbsp;Zixiao Li","doi":"10.1016/j.jneumeth.2025.110518","DOIUrl":"10.1016/j.jneumeth.2025.110518","url":null,"abstract":"<div><div>Stroke is a leading cause of adult disability, and restoring motor function post-stroke is critical to improving the well-being and quality of life of affected individuals. Accurate and timely assessment of motor function is essential for developing effective rehabilitation strategies and predicting recovery outcomes. Electroencephalography (EEG) offers a non-invasive, real-time monitoring of brain activity, offering personalized insights into motor impairment and recovery. Its simplicity and bedside applicability make EEG a valuable tool and a potential biomarker for brain function. In recent years, the integration of EEG with the brain-computer interface technology and neuromodulation techniques has revolutionized personalized rehabilitation therapy, offering new hope for patients with motor dysfunction following stroke. This review synthesizes evidence on EEG-derived biomarkers and their integration with brain-computer interface and neuromodulation techniques, proposing a framework for personalized rehabilitation strategies in stroke recovery.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"422 ","pages":"Article 110518"},"PeriodicalIF":2.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144329985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Primary culture of inner ear schwannoma","authors":"Jonas Scheffler ,&nbsp;Arne Liebau ,&nbsp;Eric Lehner ,&nbsp;Sandra Leisz ,&nbsp;Sabine Koitzsch ,&nbsp;Julia Reiber ,&nbsp;Anja Harder ,&nbsp;Stefan K. Plontke","doi":"10.1016/j.jneumeth.2025.110515","DOIUrl":"10.1016/j.jneumeth.2025.110515","url":null,"abstract":"<div><h3>Background</h3><div>Vestibulocochlear schwannomas (VS) are benign tumors arising from Schwann cells of the eighth cranial nerve. While VS are commonly located in the internal auditory canal (IAC) or cerebellopontine angle (CPA), a subset occurs within the inner ear, known as inner ear schwannomas (IES). Their location influences management strategies in terms of tumor control, hearing, and vestibular function. Despite the differences between IES and CPA- or IAC-located VS with respect to epidemiology, anatomical pathology, growth behavior, and clinical management, little is known about biological characteristics of IES.</div></div><div><h3>New method</h3><div>We developed a reliable technique for isolation of primary tumor cells from ten IES samples for a standardized application. Cells were isolated, processed and cultured for 28 days. Four samples were further characterized by assessing morphology and stability of schwannoma cells as well as presence of monocytic cells.</div></div><div><h3>Results</h3><div>In all samples, primary cells were successfully cultured and expanded for at least 28 days. Sequential imaging showed characteristic schwannoma cell morphology and a stable growth pattern.</div></div><div><h3>Comparison with existing methods</h3><div>While existing protocols had focused on establishing primary cultures of VS in the CPA/IAC so far, this study presents the first successful establishment of primary IES cell cultures from different locations within the inner ear.</div></div><div><h3>Conclusion</h3><div>This work is intended as a proof-of-principle to provide a valuable <em>in vitro</em> model system for investigating biological properties of IES, allowing expansion of small samples of a rare schwannoma subtype and <em>in vitro</em> analysis of new therapeutic approaches.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"422 ","pages":"Article 110515"},"PeriodicalIF":2.7,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144329984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comparative study of rigid-body registration algorithms for the alignment of longitudinal structural MRI of the brain","authors":"Yazdan Rezaee Jouryabi ,&nbsp;Reza Lashgari ,&nbsp;Babak A. Ardekani ,&nbsp;for the Alzheimer’s Disease Neuroimaging Initiative","doi":"10.1016/j.jneumeth.2025.110517","DOIUrl":"10.1016/j.jneumeth.2025.110517","url":null,"abstract":"<div><h3>Background</h3><div>Longitudinal structural MRI (sMRI) may be used to characterize brain morphological changes over time. A key requirement is accurate rigid-body alignment of longitudinal sMRI.</div></div><div><h3>New method</h3><div>We have developed the <em>automatic temporal registration algorithm</em> (ATRA) for this purpose. ATRA is a landmark-based approach capable of registering dozens of sMRI simultaneously.</div></div><div><h3>Comparison with existing methods</h3><div>The aim of this research was to evaluate the accuracy and inverse-consistency of ATRA in comparison to FSL, FreeSurfer, and ANTS. Absent a ground truth, it is only possible to determine the degree of discrepancy between algorithms. We propose that if the discrepancy exceeds a certain threshold, the relative accuracy of algorithms could be determined visually. We computed the discrepancy between ATRA and each of the other three methods for the alignment of 150 pairs of longitudinal sMRI.</div></div><div><h3>Results</h3><div>We visually rated the accuracy of alignments in cases where the discrepancy was greater than .5 mm while the rater was agnostic to the registration method. In those instances, ATRA was considered more accurate than FSL in 46 out of 48 cases (p &lt; .0001), more accurate than FreeSurfer in 6 out of 7 cases (p = .0625), and more accurate than ANTS in all 6 cases (p &lt; .05). ATRA was also significantly more inverse-consistent than all other methods. FreeSurfer was more inverse-consistent than FSL and ANTS, while ANTS outperformed FSL (p &lt; .0001 for all 6 pairwise comparisons).</div></div><div><h3>Conclusions</h3><div>In addition to being capable of performing unbiased group-wise registration, ATRA is the most accurate algorithm in comparison to several commonly used rigid-body alignment methods.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"422 ","pages":"Article 110517"},"PeriodicalIF":2.7,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Making oscillation detection more robust","authors":"Kieran A. Pawluk ,&nbsp;Tamari Shalamberidze ,&nbsp;Jeremy B. Caplan","doi":"10.1016/j.jneumeth.2025.110510","DOIUrl":"10.1016/j.jneumeth.2025.110510","url":null,"abstract":"<div><h3>Background:</h3><div>Neural oscillations are important for understanding cognitive functions. To quantify them, certain methods, including <em>Better OSCillation detection</em> (BOSC), distinguish oscillatory activity from non-oscillatory 1/f background activity and derive detection thresholds in order to disregard most background signal. When successful, this produces detection criteria that are fairly calibrated across frequencies. However, if the background estimate is misaligned, this can backfire and potentially introduce a frequency bias.</div></div><div><h3>New method:</h3><div>The optimized BOSC method incorporates several improvements after testing each independently and as combinations before comparing them all together with the standard BOSC method. The improvements in question are: removing high-power values across frequencies, using median rather than mean power values, and robust regression.</div></div><div><h3>Results:</h3><div>The new BOSC method showed enhanced performance when using shorter time windows and when substantial power existed at one end of the measured spectrum. Synthetic signals were used to demonstrate further versatility and the limitations of the new method.</div></div><div><h3>Comparison with existing methods:</h3><div>The standard BOSC method fared reasonably well aside from some extreme edge cases. Outcomes suggested that at very short time windows, or when artifacts or lopsided power spectra are a concern, the optimized BOSC method could result in a more selective fit that shows greater alignment with the colored-noise background signal.</div></div><div><h3>Conclusion:</h3><div>The standard BOSC method performs well in many typical scenarios, but the optimized version is ideal for less conventional scenarios and addresses many of the shortcomings of the standard method in these cases.</div></div>","PeriodicalId":16415,"journal":{"name":"Journal of Neuroscience Methods","volume":"422 ","pages":"Article 110510"},"PeriodicalIF":2.7,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144310046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}