Neuroinformatics最新文献_第2页

Detection of Schizophrenia from EEG Signals using Selected Statistical Moments of MFC Coefficients and Ensemble Learning 利用 MFC 系数的选定统计矩和集合学习从脑电图信号中检测精神分裂症

IF 3 4区医学

Neuroinformatics Pub Date : 2024-09-19 DOI: 10.1007/s12021-024-09684-4

Ashima Tyagi, Vibhav Prakash Singh, Manoj Madhava Gore

{"title":"Detection of Schizophrenia from EEG Signals using Selected Statistical Moments of MFC Coefficients and Ensemble Learning","authors":"Ashima Tyagi, Vibhav Prakash Singh, Manoj Madhava Gore","doi":"10.1007/s12021-024-09684-4","DOIUrl":"https://doi.org/10.1007/s12021-024-09684-4","url":null,"abstract":"Schizophrenia is a mental disorder characterized by neurophysiological dysfunctions that result in disturbances in thinking, perception, and behavior. Early identification of schizophrenia can help prevent potential complications and facilitate effective treatment and management of the condition. This paper proposes a computer aided diagnosis system for the early detection of schizophrenia using 19-channel Electroencephalography (EEG) signals from 28 subjects, leveraging statistical moments of Mel-frequency Cepstral Coefficients (MFCC) and ensemble learning. Initially, the EEG signals are passed through a high-pass filter to mitigate noise and remove extraneous data. The feature extraction technique is then employed to extract MFC coefficients from the filtered EEG signals. The dimensionality of these coefficients is reduced by computing their statistical moments, which include the mean, standard deviation, skewness, kurtosis, and energy. Subsequently, the Support Vector Machine based Recursive Feature Elimination (SVM-RFE) is applied to identify pertinent features from the statistical moments of the MFC coefficients. These SVM-RFE-based selected features serve as input for three base classifiers: Support Vector Machine, k-Nearest Neighbors, and Logistic Regression. Additionally, an ensemble learning approach, which combines the predictions of the three classifiers through majority voting, is introduced to enhance schizophrenia detection performance and generalize the results of the proposed approach. The study’s findings demonstrate that the ensemble model, combined with SVM-RFE-based selected statistical moments of MFCC, achieves encouraging detection performance, highlighting the potential of machine learning techniques in advancing the diagnostic process of schizophrenia.","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142257729","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}

引用次数: 0

MBV-Pipe: A One-Stop Toolbox for Assessing Mouse Brain Morphological Changes for Cross-Scale Studies MBV-Pipe：用于跨尺度研究的小鼠脑形态变化评估一站式工具箱

IF 3 4区医学

Neuroinformatics Pub Date : 2024-09-16 DOI: 10.1007/s12021-024-09687-1

Wentao Jiang, Xinyi Liu, Ming Song, Zhengyi Yang, Lan Sun, Tianzi Jiang

{"title":"MBV-Pipe: A One-Stop Toolbox for Assessing Mouse Brain Morphological Changes for Cross-Scale Studies","authors":"Wentao Jiang, Xinyi Liu, Ming Song, Zhengyi Yang, Lan Sun, Tianzi Jiang","doi":"10.1007/s12021-024-09687-1","DOIUrl":"https://doi.org/10.1007/s12021-024-09687-1","url":null,"abstract":"Mouse models are crucial for neuroscience research, yet discrepancies arise between macro- and meso-scales due to sample preparation altering brain morphology. The absence of an accessible toolbox for magnetic resonance imaging (MRI) data processing presents a challenge for assessing morphological changes in the mouse brain. To address this, we developed the MBV-Pipe (Mouse Brain Volumetric Statistics-Pipeline) toolbox, integrating the methods of Diffeomorphic Anatomical Registration Through Exponentiated Lie Algebra (DARTEL)-Voxel-based morphometry (VBM) and Tract-Based Spatial Statistics (TBSS) to evaluate brain tissue volume and white matter integrity. To validate the reliability of MBV-Pipe, brain MRI data from seven mice at three time points (in vivo, post-perfusion, and post-fixation) were acquired using a 9.4T ultra-high MRI system. Employing the MBV-Pipe toolbox, we discerned substantial volumetric changes in the mouse brain following perfusion relative to the in vivo condition, with the fixation process inducing only negligible variations. Importantly, the white matter integrity was found to be largely stable throughout the sample preparation procedures. The MBV-Pipe source code is publicly available and includes a user-friendly GUI for facilitating quality control and experimental protocol optimization, which holds promise for advancing mouse brain research in the future.","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142257727","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}

引用次数: 0

Morphology and Texture-Guided Deep Neural Network for Intracranial Aneurysm Segmentation in 3D TOF-MRA 用于三维 TOF-MRA 颅内动脉瘤分割的形态学和纹理引导的深度神经网络

IF 3 4区医学

Neuroinformatics Pub Date : 2024-09-11 DOI: 10.1007/s12021-024-09683-5

Maysam Orouskhani, Negar Firoozeh, Huayu Wang, Yan Wang, Hanrui Shi, Weijing Li, Beibei Sun, Jianjian Zhang, Xiao Li, Huilin Zhao, Mahmud Mossa-Basha, Jenq-Neng Hwang, Chengcheng Zhu

{"title":"Morphology and Texture-Guided Deep Neural Network for Intracranial Aneurysm Segmentation in 3D TOF-MRA","authors":"Maysam Orouskhani, Negar Firoozeh, Huayu Wang, Yan Wang, Hanrui Shi, Weijing Li, Beibei Sun, Jianjian Zhang, Xiao Li, Huilin Zhao, Mahmud Mossa-Basha, Jenq-Neng Hwang, Chengcheng Zhu","doi":"10.1007/s12021-024-09683-5","DOIUrl":"https://doi.org/10.1007/s12021-024-09683-5","url":null,"abstract":"This study concentrates on the segmentation of intracranial aneurysms, a pivotal aspect of diagnosis and treatment planning. We aim to overcome the inherent instance imbalance and morphological variability by introducing a novel morphology and texture loss reweighting approach. Our innovative method involves the incorporation of tailored weights within the loss function of deep neural networks. Specifically designed to account for aneurysm size, shape, and texture, this approach strategically guides the model to focus on capturing discriminative information from imbalanced features. The study conducted extensive experimentation utilizing ADAM and RENJI TOF-MRA datasets to validate the proposed approach. The results of our experimentation demonstrate the remarkable effectiveness of the introduced methodology in improving aneurysm segmentation accuracy. By dynamically adapting to the variances present in aneurysm features, our model showcases promising outcomes for accurate diagnostic insights. The nuanced consideration of morphological and textural nuances within the loss function proves instrumental in overcoming the challenge posed by instance imbalance. In conclusion, our study presents a nuanced solution to the intricate challenge of intracranial aneurysm segmentation. The proposed morphology and texture loss reweighting approach, with its tailored weights and dynamic adaptability, proves to be instrumental in enhancing segmentation precision. The promising outcomes from our experimentation suggest the potential for accurate diagnostic insights and informed treatment strategies, marking a significant advancement in this critical domain of medical imaging.","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182159","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}

引用次数: 0

Understanding Learning from EEG Data: Combining Machine Learning and Feature Engineering Based on Hidden Markov Models and Mixed Models 从脑电图数据中理解学习：基于隐马尔可夫模型和混合模型的机器学习与特征工程相结合

IF 3 4区医学

Neuroinformatics Pub Date : 2024-09-10 DOI: 10.1007/s12021-024-09690-6

Gabriel R. Palma, Conor Thornberry, Seán Commins, Rafael A. Moral

{"title":"Understanding Learning from EEG Data: Combining Machine Learning and Feature Engineering Based on Hidden Markov Models and Mixed Models","authors":"Gabriel R. Palma, Conor Thornberry, Seán Commins, Rafael A. Moral","doi":"10.1007/s12021-024-09690-6","DOIUrl":"https://doi.org/10.1007/s12021-024-09690-6","url":null,"abstract":"Theta oscillations, ranging from 4-8 Hz, play a significant role in spatial learning and memory functions during navigation tasks. Frontal theta oscillations are thought to play an important role in spatial navigation and memory. Electroencephalography (EEG) datasets are very complex, making any changes in the neural signal related to behaviour difficult to interpret. However, multiple analytical methods are available to examine complex data structures, especially machine learning-based techniques. These methods have shown high classification performance, and their combination with feature engineering enhances their capability. This paper proposes using hidden Markov and linear mixed effects models to extract features from EEG data. Based on the engineered features obtained from frontal theta EEG data during a spatial navigation task in two key trials (first, last) and between two conditions (learner and non-learner), we analysed the performance of six machine learning methods on classifying learner and non-learner participants. We also analysed how different standardisation methods used to pre-process the EEG data contribute to classification performance. We compared the classification performance of each trial with data gathered from the same subjects, including solely coordinate-based features, such as idle time and average speed. We found that more machine learning methods perform better classification using coordinate-based data. However, only deep neural networks achieved an area under the ROC curve higher than 80% using the theta EEG data alone. Our findings suggest that standardising the theta EEG data and using deep neural networks enhances the classification of learner and non-learner subjects in a spatial learning task.","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182162","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}

引用次数: 0

AnNoBrainer, An Automated Annotation of Mouse Brain Images using Deep Learning. AnNoBrainer，利用深度学习自动标注小鼠大脑图像。

IF 2.7 4区医学

Neuroinformatics Pub Date : 2024-08-07 DOI: 10.1007/s12021-024-09679-1

Roman Peter, Petr Hrobar, Josef Navratil, Martin Vagenknecht, Jindrich Soukup, Keiko Tsuji, Nestor X Barrezueta, Anna C Stoll, Renee C Gentzel, Jonathan A Sugam, Jacob Marcus, Danny A Bitton

{"title":"AnNoBrainer, An Automated Annotation of Mouse Brain Images using Deep Learning.","authors":"Roman Peter, Petr Hrobar, Josef Navratil, Martin Vagenknecht, Jindrich Soukup, Keiko Tsuji, Nestor X Barrezueta, Anna C Stoll, Renee C Gentzel, Jonathan A Sugam, Jacob Marcus, Danny A Bitton","doi":"10.1007/s12021-024-09679-1","DOIUrl":"https://doi.org/10.1007/s12021-024-09679-1","url":null,"abstract":"Annotation of multiple regions of interest across the whole mouse brain is an indispensable process for quantitative evaluation of a multitude of study endpoints in neuroscience digital pathology. Prior experience and domain expert knowledge are the key aspects for image annotation quality and consistency. At present, image annotation is often achieved manually by certified pathologists or trained technicians, limiting the total throughput of studies performed at neuroscience digital pathology labs. It may also mean that simpler and quicker methods of examining tissue samples are used by non-pathologists, especially in the early stages of research and preclinical studies. To address these limitations and to meet the growing demand for image analysis in a pharmaceutical setting, we developed AnNoBrainer, an open-source software tool that leverages deep learning, image registration, and standard cortical brain templates to automatically annotate individual brain regions on 2D pathology slides. Application of AnNoBrainer to a published set of pathology slides from transgenic mice models of synucleinopathy revealed comparable accuracy, increased reproducibility, and a significant reduction (~ 50%) in time spent on brain annotation, quality control and labelling compared to trained scientists in pathology. Taken together, AnNoBrainer offers a rapid, accurate, and reproducible automated annotation of mouse brain images that largely meets the experts' histopathological assessment standards (> 85% of cases) and enables high-throughput image analysis workflows in digital pathology labs.","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141898673","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}

引用次数: 0

Assessment of Sports Concussion in Female Athletes: A Role for Neuroinformatics? 评估女运动员的运动性脑震荡：神经信息学的作用？

IF 2.7 4区医学

Neuroinformatics Pub Date : 2024-07-30 DOI: 10.1007/s12021-024-09680-8

Rachel Edelstein, Sterling Gutterman, Benjamin Newman, John Darrell Van Horn

{"title":"Assessment of Sports Concussion in Female Athletes: A Role for Neuroinformatics?","authors":"Rachel Edelstein, Sterling Gutterman, Benjamin Newman, John Darrell Van Horn","doi":"10.1007/s12021-024-09680-8","DOIUrl":"https://doi.org/10.1007/s12021-024-09680-8","url":null,"abstract":"Over the past decade, the intricacies of sports-related concussions among female athletes have become readily apparent. Traditional clinical methods for diagnosing concussions suffer limitations when applied to female athletes, often failing to capture subtle changes in brain structure and function. Advanced neuroinformatics techniques and machine learning models have become invaluable assets in this endeavor. While these technologies have been extensively employed in understanding concussion in male athletes, there remains a significant gap in our comprehension of their effectiveness for female athletes. With its remarkable data analysis capacity, machine learning offers a promising avenue to bridge this deficit. By harnessing the power of machine learning, researchers can link observed phenotypic neuroimaging data to sex-specific biological mechanisms, unraveling the mysteries of concussions in female athletes. Furthermore, embedding methods within machine learning enable examining brain architecture and its alterations beyond the conventional anatomical reference frame. In turn, allows researchers to gain deeper insights into the dynamics of concussions, treatment responses, and recovery processes. This paper endeavors to address the crucial issue of sex differences in multimodal neuroimaging experimental design and machine learning approaches within female athlete populations, ultimately ensuring that they receive the tailored care they require when facing the challenges of concussions. Through better data integration, feature identification, knowledge representation, validation, etc., neuroinformaticists, are ideally suited to bring clarity, context, and explainabilty to the study of sports-related head injuries in males and in females, and helping to define recovery.","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141793888","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}

引用次数: 0

Characteristics of the Structural Connectivity in Patients with Brain Injury and Chronic Health Symptoms: A Pilot Study. 脑损伤和慢性健康症状患者的结构连通性特征：一项试点研究

IF 2.7 4区医学

Neuroinformatics Pub Date : 2024-07-11 DOI: 10.1007/s12021-024-09681-7

Xiaojian Kang, Byung C Yoon, Emily Grossner, Maheen M Adamson

{"title":"Characteristics of the Structural Connectivity in Patients with Brain Injury and Chronic Health Symptoms: A Pilot Study.","authors":"Xiaojian Kang, Byung C Yoon, Emily Grossner, Maheen M Adamson","doi":"10.1007/s12021-024-09681-7","DOIUrl":"https://doi.org/10.1007/s12021-024-09681-7","url":null,"abstract":"Diffusion properties from diffusion tensor imaging (DTI) are exquisitely sensitive to white matter abnormalities incurred during traumatic brain injury (TBI), especially for those patients with chronic post-TBI symptoms such as headaches, dizziness, fatigue, etc. The evaluation of structural and functional connectivity using DTI has become a promising method for identifying subtle alterations in brain connectivity associated with TBI that are otherwise not visible with conventional imaging. This study assessed whether TBI patients with (n = 17) or without (n = 16) chronic symptoms (TBIcs/TBIncs) exhibit any changes in structural connectivity (SC) and mean fractional anisotropy (mFA) of intra- and inter-hemispheric connections when compared to a control group (CG) (n = 13). Reductions in SC and mFA were observed for TBIcs compared to CG, but not for TBIncs. More connections were found to have mFA reductions than SC reductions. On the whole, SC is dominated by ipsilateral connections for all the groups after the comparison of contralateral and ipsilateral connections. More contra-ipsi reductions of mFA were found for TBIcs than TBIncs compared to CG. These findings suggest that TBI patients with chronic symptoms not only demonstrate decreased global and regional mFA but also reduced structural network connectivity.","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141581374","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}

引用次数: 0

Classifying Neuronal Cell Types Based on Shared Electrophysiological Information from Humans and Mice. 根据人类和小鼠共享的电生理信息对神经元细胞类型进行分类

IF 2.7 4区医学

Neuroinformatics Pub Date : 2024-07-08 DOI: 10.1007/s12021-024-09675-5

Ofek Ophir, Orit Shefi, Ofir Lindenbaum

{"title":"Classifying Neuronal Cell Types Based on Shared Electrophysiological Information from Humans and Mice.","authors":"Ofek Ophir, Orit Shefi, Ofir Lindenbaum","doi":"10.1007/s12021-024-09675-5","DOIUrl":"https://doi.org/10.1007/s12021-024-09675-5","url":null,"abstract":"The brain is an intricate system that controls a variety of functions. It consists of a vast number of cells that exhibit diverse characteristics. To understand brain function in health and disease, it is crucial to classify neurons accurately. Recent advancements in machine learning have provided a way to classify neurons based on their electrophysiological activity. This paper presents a deep-learning framework that classifies neurons solely on this basis. The framework uses data from the Allen Cell Types database, which contains a survey of biological features derived from single-cell recordings from mice and humans. The shared information from both sources is used to classify neurons into their broad types with the help of a joint model. An accurate domain-adaptive model, integrating electrophysiological data from both mice and humans, is implemented. Furthermore, data from mouse neurons, which also includes labels of transgenic mouse lines, is further classified into subtypes using an interpretable neural network model. The framework provides state-of-the-art results in terms of accuracy and precision while also providing explanations for the predictions.","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555808","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}

引用次数: 0

Photogrammetry scans for neuroanatomy education - a new multi-camera system: technical note. 用于神经解剖学教育的摄影测量扫描--新型多摄像头系统：技术说明。

IF 2.7 4区医学

Neuroinformatics Pub Date : 2024-07-01 Epub Date: 2024-06-13 DOI: 10.1007/s12021-024-09672-8

André S B Oliveira, Luciano C P C Leonel, Megan M J Bauman, Alessandro De Bonis, Edward R LaHood, Stephen Graepel, Michael J Link, Carlos D Pinheiro-Neto, Nirusha Lachman, Jonathan M Morris, Maria Peris-Celda

{"title":"Photogrammetry scans for neuroanatomy education - a new multi-camera system: technical note.","authors":"André S B Oliveira, Luciano C P C Leonel, Megan M J Bauman, Alessandro De Bonis, Edward R LaHood, Stephen Graepel, Michael J Link, Carlos D Pinheiro-Neto, Nirusha Lachman, Jonathan M Morris, Maria Peris-Celda","doi":"10.1007/s12021-024-09672-8","DOIUrl":"10.1007/s12021-024-09672-8","url":null,"abstract":"Photogrammetry scans has directed attention to the development of advanced camera systems to improve the creation of three-dimensional (3D) models, especially for educational and medical-related purposes. This could be a potential cost-effective method for neuroanatomy education, especially when access to laboratory-based learning is limited. The aim of this study was to describe a new photogrammetry system based on a 5 Digital Single-Lens Reflex (DSLR) cameras setup to optimize accuracy of neuroanatomical 3D models. One formalin-fixed brain and specimen and one dry skull were used for dissections and scanning using the photogrammetry technique. After each dissection, the specimens were placed inside a new MedCreator® scanner (MedReality, Thyng, Chicago, IL) to be scanned with the final 3D model being displayed on SketchFab® (Epic, Cary, NC) and MedReality® platforms. The scanner consisted of 5 cameras arranged vertically facing the specimen, which was positioned on a platform in the center of the scanner. The new multi-camera system contains automated software packages, which allowed for quick rendering and creation of a high-quality 3D models. Following uploading the 3D models to the SketchFab® and MedReality® platforms for display, the models can be freely manipulated in various angles and magnifications in any devices free of charge for users. Therefore, photogrammetry scans with this new multi-camera system have the potential to enhance the accuracy and resolution of the 3D models, along with shortening creation time of the models. This system can serve as an important tool to optimize neuroanatomy education and ultimately, improve patient outcomes.","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141312062","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}

引用次数: 0

Solving the Pervasive Problem of Protocol Non-Compliance in MRI using an Open-Source tool mrQA. 使用开源工具 mrQA 解决核磁共振成像中普遍存在的不遵守协议问题。

IF 2.7 4区医学

Neuroinformatics Pub Date : 2024-07-01 Epub Date: 2024-06-11 DOI: 10.1007/s12021-024-09668-4

Harsh Sinha, Pradeep Reddy Raamana

{"title":"Solving the Pervasive Problem of Protocol Non-Compliance in MRI using an Open-Source tool mrQA.","authors":"Harsh Sinha, Pradeep Reddy Raamana","doi":"10.1007/s12021-024-09668-4","DOIUrl":"10.1007/s12021-024-09668-4","url":null,"abstract":"Pooling data across diverse sources acquired by multisite consortia requires compliance with a predefined reference protocol i.e., ensuring different sites and scanners for a given project have used identical or compatible MR physics parameter values. Traditionally, this has been an arduous and manual process due to difficulties in working with the complicated DICOM standard and lack of resources allocated towards protocol compliance. Moreover, issues of protocol compliance is often overlooked for lack of realization that parameter values are routinely improvised/modified locally at various sites. The inconsistencies in acquisition protocols can reduce SNR, statistical power, and in the worst case, may invalidate the results altogether. An open-source tool, mrQA was developed to automatically assess protocol compliance on standard dataset formats such as DICOM and BIDS, and to study the patterns of non-compliance in over 20 open neuroimaging datasets, including the large ABCD study. The results demonstrate that the lack of compliance is rather pervasive. The frequent sources of non-compliance include but are not limited to deviations in Repetition Time, Echo Time, Flip Angle, and Phase Encoding Direction. It was also observed that GE and Philips scanners exhibited higher rates of non-compliance relative to the Siemens scanners in the ABCD dataset. Continuous monitoring for protocol compliance is strongly recommended before any pre/post-processing, ideally right after the acquisition, to avoid the silent propagation of severe/subtle issues. Although, this study focuses on neuroimaging datasets, the proposed tool mrQA can work with any DICOM-based datasets.","PeriodicalId":49761,"journal":{"name":"Neuroinformatics","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11329586/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141301974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0