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1.
Annu Rev Neurosci ; 43: 441-464, 2020 07 08.
Artículo en Inglés | MEDLINE | ID: mdl-32283996

RESUMEN

As acquiring bigger data becomes easier in experimental brain science, computational and statistical brain science must achieve similar advances to fully capitalize on these data. Tackling these problems will benefit from a more explicit and concerted effort to work together. Specifically, brain science can be further democratized by harnessing the power of community-driven tools, which both are built by and benefit from many different people with different backgrounds and expertise. This perspective can be applied across modalities and scales and enables collaborations across previously siloed communities.


Asunto(s)
Macrodatos , Encéfalo/fisiología , Biología Computacional , Red Nerviosa/fisiología , Animales , Biología Computacional/métodos , Bases de Datos Genéticas , Expresión Génica/fisiología , Humanos
2.
Nat Methods ; 21(5): 804-808, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38191935

RESUMEN

Neuroimaging research requires purpose-built analysis software, which is challenging to install and may produce different results across computing environments. The community-oriented, open-source Neurodesk platform ( https://www.neurodesk.org/ ) harnesses a comprehensive and growing suite of neuroimaging software containers. Neurodesk includes a browser-accessible virtual desktop, command-line interface and computational notebook compatibility, allowing for accessible, flexible, portable and fully reproducible neuroimaging analysis on personal workstations, high-performance computers and the cloud.


Asunto(s)
Neuroimagen , Programas Informáticos , Neuroimagen/métodos , Humanos , Interfaz Usuario-Computador , Reproducibilidad de los Resultados , Encéfalo/diagnóstico por imagen
3.
PLoS Biol ; 21(6): e3002133, 2023 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-37390046

RESUMEN

Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.


Asunto(s)
Encéfalo , Neurociencias , Animales , Humanos , Ratones , Ecosistema , Neuronas
4.
Nat Methods ; 19(12): 1568-1571, 2022 12.
Artículo en Inglés | MEDLINE | ID: mdl-36456786

RESUMEN

Reference anatomies of the brain ('templates') and corresponding atlases are the foundation for reporting standardized neuroimaging results. Currently, there is no registry of templates and atlases; therefore, the redistribution of these resources occurs either bundled within existing software or in ad hoc ways such as downloads from institutional sites and general-purpose data repositories. We introduce TemplateFlow as a publicly available framework for human and non-human brain models. The framework combines an open database with software for access, management, and vetting, allowing scientists to share their resources under FAIR-findable, accessible, interoperable, and reusable-principles. TemplateFlow enables multifaceted insights into brains across species, and supports multiverse analyses testing whether results generalize across standard references, scales, and in the long term, species.


Asunto(s)
Fenómenos Fisiológicos del Sistema Nervioso , Neuroimagen , Encéfalo , Bases de Datos Factuales , Solución de Problemas
5.
Radiology ; 309(1): e230096, 2023 10.
Artículo en Inglés | MEDLINE | ID: mdl-37906015

RESUMEN

Background Clinically acquired brain MRI scans represent a valuable but underused resource for investigating neurodevelopment due to their technical heterogeneity and lack of appropriate controls. These barriers have curtailed retrospective studies of clinical brain MRI scans compared with more costly prospectively acquired research-quality brain MRI scans. Purpose To provide a benchmark for neuroanatomic variability in clinically acquired brain MRI scans with limited imaging pathology (SLIPs) and to evaluate if growth charts from curated clinical MRI scans differed from research-quality MRI scans or were influenced by clinical indication for the scan. Materials and Methods In this secondary analysis of preexisting data, clinical brain MRI SLIPs from an urban pediatric health care system (individuals aged ≤22 years) were scanned across nine 3.0-T MRI scanners. The curation process included manual review of signed radiology reports and automated and manual quality review of images without gross pathology. Global and regional volumetric imaging phenotypes were measured using two image segmentation pipelines, and clinical brain growth charts were quantitatively compared with charts derived from a large set of research controls in the same age range by means of Pearson correlation and age at peak volume. Results The curated clinical data set included 532 patients (277 male; median age, 10 years [IQR, 5-14 years]; age range, 28 days after birth to 22 years) scanned between 2005 and 2020. Clinical brain growth charts were highly correlated with growth charts derived from research data sets (22 studies, 8346 individuals [4947 male]; age range, 152 days after birth to 22 years) in terms of normative developmental trajectories predicted by the models (median r = 0.979). Conclusion The clinical indication of the scans did not significantly bias the output of clinical brain charts. Brain growth charts derived from clinical controls with limited imaging pathology were highly correlated with brain charts from research controls, suggesting the potential of curated clinical MRI scans to supplement research data sets. © RSNA, 2023 Supplemental material is available for this article. See also the editorial by Ertl-Wagner and Pai in this issue.


Asunto(s)
Encéfalo , Gráficos de Crecimiento , Humanos , Masculino , Niño , Recién Nacido , Estudios Retrospectivos , Encéfalo/diagnóstico por imagen , Encéfalo/patología , Imagen por Resonancia Magnética/métodos , Cabeza
6.
Histochem Cell Biol ; 160(3): 223-251, 2023 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-37428210

RESUMEN

A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself-OME-Zarr-along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain-the file format that underlies so many personal, institutional, and global data management and analysis tasks.


Asunto(s)
Microscopía , Programas Informáticos , Humanos , Apoyo Comunitario
7.
BMC Psychiatry ; 23(1): 757, 2023 10 17.
Artículo en Inglés | MEDLINE | ID: mdl-37848857

RESUMEN

BACKGROUND: Adolescence is characterized by a heightened vulnerability for Major Depressive Disorder (MDD) onset, and currently, treatments are only effective for roughly half of adolescents with MDD. Accordingly, novel interventions are urgently needed. This study aims to establish mindfulness-based real-time fMRI neurofeedback (mbNF) as a non-invasive approach to downregulate the default mode network (DMN) in order to decrease ruminatory processes and depressive symptoms. METHODS: Adolescents (N = 90) with a current diagnosis of MDD ages 13-18-years-old will be randomized in a parallel group, two-arm, superiority trial to receive either 15 or 30 min of mbNF with a 1:1 allocation ratio. Real-time neurofeedback based on activation of the frontoparietal network (FPN) relative to the DMN will be displayed to participants via the movement of a ball on a computer screen while participants practice mindfulness in the scanner. We hypothesize that within-DMN (medial prefrontal cortex [mPFC] with posterior cingulate cortex [PCC]) functional connectivity will be reduced following mbNF (Aim 1: Target Engagement). Additionally, we hypothesize that participants in the 30-min mbNF condition will show greater reductions in within-DMN functional connectivity (Aim 2: Dosing Impact on Target Engagement). Aim 1 will analyze data from all participants as a single-group, and Aim 2 will leverage the randomized assignment to analyze data as a parallel-group trial. Secondary analyses will probe changes in depressive symptoms and rumination. DISCUSSION: Results of this study will determine whether mbNF reduces functional connectivity within the DMN among adolescents with MDD, and critically, will identify the optimal dosing with respect to DMN modulation as well as reduction in depressive symptoms and rumination. TRIAL REGISTRATION: This study has been registered with clinicaltrials.gov, most recently updated on July 6, 2023 (trial identifier: NCT05617495).


Asunto(s)
Trastorno Depresivo Mayor , Atención Plena , Neurorretroalimentación , Humanos , Adolescente , Trastorno Depresivo Mayor/diagnóstico por imagen , Trastorno Depresivo Mayor/terapia , Imagen por Resonancia Magnética/métodos , Neurorretroalimentación/métodos , Giro del Cíngulo/diagnóstico por imagen , Encéfalo/diagnóstico por imagen , Mapeo Encefálico/métodos
8.
Neuroimage ; 264: 119737, 2022 12 01.
Artículo en Inglés | MEDLINE | ID: mdl-36356823

RESUMEN

Brain network interactions are commonly assessed via functional (network) connectivity, captured as an undirected matrix of Pearson correlation coefficients. Functional connectivity can represent static and dynamic relations, but often these are modeled using a fixed choice for the data window Alternatively, deep learning models may flexibly learn various representations from the same data based on the model architecture and the training task. However, the representations produced by deep learning models are often difficult to interpret and require additional posthoc methods, e.g., saliency maps. In this work, we integrate the strengths of deep learning and functional connectivity methods while also mitigating their weaknesses. With interpretability in mind, we present a deep learning architecture that exposes a directed graph layer that represents what the model has learned about relevant brain connectivity. A surprising benefit of this architectural interpretability is significantly improved accuracy in discriminating controls and patients with schizophrenia, autism, and dementia, as well as age and gender prediction from functional MRI data. We also resolve the window size selection problem for dynamic directed connectivity estimation as we estimate windowing functions from the data, capturing what is needed to estimate the graph at each time-point. We demonstrate efficacy of our method in comparison with multiple existing models that focus on classification accuracy, unlike our interpretability-focused architecture. Using the same data but training different models on their own discriminative tasks we are able to estimate task-specific directed connectivity matrices for each subject. Results show that the proposed approach is also more robust to confounding factors compared to standard dynamic functional connectivity models. The dynamic patterns captured by our model are naturally interpretable since they highlight the intervals in the signal that are most important for the prediction. The proposed approach reveals that differences in connectivity among sensorimotor networks relative to default-mode networks are an important indicator of dementia and gender. Dysconnectivity between networks, specially sensorimotor and visual, is linked with schizophrenic patients, however schizophrenic patients show increased intra-network default-mode connectivity compared to healthy controls. Sensorimotor connectivity was important for both dementia and schizophrenia prediction, but schizophrenia is more related to dysconnectivity between networks whereas, dementia bio-markers were mostly intra-network connectivity.


Asunto(s)
Demencia , Esquizofrenia , Humanos , Imagen por Resonancia Magnética/métodos , Mapeo Encefálico/métodos , Encéfalo/diagnóstico por imagen , Esquizofrenia/diagnóstico por imagen
9.
Nat Methods ; 16(1): 111-116, 2019 01.
Artículo en Inglés | MEDLINE | ID: mdl-30532080

RESUMEN

Preprocessing of functional magnetic resonance imaging (fMRI) involves numerous steps to clean and standardize the data before statistical analysis. Generally, researchers create ad hoc preprocessing workflows for each dataset, building upon a large inventory of available tools. The complexity of these workflows has snowballed with rapid advances in acquisition and processing. We introduce fMRIPrep, an analysis-agnostic tool that addresses the challenge of robust and reproducible preprocessing for fMRI data. fMRIPrep automatically adapts a best-in-breed workflow to the idiosyncrasies of virtually any dataset, ensuring high-quality preprocessing without manual intervention. By introducing visual assessment checkpoints into an iterative integration framework for software testing, we show that fMRIPrep robustly produces high-quality results on a diverse fMRI data collection. Additionally, fMRIPrep introduces less uncontrolled spatial smoothness than observed with commonly used preprocessing tools. fMRIPrep equips neuroscientists with an easy-to-use and transparent preprocessing workflow, which can help ensure the validity of inference and the interpretability of results.


Asunto(s)
Imagen por Resonancia Magnética/métodos , Flujo de Trabajo , Mapeo Encefálico/métodos , Humanos , Procesamiento de Imagen Asistido por Computador/métodos , Reproducibilidad de los Resultados
10.
Hum Brain Mapp ; 42(7): 1945-1951, 2021 05.
Artículo en Inglés | MEDLINE | ID: mdl-33522661

RESUMEN

Having the means to share research data openly is essential to modern science. For human research, a key aspect in this endeavor is obtaining consent from participants, not just to take part in a study, which is a basic ethical principle, but also to share their data with the scientific community. To ensure that the participants' privacy is respected, national and/or supranational regulations and laws are in place. It is, however, not always clear to researchers what the implications of those are, nor how to comply with them. The Open Brain Consent (https://open-brain-consent.readthedocs.io) is an international initiative that aims to provide researchers in the brain imaging community with information about data sharing options and tools. We present here a short history of this project and its latest developments, and share pointers to consent forms, including a template consent form that is compliant with the EU general data protection regulation. We also share pointers to an associated data user agreement that is not only useful in the EU context, but also for any researchers dealing with personal (clinical) data elsewhere.


Asunto(s)
Encéfalo/diagnóstico por imagen , Difusión de la Información , Consentimiento Informado , Neuroimagen , Sujetos de Investigación , Humanos , Difusión de la Información/ética , Consentimiento Informado/ética , Neuroimagen/ética
11.
Cerebellum ; 20(3): 392-401, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33210245

RESUMEN

Adolescents with anxiety disorders exhibit excessive emotional and somatic arousal. Neuroimaging studies have shown abnormal cerebral cortical activation and connectivity in this patient population. The specific role of cerebellar output circuitry, specifically the dentate nuclei (DN), in adolescent anxiety disorders remains largely unexplored. Resting-state functional connectivity analyses have parcellated the DN, the major output nuclei of the cerebellum, into three functional territories (FTs) that include default-mode, salience-motor, and visual networks. The objective of this study was to understand whether FTs of the DN are implicated in adolescent anxiety disorders. Forty-one adolescents (mean age 15.19 ± 0.82, 26 females) with one or more anxiety disorders and 55 age- and gender-matched healthy controls completed resting-state fMRI scans and a self-report survey on anxiety symptoms. Seed-to-voxel functional connectivity analyses were performed using the FTs from DN parcellation. Brain connectivity metrics were then correlated with State-Trait Anxiety Inventory (STAI) measures within each group. Adolescents with an anxiety disorder showed significant hyperconnectivity between salience-motor DN FT and cerebral cortical salience-motor regions compared to controls. Salience-motor FT connectivity with cerebral cortical sensorimotor regions was significantly correlated with STAI-trait scores in HC (R2 = 0.41). Here, we report DN functional connectivity differences in adolescents diagnosed with anxiety, as well as in HC with variable degrees of anxiety traits. These observations highlight the relevance of DN as a potential clinical and sub-clinical marker of anxiety.


Asunto(s)
Trastornos de Ansiedad/diagnóstico por imagen , Cerebelo/diagnóstico por imagen , Adolescente , Mapeo Encefálico , Femenino , Humanos , Imagen por Resonancia Magnética , Masculino , Movimiento/fisiología , Red Nerviosa/diagnóstico por imagen , Pruebas Neuropsicológicas , Autoinforme
12.
J Med Internet Res ; 23(11): e22369, 2021 11 11.
Artículo en Inglés | MEDLINE | ID: mdl-34762054

RESUMEN

BACKGROUND: Universal access to assessment and treatment of mental health and learning disorders remains a significant and unmet need. There are many people without access to care because of economic, geographic, and cultural barriers, as well as the limited availability of clinical experts who could help advance our understanding and treatment of mental health. OBJECTIVE: This study aims to create an open, configurable software platform to build clinical measures, mobile assessments, tasks, and interventions without programming expertise. Specifically, our primary requirements include an administrator interface for creating and scheduling recurring and customized questionnaires where end users receive and respond to scheduled notifications via an iOS or Android app on a mobile device. Such a platform would help relieve overwhelmed health systems and empower remote and disadvantaged subgroups in need of accurate and effective information, assessment, and care. This platform has the potential to advance scientific research by supporting the collection of data with instruments tailored to specific scientific questions from large, distributed, and diverse populations. METHODS: We searched for products that satisfy these requirements. We designed and developed a new software platform called MindLogger, which exceeds the requirements. To demonstrate the platform's configurability, we built multiple applets (collections of activities) within the MindLogger mobile app and deployed several of them, including a comprehensive set of assessments underway in a large-scale, longitudinal mental health study. RESULTS: Of the hundreds of products we researched, we found 10 that met our primary requirements with 4 that support end-to-end encryption, 2 that enable restricted access to individual users' data, 1 that provides open-source software, and none that satisfy all three. We compared features related to information presentation and data capture capabilities; privacy and security; and access to the product, code, and data. We successfully built MindLogger mobile and web applications, as well as web browser-based tools for building and editing new applets and for administering them to end users. MindLogger has end-to-end encryption, enables restricted access, is open source, and supports a variety of data collection features. One applet is currently collecting data from children and adolescents in our mental health study, and other applets are in different stages of testing and deployment for use in clinical and research settings. CONCLUSIONS: We demonstrated the flexibility and applicability of the MindLogger platform through its deployment in a large-scale, longitudinal, mobile mental health study and by building a variety of other mental health-related applets. With this release, we encourage a broad range of users to apply the MindLogger platform to create and test applets to advance health care and scientific research. We hope that increasing the availability of applets designed to assess and administer interventions will facilitate access to health care in the general population.


Asunto(s)
Aplicaciones Móviles , Psiquiatría , Telemedicina , Adolescente , Humanos , Salud Mental , Encuestas y Cuestionarios
13.
Cerebellum ; 19(1): 16-29, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31321675

RESUMEN

A patient diagnosed with developmental delay, intellectual disability, and autistic and obsessive-compulsive symptoms was found to have a posterior fossa arachnoid cyst (PFAC) compressing the cerebellum. The patient was referred to our Ataxia Unit for consideration of surgical drainage of the cyst to improve his clinical constellation. This scenario led to an in-depth analysis including a literature review, functional resting-state MRI analysis of our patient compared to a group of controls, and genetic testing. While it is reasonable to consider that there may be a causal relationship between PFAC and neurodevelopmental or psychiatric symptoms in some patients, there is also a nontrivial prevalence of PFAC in the asymptomatic population and a significant possibility that many PFAC are incidental findings in the context of primary cognitive or psychiatric symptoms. Our functional MRI analysis is the first to examine brain function, and to report cerebellar dysfunction, in a patient presenting with cognitive/psychiatric symptoms found to have a structural abnormality compressing the cerebellum. These neuroimaging findings are inherently limited due to their correlational nature but provide unprecedented evidence suggesting that cerebellar compression may be associated with cerebellar dysfunction. Exome gene sequencing revealed additional etiological possibilities, highlighting the complexity of this field of cerebellar clinical and scientific practice. Our findings and discussion may guide future investigations addressing an important knowledge gap-namely, is there a link between cerebellar compression (including arachnoid cysts and possibly other forms of cerebellar compression such as Chiari malformation), cerebellar dysfunction (including fMRI abnormalities reported here), and neuropsychiatric symptoms?


Asunto(s)
Quistes Aracnoideos/diagnóstico por imagen , Enfermedades Cerebelosas/diagnóstico por imagen , Cerebelo/diagnóstico por imagen , Trastornos Mentales/diagnóstico por imagen , Trastornos del Neurodesarrollo/diagnóstico por imagen , Adulto , Quistes Aracnoideos/complicaciones , Quistes Aracnoideos/cirugía , Enfermedades Cerebelosas/complicaciones , Enfermedades Cerebelosas/cirugía , Cerebelo/cirugía , Humanos , Imagen por Resonancia Magnética/métodos , Masculino , Trastornos Mentales/complicaciones , Trastornos Mentales/cirugía , Trastornos del Neurodesarrollo/complicaciones , Trastornos del Neurodesarrollo/cirugía
14.
J Med Internet Res ; 22(10): e22635, 2020 10 12.
Artículo en Inglés | MEDLINE | ID: mdl-32936777

RESUMEN

BACKGROUND: The COVID-19 pandemic is impacting mental health, but it is not clear how people with different types of mental health problems were differentially impacted as the initial wave of cases hit. OBJECTIVE: The aim of this study is to leverage natural language processing (NLP) with the goal of characterizing changes in 15 of the world's largest mental health support groups (eg, r/schizophrenia, r/SuicideWatch, r/Depression) found on the website Reddit, along with 11 non-mental health groups (eg, r/PersonalFinance, r/conspiracy) during the initial stage of the pandemic. METHODS: We created and released the Reddit Mental Health Dataset including posts from 826,961 unique users from 2018 to 2020. Using regression, we analyzed trends from 90 text-derived features such as sentiment analysis, personal pronouns, and semantic categories. Using supervised machine learning, we classified posts into their respective support groups and interpreted important features to understand how different problems manifest in language. We applied unsupervised methods such as topic modeling and unsupervised clustering to uncover concerns throughout Reddit before and during the pandemic. RESULTS: We found that the r/HealthAnxiety forum showed spikes in posts about COVID-19 early on in January, approximately 2 months before other support groups started posting about the pandemic. There were many features that significantly increased during COVID-19 for specific groups including the categories "economic stress," "isolation," and "home," while others such as "motion" significantly decreased. We found that support groups related to attention-deficit/hyperactivity disorder, eating disorders, and anxiety showed the most negative semantic change during the pandemic out of all mental health groups. Health anxiety emerged as a general theme across Reddit through independent supervised and unsupervised machine learning analyses. For instance, we provide evidence that the concerns of a diverse set of individuals are converging in this unique moment of history; we discovered that the more users posted about COVID-19, the more linguistically similar (less distant) the mental health support groups became to r/HealthAnxiety (ρ=-0.96, P<.001). Using unsupervised clustering, we found the suicidality and loneliness clusters more than doubled in the number of posts during the pandemic. Specifically, the support groups for borderline personality disorder and posttraumatic stress disorder became significantly associated with the suicidality cluster. Furthermore, clusters surrounding self-harm and entertainment emerged. CONCLUSIONS: By using a broad set of NLP techniques and analyzing a baseline of prepandemic posts, we uncovered patterns of how specific mental health problems manifest in language, identified at-risk users, and revealed the distribution of concerns across Reddit, which could help provide better resources to its millions of users. We then demonstrated that textual analysis is sensitive to uncover mental health complaints as they appear in real time, identifying vulnerable groups and alarming themes during COVID-19, and thus may have utility during the ongoing pandemic and other world-changing events such as elections and protests.


Asunto(s)
Ansiedad/diagnóstico , Ansiedad/epidemiología , Infecciones por Coronavirus/epidemiología , Salud Mental/estadística & datos numéricos , Procesamiento de Lenguaje Natural , Neumonía Viral/epidemiología , Grupos de Autoayuda/estadística & datos numéricos , Medios de Comunicación Sociales/estadística & datos numéricos , Adolescente , Adulto , Ansiedad/psicología , Betacoronavirus , Trastorno de Personalidad Limítrofe/epidemiología , Trastorno de Personalidad Limítrofe/psicología , COVID-19 , Femenino , Salud Global , Humanos , Masculino , Persona de Mediana Edad , Pandemias , SARS-CoV-2 , Trastornos por Estrés Postraumático/epidemiología , Trastornos por Estrés Postraumático/psicología , Ideación Suicida , Adulto Joven
15.
Proc Natl Acad Sci U S A ; 113(44): 12574-12579, 2016 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-27791099

RESUMEN

Understanding how the structure of cognition arises from the topographical organization of the cortex is a primary goal in neuroscience. Previous work has described local functional gradients extending from perceptual and motor regions to cortical areas representing more abstract functions, but an overarching framework for the association between structure and function is still lacking. Here, we show that the principal gradient revealed by the decomposition of connectivity data in humans and the macaque monkey is anchored by, at one end, regions serving primary sensory/motor functions and at the other end, transmodal regions that, in humans, are known as the default-mode network (DMN). These DMN regions exhibit the greatest geodesic distance along the cortical surface-and are precisely equidistant-from primary sensory/motor morphological landmarks. The principal gradient also provides an organizing spatial framework for multiple large-scale networks and characterizes a spectrum from unimodal to heteromodal activity in a functional metaanalysis. Together, these observations provide a characterization of the topographical organization of cortex and indicate that the role of the DMN in cognition might arise from its position at one extreme of a hierarchy, allowing it to process transmodal information that is unrelated to immediate sensory input.


Asunto(s)
Encéfalo/fisiología , Red Nerviosa/fisiología , Sensación/fisiología , Corteza Sensoriomotora/fisiología , Animales , Mapeo Encefálico , Humanos , Macaca , Imagen por Resonancia Magnética/métodos , Modelos Neurológicos
16.
PLoS Comput Biol ; 13(2): e1005350, 2017 02.
Artículo en Inglés | MEDLINE | ID: mdl-28231282

RESUMEN

Mindboggle (http://mindboggle.info) is an open source brain morphometry platform that takes in preprocessed T1-weighted MRI data and outputs volume, surface, and tabular data containing label, feature, and shape information for further analysis. In this article, we document the software and demonstrate its use in studies of shape variation in healthy and diseased humans. The number of different shape measures and the size of the populations make this the largest and most detailed shape analysis of human brains ever conducted. Brain image morphometry shows great potential for providing much-needed biological markers for diagnosing, tracking, and predicting progression of mental health disorders. Very few software algorithms provide more than measures of volume and cortical thickness, while more subtle shape measures may provide more sensitive and specific biomarkers. Mindboggle computes a variety of (primarily surface-based) shapes: area, volume, thickness, curvature, depth, Laplace-Beltrami spectra, Zernike moments, etc. We evaluate Mindboggle's algorithms using the largest set of manually labeled, publicly available brain images in the world and compare them against state-of-the-art algorithms where they exist. All data, code, and results of these evaluations are publicly available.


Asunto(s)
Algoritmos , Puntos Anatómicos de Referencia/diagnóstico por imagen , Encefalopatías/diagnóstico por imagen , Encefalopatías/patología , Encéfalo/patología , Imagen de Difusión por Resonancia Magnética , Femenino , Humanos , Interpretación de Imagen Asistida por Computador , Imagenología Tridimensional , Masculino , Tamaño de los Órganos , Reconocimiento de Normas Patrones Automatizadas , Reproducibilidad de los Resultados , Sensibilidad y Especificidad , Programas Informáticos , Técnica de Sustracción
17.
PLoS Comput Biol ; 13(3): e1005209, 2017 03.
Artículo en Inglés | MEDLINE | ID: mdl-28278228

RESUMEN

The rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world. In this work, we introduce a framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and described in compliance with the Brain Imaging Data Structure (BIDS). The portability of these applications (BIDS Apps) is achieved by using container technologies that encapsulate all binary and other dependencies in one convenient package. BIDS Apps run on all three major operating systems with no need for complex setup and configuration and thanks to the comprehensiveness of the BIDS standard they require little manual user input. Previous containerized data processing solutions were limited to single user environments and not compatible with most multi-tenant High Performance Computing systems. BIDS Apps overcome this limitation by taking advantage of the Singularity container technology. As a proof of concept, this work is accompanied by 22 ready to use BIDS Apps, packaging a diverse set of commonly used neuroimaging algorithms.


Asunto(s)
Encéfalo/anatomía & histología , Interpretación de Imagen Asistida por Computador/métodos , Neuroimagen/métodos , Sistemas de Información Radiológica/organización & administración , Programas Informáticos , Interfaz Usuario-Computador , Algoritmos , Humanos , Imagen por Resonancia Magnética/métodos
18.
Neuroimage ; 156: 456-465, 2017 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-28416451

RESUMEN

Aligning brain structures across individuals is a central prerequisite for comparative neuroimaging studies. Typically, registration approaches assume a strong association between the features used for alignment, such as macro-anatomy, and the variable observed, such as functional activation or connectivity. Here, we propose to use the structure of intrinsic resting state fMRI signal correlation patterns as a basis for alignment of the cortex in functional studies. Rather than assuming the spatial correspondence of functional structures between subjects, we have identified locations with similar connectivity profiles across subjects. We mapped functional connectivity relationships within the brain into an embedding space, and aligned the resulting maps of multiple subjects. We then performed a diffeomorphic alignment of the cortical surfaces, driven by the corresponding features in the joint embedding space. Results show that functional alignment based on resting state fMRI identifies functionally homologous regions across individuals with higher accuracy than alignment based on the spatial correspondence of anatomy. Further, functional alignment enables measurement of the strength of the anatomo-functional link across the cortex, and reveals the uneven distribution of this link. Stronger anatomo-functional dissociation was found in higher association areas compared to primary sensory- and motor areas. Functional alignment based on resting state features improves group analysis of task based functional MRI data, increasing statistical power and improving the delineation of task-specific core regions. Finally, a comparison of the anatomo-functional dissociation between cohorts is demonstrated with a group of left and right handed subjects.


Asunto(s)
Mapeo Encefálico/métodos , Encéfalo/diagnóstico por imagen , Procesamiento de Imagen Asistido por Computador/métodos , Imagen por Resonancia Magnética/métodos , Vías Nerviosas/diagnóstico por imagen , Adulto , Femenino , Humanos , Masculino
19.
Neuroimage ; 124(Pt B): 1242-1244, 2016 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-25869863

RESUMEN

NeuroVault.org is dedicated to storing outputs of analyses in the form of statistical maps, parcellations and atlases, a unique strategy that contrasts with most neuroimaging repositories that store raw acquisition data or stereotaxic coordinates. Such maps are indispensable for performing meta-analyses, validating novel methodology, and deciding on precise outlines for regions of interest (ROIs). NeuroVault is open to maps derived from both healthy and clinical populations, as well as from various imaging modalities (sMRI, fMRI, EEG, MEG, PET, etc.). The repository uses modern web technologies such as interactive web-based visualization, cognitive decoding, and comparison with other maps to provide researchers with efficient, intuitive tools to improve the understanding of their results. Each dataset and map is assigned a permanent Universal Resource Locator (URL), and all of the data is accessible through a REST Application Programming Interface (API). Additionally, the repository supports the NIDM-Results standard and has the ability to parse outputs from popular FSL and SPM software packages to automatically extract relevant metadata. This ease of use, modern web-integration, and pioneering functionality holds promise to improve the workflow for making inferences about and sharing whole-brain statistical maps.


Asunto(s)
Mapeo Encefálico/estadística & datos numéricos , Bases de Datos Factuales , Difusión de la Información , Acceso a la Información , Humanos , Procesamiento de Imagen Asistido por Computador , Imagen por Resonancia Magnética , Neuroimagen
20.
Alzheimers Dement ; 12(6): 645-53, 2016 06.
Artículo en Inglés | MEDLINE | ID: mdl-27079753

RESUMEN

Identifying accurate biomarkers of cognitive decline is essential for advancing early diagnosis and prevention therapies in Alzheimer's disease. The Alzheimer's disease DREAM Challenge was designed as a computational crowdsourced project to benchmark the current state-of-the-art in predicting cognitive outcomes in Alzheimer's disease based on high dimensional, publicly available genetic and structural imaging data. This meta-analysis failed to identify a meaningful predictor developed from either data modality, suggesting that alternate approaches should be considered for prediction of cognitive performance.


Asunto(s)
Enfermedad de Alzheimer/complicaciones , Trastornos del Conocimiento/diagnóstico , Trastornos del Conocimiento/etiología , Enfermedad de Alzheimer/genética , Apolipoproteínas E/genética , Biomarcadores , Trastornos del Conocimiento/genética , Biología Computacional , Bases de Datos Bibliográficas/estadística & datos numéricos , Humanos , Valor Predictivo de las Pruebas
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