[ { "key": "9BA7EWM8", "version": 5, "library": { "type": "group", "id": 324604, "name": "functional-connectivity", "links": { "alternate": { "href": "https://www.zotero.org/groups/functional-connectivity", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/324604/items/9BA7EWM8", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/functional-connectivity/items/9BA7EWM8", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1735204, "username": "yatsenko", "name": "Dimitri Yatsenko", "links": { "alternate": { "href": "https://www.zotero.org/yatsenko", "type": "text/html" } } }, "creatorSummary": "Lee et al.", "parsedDate": "2003-06", "numChildren": 0 }, "data": { "key": "9BA7EWM8", "version": 5, "itemType": "journalArticle", "title": "A report of the functional connectivity workshop, Dusseldorf 2002", "creators": [ { "creatorType": "author", "firstName": "Lucy", "lastName": "Lee" }, { "creatorType": "author", "firstName": "Lee M", "lastName": "Harrison" }, { "creatorType": "author", "firstName": "Andrea", "lastName": "Mechelli" } ], "abstractNote": "This report provides a commentary on the issues presented and discussed at the recent “Functional Brain Connectivity” workshop, held in Dusseldorf, Germany. The workshop brought together researchers using different approaches to study connectivity in the brain, providing them with an opportunity to share conceptual, mathematical, and experimental ideas and to develop strategies and collaborations for future work on functional integration. The main themes that emerged included: (1) the importance of anatomical knowledge in understanding functional interactions the brain; (2) the need to establish common definitions for terms used across disciplines; (3) the need to develop a satisfactory framework for inferring causality from functional imaging and EEG/MEG data; (4) the importance of analytic tools that capture the dynamics of neural interactions; and (5) the role of experimental paradigms that exploit the functional imaging of perturbations to cortical interactions.", "publicationTitle": "NeuroImage", "publisher": "", "place": "", "date": "June 2003", "volume": "19", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "457-465", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "NeuroImage", "DOI": "10.1016/S1053-8119(03)00062-4", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S1053811903000624", "accessDate": "2015-01-30T23:28:48Z", "PMID": "", "PMCID": "", "ISSN": "1053-8119", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2015-01-30T23:35:47Z", "dateModified": "2015-01-30T23:35:47Z" } }, { "key": "TK4JDAUZ", "version": 6, "library": { "type": "group", "id": 324604, "name": "functional-connectivity", "links": { "alternate": { "href": "https://www.zotero.org/groups/functional-connectivity", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/324604/items/TK4JDAUZ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/functional-connectivity/items/TK4JDAUZ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1735204, "username": "yatsenko", "name": "Dimitri Yatsenko", "links": { "alternate": { "href": "https://www.zotero.org/yatsenko", "type": "text/html" } } }, "lastModifiedByUser": { "id": 1279562, "username": "gdenfield", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/gdenfield", "type": "text/html" } } }, "creatorSummary": "Wang et al.", "parsedDate": "2014-12-09", "numChildren": 1 }, "data": { "key": "TK4JDAUZ", "version": 6, "itemType": "journalArticle", "title": "A systematic framework for functional connectivity measures", "creators": [ { "creatorType": "author", "firstName": "Huifang E.", "lastName": "Wang" }, { "creatorType": "author", "firstName": "Christian G.", "lastName": "Bénar" }, { "creatorType": "author", "firstName": "Pascale P.", "lastName": "Quilichini" }, { "creatorType": "author", "firstName": "Karl J.", "lastName": "Friston" }, { "creatorType": "author", "firstName": "Viktor K.", "lastName": "Jirsa" }, { "creatorType": "author", "firstName": "Christophe", "lastName": "Bernard" } ], "abstractNote": "Various methods have been proposed to characterize the functional connectivity between nodes in a network measured with different modalities (electrophysiology, functional magnetic resonance imaging etc.). Since different measures of functional connectivity yield different results for the same dataset, it is important to assess when and how they can be used. In this work, we provide a systematic framework for evaluating the performance of a large range of functional connectivity measures—based upon a comprehensive portfolio of models generating measurable responses. Specifically, we benchmarked 42 methods using 10,000 simulated datasets from 5 different types of generative models with different connectivity structures. Since all functional connectivity methods require the setting of some parameters (window size and number, model order etc.), we first optimized these parameters using performance criteria based upon (threshold free) ROC analysis. We then evaluated the performance of the methods on data simulated with different types of models. Finally, we assessed the performance of the methods against different levels of signal-to-noise ratios and network configurations. A MATLAB toolbox is provided to perform such analyses using other methods and simulated datasets.", "publicationTitle": "Frontiers in Neuroscience", "publisher": "", "place": "", "date": "2014-12-09", "volume": "8", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Front Neurosci", "DOI": "10.3389/fnins.2014.00405", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260483/", "accessDate": "2015-01-30T23:26:42Z", "PMID": "25538556", "PMCID": "PMC4260483", "ISSN": "1662-4548", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2015-01-30T23:34:15Z", "dateModified": "2015-01-30T23:34:15Z" } }, { "key": "P2I6TH8M", "version": 4, "library": { "type": "group", "id": 324604, "name": "functional-connectivity", "links": { "alternate": { "href": "https://www.zotero.org/groups/functional-connectivity", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/324604/items/P2I6TH8M", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/functional-connectivity/items/P2I6TH8M", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/324604/items/TK4JDAUZ", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1735204, "username": "yatsenko", "name": "Dimitri Yatsenko", "links": { "alternate": { "href": "https://www.zotero.org/yatsenko", "type": "text/html" } } } }, "data": { "key": "P2I6TH8M", "version": 4, "parentItem": "TK4JDAUZ", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Link", "accessDate": "2015-01-30T23:26:42Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260483/", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2015-01-30T23:34:15Z", "dateModified": "2015-01-30T23:34:15Z" } }, { "key": "4CX3D32I", "version": 3, "library": { "type": "group", "id": 324604, "name": "functional-connectivity", "links": { "alternate": { "href": "https://www.zotero.org/groups/functional-connectivity", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/324604/items/4CX3D32I", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/functional-connectivity/items/4CX3D32I", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1735204, "username": "yatsenko", "name": "Dimitri Yatsenko", "links": { "alternate": { "href": "https://www.zotero.org/yatsenko", "type": "text/html" } } }, "creatorSummary": "Friston", "parsedDate": "2011", "numChildren": 0 }, "data": { "key": "4CX3D32I", "version": 3, "itemType": "journalArticle", "title": "Functional and effective connectivity: a review", "creators": [ { "creatorType": "author", "firstName": "Karl J", "lastName": "Friston" } ], "abstractNote": "", "publicationTitle": "Brain connectivity", "publisher": "", "place": "", "date": "2011", "volume": "1", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "13–36", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2015-01-30T23:24:39Z", "dateModified": "2015-01-30T23:24:39Z" } }, { "key": "JXM8J793", "version": 3, "library": { "type": "group", "id": 324604, "name": "functional-connectivity", "links": { "alternate": { "href": "https://www.zotero.org/groups/functional-connectivity", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/324604/items/JXM8J793", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/functional-connectivity/items/JXM8J793", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1735204, "username": "yatsenko", "name": "Dimitri Yatsenko", "links": { "alternate": { "href": "https://www.zotero.org/yatsenko", "type": "text/html" } } }, "creatorSummary": "Yatsenko et al.", "parsedDate": "2015-01", "numChildren": 0 }, "data": { "key": "JXM8J793", "version": 3, "itemType": "journalArticle", "title": "Improved estimation and interpretation of correlations in neural circuits", "creators": [ { "creatorType": "author", "firstName": "Dimitri", "lastName": "Yatsenko" }, { "creatorType": "author", "firstName": "Krešimir", "lastName": "Josić" }, { "creatorType": "author", "firstName": "Alexander S.", "lastName": "Ecker" }, { "creatorType": "author", "firstName": "Emmanouil", "lastName": "Froudarakis" }, { "creatorType": "author", "firstName": "R. James", "lastName": "Cotton" }, { "creatorType": "author", "firstName": "Andreas S.", "lastName": "Tolias" } ], "abstractNote": "", "publicationTitle": "PLoS Computational Biology", "publisher": "", "place": "", "date": "January, 2015", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2015-01-30T23:23:08Z", "dateModified": "2015-01-30T23:23:08Z" } }, { "key": "BFK5T99U", "version": 2, "library": { "type": "group", "id": 324604, "name": "functional-connectivity", "links": { "alternate": { "href": "https://www.zotero.org/groups/functional-connectivity", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/324604/items/BFK5T99U", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/functional-connectivity/items/BFK5T99U", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1735204, "username": "yatsenko", "name": "Dimitri Yatsenko", "links": { "alternate": { "href": "https://www.zotero.org/yatsenko", "type": "text/html" } } }, "creatorSummary": "Harris and Shepherd", "parsedDate": "2015-02", "numChildren": 0 }, "data": { "key": "BFK5T99U", "version": 2, "itemType": "journalArticle", "title": "The neocortical circuit: themes and variations", "creators": [ { "creatorType": "author", "firstName": "Kenneth D.", "lastName": "Harris" }, { "creatorType": "author", "firstName": "Gordon M. G.", "lastName": "Shepherd" } ], "abstractNote": "Similarities in neocortical circuit organization across areas and species suggest a common strategy to process diverse types of information, including sensation from diverse modalities, motor control and higher cognitive processes. Cortical neurons belong to a small number of main classes. The properties of these classes, including their local and long-range connectivity, developmental history, gene expression, intrinsic physiology and in vivo activity patterns, are remarkably similar across areas. Each class contains subclasses; for a rapidly growing number of these, conserved patterns of input and output connections are also becoming evident. The ensemble of circuit connections constitutes a basic circuit pattern that appears to be repeated across neocortical areas, with area- and species-specific modifications. Such 'serially homologous' organization may adapt individual neocortical regions to the type of information each must process.", "publicationTitle": "Nature Neuroscience", "publisher": "", "place": "", "date": "February 2015", "volume": "18", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "170-181", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Neurosci", "DOI": "10.1038/nn.3917", "citationKey": "", "url": "http://www.nature.com.ezproxyhost.library.tmc.edu/neuro/journal/v18/n2/full/nn.3917.html", "accessDate": "2015-01-29T19:51:25Z", "PMID": "", "PMCID": "", "ISSN": "1097-6256", "archive": "", "archiveLocation": "", "shortTitle": "The neocortical circuit", "language": "en", "libraryCatalog": "www.nature.com.ezproxyhost.library.tmc.edu", "callNumber": "", "rights": "© 2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2015-01-30T23:22:46Z", "dateModified": "2015-01-30T23:22:46Z" } } ]