RRID | Searching in Community Resources

<!DOCTYPE html>    <html lang="en">  <head> <title>RRID | Searching in Community Resources</title>  <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="description" content="Results for the query '*' in resources across SciCrunch: Registry"> <meta name="author" content=""> <meta name="google-site-verification" content="vhe7FXQ5uQHNwM10raiS4rO23GgbFW6-iyRfapxGPJc" />  <link rel="shortcut icon" href="/favicon.ico">  <link rel="stylesheet" href="/css/main.css"> <link rel="stylesheet" href="/assets/plugins/bootstrap/css/bootstrap.min.css"> <link rel="stylesheet" href="/assets/plugins/sky-forms/version-2.0.1/css/custom-sky-forms.css"> <link rel="stylesheet" href="/assets/css/style.css">  <link rel="stylesheet" href="/assets/plugins/line-icons/line-icons.css"> <link rel="stylesheet" href="/assets/plugins/font-awesome/css/font-awesome.min.css"> <link rel="stylesheet" href="/assets/plugins/owl-carousel/owl-carousel/owl.carousel.css">  <link rel="stylesheet" href="/assets/css/pages/page_search_inner.css"> <link rel="stylesheet" href="/assets/css/pages/page_search_inner_tables.css"> <link rel="stylesheet" href="/assets/plugins/scrollbar/src/perfect-scrollbar.css">  <link rel="stylesheet" href="/assets/css/themes/default.css" id="style_color"> <link rel="stylesheet" href="/assets/css/pages/page_log_reg_v2.css"> <link rel="stylesheet" href="/assets/css/shop/shop.blocks.css">  <link rel="stylesheet" href="/assets/css/custom.css"> <link rel="stylesheet" href="/css/community-search.css"> <link rel="stylesheet" href="/css/joyride-2.0.3.css"> <link rel="stylesheet" href="/js/Highcharts-6.0.7/code/css/highcharts.css"> <script type="text/javascript" src="/assets/plugins/jquery-3.4.1.min.js"></script> <script type="text/javascript" src="/js/main.js"></script> <script src="/js/angular-1.7.9/angular.min.js"></script> <script src="/js/ui-bootstrap-tpls-2.5.0.min.js"></script> <script src="/js/angular-1.7.9/angular-sanitize.js"></script> <script src="/js/module-error.js"></script> <script src="/js/module-resource.js"></script>  <style> #loading { background: #F7F7FF; display: none; } .page-overlay { width: 100%; height: 100%; z-index: 1000; top: 0; left: 0; position: fixed; } #restarting-warning { background: #FFF7F7; display: none; } #try-again-later-warning { display: none; } .center-style-1 { display: table; position: absolute; height: 100%; width: 100%; } .center-style-2 { display: table-cell; vertical-align: middle; } .center-style-3 { margin-left: auto; margin-right: auto; } </style> <script> window.page_loaded = false; function pageLoad() { document.getElementById("loading").style.display = "none"; document.getElementById("full-page").style.display = "block"; window.page_loaded = window.okSearchStatus; clearTimeout(window.reloadTimeout); checkReloadSearchPage(); } function checkReloadSearchPage() { document.getElementById("loading").style.display = "none"; document.getElementById("full-page").style.display = "block"; if(!window.page_loaded) { if(window.location.search.indexOf("restarted") === -1) { document.getElementById("restarting-warning").style.display = "block"; setTimeout(function() { var sep = window.location.search.indexOf("?") === -1 ? 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Many functions will not work if you continue with JavaScript disabled. </div> </noscript> <div id="loading" class="page-overlay"> <div class="center-style-1"> <div class="center-style-2"> <div class="center-style-3"> <center> <h2>Searching across hundreds of databases <i class="fa fa-cog fa-spin"></i></h2> <img src="/images/scicrunch.png" style="height: 100px" /> </center> </div> </div> </div> </div> <div id="restarting-warning" class="page-overlay"> <div class="center-style-1"> <div class="center-style-2"> <div class="center-style-3"> <center> <h2>Our searching services are busy right now. Your search will reload in five seconds.</h2> </center> </div> </div> </div> </div> <div id="try-again-later-warning" class="alert alert-warning" role="alert"> Our searching services are busy right now. Please try again later. </div> <script>document.getElementById("loading").style.display = "block";</script> <div id="full-page"> <script>document.getElementById("full-page").style.display = "none";</script> <script> window.okSearchStatus = true</script> <div class="wrapper-background" style="overflow:auto ">  <style> .header .navbar-default .navbar-nav > li > a:hover, .header .navbar-default .navbar-nav > .active > a { color: #0095FE; border-bottom: solid 2px #0095FE; } .header .dropdown-menu { border-top: solid 2px #0095FE; } .header .navbar .nav > li > .search:hover { color: #0095FE; background: #f7f7f7; border-bottom-color: #0095FE; } .topbar .loginbar li a:hover { color: #0095FE; } .header .btn-u { background: #0095FE; } .header .btn-u:hover { background: #0095FE; } .header .container > .navbar-header, .header .container-fluid > .navbar-header, .header .container > .navbar-collapse, .header .container-fluid > .navbar-collapse { margin-bottom: -30px; } </style> <div class="header-v1" style="z-index:99"> <div class="topbar-v1 margin-bottom-20" > <div class="container"> <div class="row"> <div class="col-md-6"> </div> <div class="col-md-6"> <ul class="list-unstyled top-v1-data"> <script> (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); 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You can also add a resource to the community here. </p> </li> <li data-class="joyride-community-resources" data-text="Next" data-options="tipLocation:bottom;tipAnimation:fade"> <h2>Community Resources</h2> <p> Search through data specific to this community </p> </li> <li data-class="joyride-more-resources" data-text="Next" data-options="tipLocation:bottom;tipAnimation:fade"> <h2>More Resources</h2> <p> Search through all of SciCrunch's data. </p> </li> <li data-class="joyride-literature" data-text="Next" data-options="tipLocation:bottom;tipAnimation:fade"> <h2>Literature</h2> <p> Search through literature data. </p> </li> </ol> <script type="text/javascript"> $(function() { $(".tutorial-header-btn").click(function () { $("body").joyride(); $("body").joyride("destroy"); // joyride bug, when multiple joyrides on a page $(".joyride-next-tip").show(); $("#joyRideHeaderContent").joyride( { "postStepCallback": function(index, tip) { }, "startOffset": 0, "tip_class": false, } ); }); }); </script> <div class="container login-backing" style="display:none;position: fixed;left:0;top:0;width:100%;height:100%;z-index: 20000;background: rgba(0,0,0,.8)">  <form method="post" action="/forms/login.php?cid=510"> <div class="reg-block login-box"> <div class="login-backing close dark">X</div> <div class="reg-block-header"> <h2>Log in</h2> </div> <div class="input-group margin-bottom-20"> <span class="input-group-addon"><i class="fa fa-envelope"></i></span> <input type="text" class="form-control" name="email" placeholder="Email"> </div> <div class="input-group margin-bottom-20"> <span class="input-group-addon"><i class="fa fa-lock"></i></span> <input type="password" class="form-control" name="password" placeholder="Password"> </div> <a class="referer-link" href="/resources/join">Create an account</a><br/> <span class="simple-toggle login-backing" modal=".forgot-password" style="cursor:pointer;color:#72c02c" title="Forgot Password">Forgot password?</span><br/> <hr> <div class="row"> <div class="col-md-10 col-md-offset-1"> <button type="submit" class="btn-u btn-block">Log In</button> </div> </div> </div> </form>  </div> <div class="back-hide forgot-password no-padding"> <div class="close dark less-right">X</div> <div id="sky-form4" class="sky-form" novalidate="novalidate"> <header>Forgot Password</header> <fieldset> <p> If you have forgotten your password you can enter your email here and get a temporary password sent to your email. <div class="forgot-pw-container"> <form class="forgot-pw-form"> <div class="input-group"> <input type="text" class="form-control forgot-email" name="query" placeholder="Account Email"/> <span class="input-group-btn"> <button class="btn-u" type="submit">Send</button> </span> </div> </form> </div> </p> </fieldset> </div> </div> <script type="text/javascript" src="/js/facets-wordcloud30.js"></script> <script> document.categoryGraphData = null; </script> <link href="/css/rin.css" rel="stylesheet" /> <div class="rin"> <div class="report"> <div class="header-scicrunch"> <div class="container"> <div class="row"> <div> <h1 style="margin-top:10px"> Tools  <a target='_self' href='https://rrid.site/rin/rrids' class='btn btn-primary'><i class='fa fa-bars'></i> Select Another Resource Report Type</a> </h1> <ol class="breadcrumb"> <li> <a class="color-white " target="_self" href="https://rrid.site" > Home </a> </li> <li> <a class="color-white " target="_self" href="https://rrid.site/rin/rrids" > Resource Reports </a> </li> <li> <a class="color-white active" target="_self" > Tools </a> </li> </ol> </div> </div> </div> </div> <div class="header-background-resolver"></div> <div class="row"> <div class="container"> <div class="wrapper"> <div class="row"> <div class="col-md-12"> <div> <div class="row"> <div class="col-md-12"> <p style="margin-bottom: 0px" class="truncate-medium" id="sc-descr"><a href="https://scicrunch.org/scicrunch/about/sources/nlx_144509-1">SciCrunch Registry</a> is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to <a href="https://scicrunch.org/create/resource">register your resource</a>.</p> </div> <div class="col-md-12 results-number" style="margin-top:10px;"> <style> .search-block-v2 h2 { color: #585f69; 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}); $(".hidden-default-toggle").click(function() { $(".hidden-default").slideToggle(); }); }); </script> <br/> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&filter[]=gte:20241103">See new records</a> <hr /> <h3>Options</h3> <ul class="list-group"> <li class="list-group-item"><a href="#" class="btn-login">Log in for Collection Options</a></li> </ul> <hr class="hr-small" /> <h3>Current Facets and Filters</h3><ul class="list-unstyled"><li>Keywords:analysis (facet)<a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29"><i class="fa red-x fa-times-circle"></i></a></li><li>Related Resources:neuroimaging tools and resources collaboratory (nitrc) (facet)<a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis"><i class="fa red-x fa-times-circle"></i></a></li></ul><hr style="margin-top:10px;margin-bottom:15px;"/> <div> <h3>Facets</h3> <form class="multi-facets" url="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29"> <ul class="list-group sidebar-nav-v1" id="sidebar-nav"> <li class="list-group-item list-toggle" data-toggle="collapse" data-parent="#sidebar-nav" href="#collapse-Resource_Type"> <a href="javascript:void(0)">Resource Type</a> <ul id="collapse-Resource_Type" class="collapse"> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&facet[]=Resource%20Type%3Asoftware%20resource" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="37" title="software resource"> software resource (37) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="software%20resource" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&facet[]=Resource%20Type%3Asoftware%20application" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="33" title="software application"> software application (33) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="software%20application" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&facet[]=Resource%20Type%3Adata%20processing%20software" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="30" title="data processing software"> data processing soft... (30) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="data%20processing%20software" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&facet[]=Resource%20Type%3Aimage%20analysis%20software" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="17" title="image analysis software"> image analysis softw... (17) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="image%20analysis%20software" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&facet[]=Resource%20Type%3Asoftware%20toolkit" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="14" title="software toolkit"> software toolkit (14) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="software%20toolkit" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&facet[]=Resource%20Type%3Adata%20analysis%20software" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="9" title="data analysis software"> data analysis softwa... 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It is hoped that this helps the tool developers to get their tools to a larger user community and to reduce redundancy (or at least utilize tool redundancy to facilitate optimal tool design) in tool development. This also helps tool users in identification of the existing tools for specific problems as they arise. The registry is designed to be self-moderated. This means that all tool entries are owned by some responsible party who enters the tool information, and keeps it up to date via the Web.</p> <p></p> <p> <strong>Proper citation:</strong> Internet Analysis Tools Registry (RRID:SCR_005638) <a href="javascript:void(0)" onclick="copyTextToClipboard('Internet Analysis Tools Registry (RRID:SCR_005638)', 'rrid:scr_005638')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_005638" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_006204/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_006204">Brede Toolbox <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_006204 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 1+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_006204&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://neuro.imm.dtu.dk/software/brede/">http://neuro.imm.dtu.dk/software/brede/ <i class='fa fa-external-link'></i></a></p> <p>A package for neuroinformatics and neuroimaging analysis mostly programmed in Matlab with a few additional programs in Python and Perl. It allows coordinate-based meta-analysis and visualization, neuroimaging analysis of voxel or regional data - not the original data but rather the summary images (e.g., statistical parametric images) and location data in stereotactic space. Among the algorithms implemented are kernel density estimation (for coordinate-based meta-analysis), independent component analysis, non-negative matrix factorization, k-means clustering, singular value decomposition, partial correlation analysis with permutation testing and partial canonical correlation analysis. Visualization of coordinate, surfaces and volumes are possible in 2D and 3D. Generation of HTML for results are possible and algorithms can be accessed from the command line or via a flexible graphical interface. With the Brede Toolbox comes the Brede Database with a small coordinate database from published neuroimaging studies, and ontologies for, e.g., brain function and brain regions.</p> <p></p> <p> <strong>Proper citation:</strong> Brede Toolbox (RRID:SCR_006204) <a href="javascript:void(0)" onclick="copyTextToClipboard('Brede Toolbox (RRID:SCR_006204)', 'rrid:scr_006204')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_006204" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_002823/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_002823">FSL <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_002823 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 1000+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_002823&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://www.fmrib.ox.ac.uk/fsl/">http://www.fmrib.ox.ac.uk/fsl/ <i class='fa fa-external-link'></i></a></p> <p>Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas.</p> <p></p> <p> <strong>Proper citation:</strong> FSL (RRID:SCR_002823) <a href="javascript:void(0)" onclick="copyTextToClipboard('FSL (RRID:SCR_002823)', 'rrid:scr_002823')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_002823" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_003487/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_003487">L-Measure <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_003487 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_003487&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://cng.gmu.edu:8080/Lm">http://cng.gmu.edu:8080/Lm <i class='fa fa-external-link'></i></a></p> <p>A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux.</p> <p></p> <p> <strong>Proper citation:</strong> L-Measure (RRID:SCR_003487) <a href="javascript:void(0)" onclick="copyTextToClipboard('L-Measure (RRID:SCR_003487)', 'rrid:scr_003487')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_003487" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_007109/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_007109">Cambridge Brain Activation <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_007109 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_007109&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://www.bmu.psychiatry.cam.ac.uk/software/">http://www.bmu.psychiatry.cam.ac.uk/software/ <i class='fa fa-external-link'></i></a></p> <p>Suite of programs developed for fMRI analysis in a Virtual Pipeline Laboratory facilitates combining program modules from different software packages into processing pipelines to create analysis solutions which are not possible with a single software package alone. Current pipelines include fMRI analysis, statistical testing based on randomization methods and fractal spectral analysis. Pipelines are continually being added. The software is mostly written in C. This fMRI analysis package supports batch processing and comprises the following general functions at the first level of individual image analysis: movement correction (interpolation and regression), time series modeling, data resampling in the wavelet domain, hypothesis testing at voxel and cluster levels. Additionally, there is code for second level analysis - group and factorial or ANOVA mapping - after co-registration of voxel statistic maps from individual images in a standard space. The main point of difference from other fMRI analysis packages is the emphasis throughout on the use of data resampling (permutation or randomization) as a basis for inference on individual, group and factorial test statistics at voxel and cluster levels of resolution.</p> <p></p> <p> <strong>Proper citation:</strong> Cambridge Brain Activation (RRID:SCR_007109) <a href="javascript:void(0)" onclick="copyTextToClipboard('Cambridge Brain Activation (RRID:SCR_007109)', 'rrid:scr_007109')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_007109" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_001847/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_001847">FreeSurfer <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_001847 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10000+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_001847&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://surfer.nmr.mgh.harvard.edu/">http://surfer.nmr.mgh.harvard.edu/ <i class='fa fa-external-link'></i></a></p> <p>Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS.</p> <p></p> <p> <strong>Proper citation:</strong> FreeSurfer (RRID:SCR_001847) <a href="javascript:void(0)" onclick="copyTextToClipboard('FreeSurfer (RRID:SCR_001847)', 'rrid:scr_001847')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_001847" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_001808/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_001808">Atlas3D <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_001808 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_001808&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://www.nesys.uio.no/Atlas3D/">http://www.nesys.uio.no/Atlas3D/ <i class='fa fa-external-link'></i></a></p> <p>A multi-platform visualization tool which allows import and visualization of 3-D atlas structures in combination with tomographic and histological image data. The tool allows visualization and analysis of the reconstructed atlas framework, surface modeling and rotation of selected structures, user-defined slicing at any chosen angle, and import of data produced by the user for merging with the atlas framework. Tomographic image data in NIfTI (Neuroimaging Informatics Technology Initiative) file format, VRML and PNG files can be imported and visualized within the atlas framework. XYZ coordinate lists are also supported. Atlases that are available with the tool include mouse brain structures (3-D reconstructed from The Mouse Brain in Stereotaxic Coordinates by Paxinos and Franklin (2001)) and rat brain structures (3-D reconstructed from The Rat Brain in Stereotaxic Coordinates by Paxinos and Watson (2005)). Experimental data can be imported in Atlas3D and warped to atlas space, using manual linear registration, with the possibility to scale, rotate, and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images.</p> <p></p> <p> <strong>Proper citation:</strong> Atlas3D (RRID:SCR_001808) <a href="javascript:void(0)" onclick="copyTextToClipboard('Atlas3D (RRID:SCR_001808)', 'rrid:scr_001808')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_001808" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_002166/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_002166">VoxBo <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_002166 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_002166&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://www.nitrc.org/projects/voxbo">http://www.nitrc.org/projects/voxbo <i class='fa fa-external-link'></i></a></p> <p>Software package for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. It provides GLM-based statistical tools, an architecture for interoperability with other tools (they encourage users to incorporate SPM and FSL into their processing pipelines), an automation system, a system for parallel distributed computing, numerous stand-alone tools, decent wiki-based documentation, and lots more.</p> <p></p> <p> <strong>Proper citation:</strong> VoxBo (RRID:SCR_002166) <a href="javascript:void(0)" onclick="copyTextToClipboard('VoxBo (RRID:SCR_002166)', 'rrid:scr_002166')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_002166" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_013141/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_013141">Neuroimaging in Python <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_013141 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_013141&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://nipy.org">http://nipy.org <i class='fa fa-external-link'></i></a></p> <p>Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration.</p> <p></p> <p> <strong>Proper citation:</strong> Neuroimaging in Python (RRID:SCR_013141) <a href="javascript:void(0)" onclick="copyTextToClipboard('Neuroimaging in Python (RRID:SCR_013141)', 'rrid:scr_013141')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_013141" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_016349/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_016349">masked ICA (mICA) Toolbox <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_016349 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 1+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_016349&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://www.nitrc.org/projects/mica/">http://www.nitrc.org/projects/mica/ <i class='fa fa-external-link'></i></a></p> <p>Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging.</p> <p></p> <p> <strong>Proper citation:</strong> masked ICA (mICA) Toolbox (RRID:SCR_016349) <a href="javascript:void(0)" onclick="copyTextToClipboard('masked ICA (mICA) Toolbox (RRID:SCR_016349)', 'rrid:scr_016349')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_016349" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_017183/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_017183">Nutil - Neuroimaging utilities <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_017183 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_017183&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://www.nitrc.org/projects/nutil/">http://www.nitrc.org/projects/nutil/ <i class='fa fa-external-link'></i></a></p> <p>Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems.</p> <p></p> <p> <strong>Proper citation:</strong> Nutil - Neuroimaging utilities (RRID:SCR_017183) <a href="javascript:void(0)" onclick="copyTextToClipboard('Nutil - Neuroimaging utilities (RRID:SCR_017183)', 'rrid:scr_017183')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_017183" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_009586/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_009586">Homer2 <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_009586 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 100+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_009586&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://www.nmr.mgh.harvard.edu/DOT/resources/homer2/home.htm">http://www.nmr.mgh.harvard.edu/DOT/resources/homer2/home.htm <i class='fa fa-external-link'></i></a></p> <p>Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data.</p> <p></p> <p> <strong>Proper citation:</strong> Homer2 (RRID:SCR_009586) <a href="javascript:void(0)" onclick="copyTextToClipboard('Homer2 (RRID:SCR_009586)', 'rrid:scr_009586')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_009586" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_009557/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_009557">DSI Studio <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_009557 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 100+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_009557&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://dsi-studio.labsolver.org">http://dsi-studio.labsolver.org <i class='fa fa-external-link'></i></a></p> <p>A software for diffusion MR images analysis. The provided functions include reconstruction (DTI, QBI, DSI, and GQI), deterministic fiber tracking, and 3D visualization. It has a window-based interface and operates on Microsoft Windows system.</p> <p></p> <p> <strong>Proper citation:</strong> DSI Studio (RRID:SCR_009557) <a href="javascript:void(0)" onclick="copyTextToClipboard('DSI Studio (RRID:SCR_009557)', 'rrid:scr_009557')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_009557" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_017260/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_017260">brainGraph <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_017260 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 1+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_017260&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="https://github.com/cwatson/braingraph/">https://github.com/cwatson/braingraph/ <i class='fa fa-external-link'></i></a></p> <p>Software R package for performing graph theory analyses of brain MRI data.</p> <p></p> <p> <strong>Proper citation:</strong> brainGraph (RRID:SCR_017260) <a href="javascript:void(0)" onclick="copyTextToClipboard('brainGraph (RRID:SCR_017260)', 'rrid:scr_017260')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_017260" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_001645/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_001645">TORTOISE <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_001645 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 50+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_001645&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://www.tortoisedti.org">http://www.tortoisedti.org <i class='fa fa-external-link'></i></a></p> <p>An integrated and flexible software package for processing of DTI data, and in general for the correction of diffusion weighted images to be used for DTI and potentially for high angular resolution diffusion imaging (HARDI) analysis. It can be run on both Linux and Mac platforms. It is composed of two modules named DIFF PREP and DIFF CALC. * DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space * DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data.</p> <p></p> <p> <strong>Proper citation:</strong> TORTOISE (RRID:SCR_001645) <a href="javascript:void(0)" onclick="copyTextToClipboard('TORTOISE (RRID:SCR_001645)', 'rrid:scr_001645')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_001645" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_002504/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_002504">Nitime <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_002504 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_002504&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://nipy.org/nitime/">http://nipy.org/nitime/ <i class='fa fa-external-link'></i></a></p> <p>Software library for time-series analysis of data from neuroscience experiments. It contains a core of numerical algorithms for time-series analysis both in the time and spectral domains, a set of container objects to represent time-series, and auxiliary objects that expose a high level interface to the numerical machinery and make common analysis tasks easy to express with compact and semantically clear code.</p> <p></p> <p> <strong>Proper citation:</strong> Nitime (RRID:SCR_002504) <a href="javascript:void(0)" onclick="copyTextToClipboard('Nitime (RRID:SCR_002504)', 'rrid:scr_002504')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_002504" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_007037/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_007037">SPM <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_007037 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 5000+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_007037&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="https://github.com/spm">https://github.com/spm <i class='fa fa-external-link'></i></a></p> <p>Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.</p> <p></p> <p> <strong>Proper citation:</strong> SPM (RRID:SCR_007037) <a href="javascript:void(0)" onclick="copyTextToClipboard('SPM (RRID:SCR_007037)', 'rrid:scr_007037')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_007037" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_002545/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_002545">SPHARM-MAT <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_002545 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 1+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_002545&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://imaging.indyrad.iupui.edu/projects/SPHARM/">http://imaging.indyrad.iupui.edu/projects/SPHARM/ <i class='fa fa-external-link'></i></a></p> <p>A matlab-based 3D shape modeling and analysis toolkit, and is designed to aid statistical shape analysis for identifying morphometric changes in 3D structures of interest related to different conditions. SPHARM-MAT is implemented based on a powerful 3D Fourier surface representation method called SPHARM, which creates parametric surface models using spherical harmonics.</p> <p></p> <p> <strong>Proper citation:</strong> SPHARM-MAT (RRID:SCR_002545) <a href="javascript:void(0)" onclick="copyTextToClipboard('SPHARM-MAT (RRID:SCR_002545)', 'rrid:scr_002545')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_002545" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_002502/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_002502">Nipype <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_002502 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 500+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_002502&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://nipy.org/nipype/">http://nipy.org/nipype/ <i class='fa fa-external-link'></i></a></p> <p>A package for writing fMRI analysis pipelines and interfacing with external analysis packages (SPM, FSL, AFNI). Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. However, this has resulted in a heterogeneous collection of specialized applications without transparent interoperability or a uniform operating interface. Nipype, an open-source, community-developed initiative under the umbrella of Nipy, is a Python project that solves these issues by providing a uniform interface to existing neuroimaging software and by facilitating interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems.</p> <p></p> <p> <strong>Proper citation:</strong> Nipype (RRID:SCR_002502) <a href="javascript:void(0)" onclick="copyTextToClipboard('Nipype (RRID:SCR_002502)', 'rrid:scr_002502')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_002502" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_002372/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Related%20Resources%3Aneuroimaging%20tools%20and%20resources%20collaboratory%20%28nitrc%29&i=rrid:scr_002372">DPARSF <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_002372 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 100+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_002372&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://rfmri.org/DPARSF">http://rfmri.org/DPARSF <i class='fa fa-external-link'></i></a></p> <p>A MATLAB toolbox forpipeline data analysis of resting-state fMRI that is based on Statistical Parametric Mapping (SPM) and a plug-in software within DPABI. After the user arranges the Digital Imaging and Communications in Medicine (DICOM) files and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (ALFF), fractional ALFF, degree centrality, voxel-mirrored homotopic connectivity (VMHC) results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. In addition, users can also use DPARSF to extract time courses from regions of interest. DPARSF basic edition is very easy to use while DPARSF advanced edition (alias: DPARSFA) is much more flexible and powerful. DPARSFA can parallel the computation for each subject, and can be used to reorient images interactively or define regions of interest interactively. 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