Merge branch 'master' into enh-spaces

ReproNim · Jul 30, 2024 · 27609fb · 27609fb
2 parents 4778034 + 5596b90
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diff --git a/.codespellrc b/.codespellrc
@@ -0,0 +1,6 @@
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+[codespell]
+skip = .git,*.pdf,*.svg,go.sum,*.css,*.min.*,.codespellrc
+check-hidden = true
+ignore-regex = \b(TE|currentY|Lew|fnndsc.childrens.harvard.edu)\b
+# ignore-words-list =
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,23 @@
+# Codespell configuration is within .codespellrc
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
diff --git a/2019_training_logistics.html b/2019_training_logistics.html
@@ -2,13 +2,13 @@
 <html lang="en">
     <head>
 
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=UA-132556733-1"></script>
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
         <script>
-            window.dataLayer = window.dataLayer || [];
-            function gtag(){dataLayer.push(arguments);}
-            gtag('js', new Date());
-            gtag('config', 'UA-132556733-1');
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+          gtag('config', 'G-WJRL86VLXW');
         </script>
 
         <meta charset="utf-8">

diff --git a/5Steps/acquisition.html b/5Steps/acquisition.html
@@ -2,13 +2,13 @@
 <html lang="en">
     <head>
 
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=UA-132556733-1"></script>
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
         <script>
-            window.dataLayer = window.dataLayer || [];
-            function gtag(){dataLayer.push(arguments);}
-            gtag('js', new Date());
-            gtag('config', 'UA-132556733-1');
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+          gtag('config', 'G-WJRL86VLXW');
         </script>
 
         <meta charset="utf-8">
@@ -82,7 +82,7 @@ <h1 class="main-page-header"><b>Data Acquisition Considerations</b> for More Rep
 <li>Use <a href="http://reproin.repronim.org">ReproIn</a> to automate conversion of your imaging data to <a href="http://bids.neuroimaging.io">BIDS</a>.
 <li>Annotate your metadata (all experimental details) as you collect it.
 	<ul>
-		<li>There are a number of ways to annotate your data.  The idea with annotations are to provide unambigous markup of your data, whether it be imaging, behavioral, clinical, etc.  One strategy is to annotate the variables you intend to collect during the study design process.  This can occur by choosing data structures that are publically available and already annotated (e.g. <a href="https://ndar.nih.gov/data_dictionary.html">NDAR</a>) or by using the tools below.  Regardless of the approach, the important aspect is to unambigously describe what the variables collected mean, their ranges, min/max, units, etc.  For more information on the desired properties for annotations, see:  <a href="https://docs.google.com/spreadsheets/d/1PKoO9wqxJy92Je1doX_a42Ey2PzFOqGTxQgSpHtu7D4/edit#gid=632728597">Federated Data Elements</a>
+		<li>There are a number of ways to annotate your data.  The idea with annotations are to provide unambiguous markup of your data, whether it be imaging, behavioral, clinical, etc.  One strategy is to annotate the variables you intend to collect during the study design process.  This can occur by choosing data structures that are publicly available and already annotated (e.g. <a href="https://ndar.nih.gov/data_dictionary.html">NDAR</a>) or by using the tools below.  Regardless of the approach, the important aspect is to unambiguously describe what the variables collected mean, their ranges, min/max, units, etc.  For more information on the desired properties for annotations, see:  <a href="https://docs.google.com/spreadsheets/d/1PKoO9wqxJy92Je1doX_a42Ey2PzFOqGTxQgSpHtu7D4/edit#gid=632728597">Federated Data Elements</a>
 			<ul>
 				<li> <a href="http://brainverse.repronim.org">BrainVerse</a> is a tool being developed which can help to annotate your variables by directly incorporating data structures from NDAR.
 				<li> <a href="https://github.com/incf-nidash/PyNIDM">PyNIDM</a> is both a Python library for creating metadata documents using the Neuroimaging Data Model (<a href="http://nidm.nidash.org/">NIDM</a>) but also contains tools such as "bidsmri2nidm" and "csv2nidm" which can be used to interactively annotate both BIDS datasets (via participants.csv file) and general CSV-formatted data files containinga header row of variables which require annotation.  The annotation process requires you to have a <a href="https://scicrunch.org/">SciCrunch</a> account and API-access key which are freely available on the site.  The tools iteratve over your variables and query the InterLex information resource looking for terms that match your variables.  If no term is found you are asked to contribute a new term definition which will be used in the InterLex and thus provide persistent annotations.

diff --git a/5Steps/design.html b/5Steps/design.html
@@ -2,13 +2,13 @@
 <html lang="en">
     <head>
 
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=UA-132556733-1"></script>
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
         <script>
-            window.dataLayer = window.dataLayer || [];
-            function gtag(){dataLayer.push(arguments);}
-            gtag('js', new Date());
-            gtag('config', 'UA-132556733-1');
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+          gtag('config', 'G-WJRL86VLXW');
         </script>
 
         <meta charset="utf-8">

diff --git a/5Steps/processing.html b/5Steps/processing.html
@@ -2,13 +2,13 @@
 <html lang="en">
     <head>
 
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=UA-132556733-1"></script>
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
         <script>
-            window.dataLayer = window.dataLayer || [];
-            function gtag(){dataLayer.push(arguments);}
-            gtag('js', new Date());
-            gtag('config', 'UA-132556733-1');
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+          gtag('config', 'G-WJRL86VLXW');
         </script>
 
         <meta charset="utf-8">

diff --git a/5Steps/publication.html b/5Steps/publication.html
@@ -2,13 +2,13 @@
 <html lang="en">
     <head>
 
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=UA-132556733-1"></script>
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
         <script>
-            window.dataLayer = window.dataLayer || [];
-            function gtag(){dataLayer.push(arguments);}
-            gtag('js', new Date());
-            gtag('config', 'UA-132556733-1');
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+          gtag('config', 'G-WJRL86VLXW');
         </script>
 
         <meta charset="utf-8">

diff --git a/5Steps/stats.html b/5Steps/stats.html
@@ -2,13 +2,13 @@
 <html lang="en">
     <head>
 
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=UA-132556733-1"></script>
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
         <script>
-            window.dataLayer = window.dataLayer || [];
-            function gtag(){dataLayer.push(arguments);}
-            gtag('js', new Date());
-            gtag('config', 'UA-132556733-1');
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+          gtag('config', 'G-WJRL86VLXW');
         </script>
 
         <meta charset="utf-8">

diff --git a/5steps.html b/5steps.html
@@ -2,13 +2,13 @@
 <html lang="en">
     <head>
 
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=UA-132556733-1"></script>
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
         <script>
-            window.dataLayer = window.dataLayer || [];
-            function gtag(){dataLayer.push(arguments);}
-            gtag('js', new Date());
-            gtag('config', 'UA-132556733-1');
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+          gtag('config', 'G-WJRL86VLXW');
         </script>
 
         <meta charset="utf-8">

diff --git a/about_us.html b/about_us.html
@@ -2,13 +2,13 @@
 <html lang="en">
     <head>
 
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=UA-132556733-1"></script>
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
         <script>
-            window.dataLayer = window.dataLayer || [];
-            function gtag(){dataLayer.push(arguments);}
-            gtag('js', new Date());
-            gtag('config', 'UA-132556733-1');
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+          gtag('config', 'G-WJRL86VLXW');
         </script>
 
         <meta charset="utf-8">

diff --git a/collaborators.html b/collaborators.html
@@ -8,5 +8,4 @@
 <body>
     <p>If you are not redirected, <a href="community.html#collaborating-projects">click here</a>.</p>
 </body>
-</html>
-
+</html>
diff --git a/community.html b/community.html
@@ -2,13 +2,13 @@
 <html lang="en">
     <head>
 
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=UA-132556733-1"></script>
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
         <script>
-            window.dataLayer = window.dataLayer || [];
-            function gtag(){dataLayer.push(arguments);}
-            gtag('js', new Date());
-            gtag('config', 'UA-132556733-1');
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+          gtag('config', 'G-WJRL86VLXW');
         </script>
 
         <meta charset="utf-8">

diff --git a/describe.html b/describe.html
@@ -2,13 +2,13 @@
 <html lang="en">
     <head>
 
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=UA-132556733-1"></script>
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
         <script>
-            window.dataLayer = window.dataLayer || [];
-            function gtag(){dataLayer.push(arguments);}
-            gtag('js', new Date());
-            gtag('config', 'UA-132556733-1');
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+          gtag('config', 'G-WJRL86VLXW');
         </script>
 
         <meta charset="utf-8">

diff --git a/discover.html b/discover.html
@@ -2,13 +2,13 @@
 <html lang="en">
     <head>
 
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=UA-132556733-1"></script>
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
         <script>
-            window.dataLayer = window.dataLayer || [];
-            function gtag(){dataLayer.push(arguments);}
-            gtag('js', new Date());
-            gtag('config', 'UA-132556733-1');
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+          gtag('config', 'G-WJRL86VLXW');
         </script>
 
         <meta charset="utf-8">

diff --git a/do.html b/do.html
@@ -2,13 +2,13 @@
 <html lang="en">
     <head>
 
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=UA-132556733-1"></script>
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
         <script>
-            window.dataLayer = window.dataLayer || [];
-            function gtag(){dataLayer.push(arguments);}
-            gtag('js', new Date());
-            gtag('config', 'UA-132556733-1');
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+          gtag('config', 'G-WJRL86VLXW');
         </script>
 
         <meta charset="utf-8">
@@ -92,7 +92,7 @@ <h3 class="main-sub-header">What are you waiting for?<br> Just <strong>Do</stron
 </ul>
 <p>
   We strongly believe in the benefits of modular design,
-  collaboration, and re-use. That is why, instead of developing a
+  collaboration, and reuse. That is why, instead of developing a
   single monolithic platform to "solve all the problems", we are
   reusing and contributing to existing projects as much as possible.
   To that end, in the scope of this project, we actively maintain
@@ -195,7 +195,7 @@ <h3><a href="https://github.com/myyoda">YODA</a> Principles</h3>
   cover the entire life-span of a research project with reliable,
   non-ambiguous tracking and orchestration of all digital products of
   a study (e.g., inputs, code, outputs). Modularization facilitates
-  the independent re-use of parts (e.g., the same data used across
+  the independent reuse of parts (e.g., the same data used across
   multiple studies, versions of a software library used repeatedly) in
   a manner that scales to dataset sizes found in cutting edge
   high-resolution neuroimaging research.</p>

diff --git a/eab.html b/eab.html
@@ -2,13 +2,13 @@
 <html lang="en">
     <head>
 
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=UA-132556733-1"></script>
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
         <script>
-            window.dataLayer = window.dataLayer || [];
-            function gtag(){dataLayer.push(arguments);}
-            gtag('js', new Date());
-            gtag('config', 'UA-132556733-1');
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+          gtag('config', 'G-WJRL86VLXW');
         </script>
 
         <meta charset="utf-8">

diff --git a/events.html b/events.html
@@ -2,13 +2,13 @@
 <html lang="en">
     <head>
 
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=UA-132556733-1"></script>
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
         <script>
-            window.dataLayer = window.dataLayer || [];
-            function gtag(){dataLayer.push(arguments);}
-            gtag('js', new Date());
-            gtag('config', 'UA-132556733-1');
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+          gtag('config', 'G-WJRL86VLXW');
         </script>
 
         <meta charset="utf-8">

diff --git a/fellows-resources.html b/fellows-resources.html
@@ -2,13 +2,13 @@
 <html lang="en">
     <head>
 
-        <!-- Global site tag (gtag.js) - Google Analytics -->
-        <script async src="https://www.googletagmanager.com/gtag/js?id=UA-132556733-1"></script>
+        <!-- Google tag (gtag.js) -->
+        <script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
         <script>
-            window.dataLayer = window.dataLayer || [];
-            function gtag(){dataLayer.push(arguments);}
-            gtag('js', new Date());
-            gtag('config', 'UA-132556733-1');
+          window.dataLayer = window.dataLayer || [];
+          function gtag(){dataLayer.push(arguments);}
+          gtag('js', new Date());
+          gtag('config', 'G-WJRL86VLXW');
         </script>
 
         <meta charset="utf-8">
@@ -97,20 +97,19 @@ <h3 class="main-sub-header">Resources developed by fellows.</h3>
                                 </dl>
                             </div>
                             <div class="col-sm-6 resource">
-
                                 <dl>
                                     <dt>Title</dt>
-                                    <dd>Brain Image Processing</dd>
+                                    <dd>Southampton Brain Image Processing Workshops</dd>
                                     <dt>Type</dt>
                                     <dd>Workshop</dd>
                                     <dt>Description</dt>
                                     <dd></dd>
                                     <dt>Audience</dt>
-                                    <dd></dd>
+                                    <dd>academics and clinicians developing image processing and data analysis methods for neurological disorders</dd>
                                     <dt>Keywords</dt>
                                     <dd></dd>
                                     <dt>Links</dt>
-                                    <dd></dd>
+                                    <dd><a href="https://sotnir.github.io/svg" target="_blank">https://sotnir.github.io/svg</a><br></dd>
                                     <dt>Fellow</dt>
                                     <dd>Yukai Zou</dd>
                                 </dl>
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,5 +8,4 @@ @@
     <body>
         <p>If you are not redirected, <a href="community.html#collaborating-projects">click here</a>.</p>
     </body>
-    </html>
+    </html>