From e0a80895179c1d3f78db12c3bdd8ab42a3d67661 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 14 Jan 2025 00:23:41 +0000
Subject: [PATCH] site deploy

Auto-generated via `{sandpaper}`
Source  : 278a4f4f2906702156b5917470dbdeafeb3b08c9
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2025-01-14 00:23:22 +0000
Message : markdown source builds

Auto-generated via `{sandpaper}`
Source  : 707ea6dbc11cd384f0d95990538434e288003445
Branch  : main
Author  : davecash75 <d.cash@ucl.ac.uk>
Time    : 2024-09-23 12:40:45 +0000
Message : Merge pull request #9 from HealthBioscienceIDEAS/4-add-quick-dcm2niix-intro

HTML anchor blocking fencepost
---
 404.html                                      |  4 +--
 CODE_OF_CONDUCT.html                          |  6 ++--
 LICENSE.html                                  |  6 ++--
 aio.html                                      | 24 +++++++-------
 command-line.html                             |  8 ++---
 diffusion-weighted-imaging.html               |  6 ++--
 functional-mri.html                           |  6 ++--
 images.html                                   |  4 +--
 imaging-data-structure-and-formats.html       |  6 ++--
 index.html                                    |  4 +--
 instructor-notes.html                         |  4 +--
 instructor/404.html                           |  4 +--
 instructor/CODE_OF_CONDUCT.html               |  6 ++--
 instructor/LICENSE.html                       |  6 ++--
 instructor/aio.html                           | 24 +++++++-------
 instructor/command-line.html                  |  8 ++---
 instructor/diffusion-weighted-imaging.html    |  6 ++--
 instructor/functional-mri.html                |  6 ++--
 instructor/images.html                        |  4 +--
 .../imaging-data-structure-and-formats.html   |  6 ++--
 instructor/index.html                         |  4 +--
 instructor/instructor-notes.html              |  4 +--
 instructor/key-points.html                    |  4 +--
 instructor/pet-imaging.html                   |  6 ++--
 instructor/profiles.html                      |  4 +--
 instructor/reference.html                     |  6 ++--
 instructor/structural-mri.html                | 12 +++----
 key-points.html                               |  4 +--
 md5sum.txt                                    | 32 +++++++++----------
 pet-imaging.html                              |  6 ++--
 pkgdown.yml                                   |  2 +-
 profiles.html                                 |  4 +--
 reference.html                                |  6 ++--
 structural-mri.html                           | 12 +++----
 34 files changed, 127 insertions(+), 127 deletions(-)

diff --git a/404.html b/404.html
index e13e2cb..938ff44 100644
--- a/404.html
+++ b/404.html
@@ -323,8 +323,8 @@ <h1>Page not found</h1>
   "url": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/404.html",
   "identifier": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/404.html",
   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
+  "dateModified": "2025-01-14",
+  "datePublished": "2025-01-14"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index b94d842..2a8dc8f 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -262,7 +262,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -345,8 +345,8 @@ <h1>Contributor Code of Conduct</h1>
   "url": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/CODE_OF_CONDUCT.html",
   "identifier": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
+  "dateModified": "2025-01-14",
+  "datePublished": "2025-01-14"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 81dd56c..bc3b2a7 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -262,7 +262,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -393,8 +393,8 @@ <h1>Licenses</h1>
   "url": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/LICENSE.html",
   "identifier": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/LICENSE.html",
   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
+  "dateModified": "2025-01-14",
+  "datePublished": "2025-01-14"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index 7911f1b..5f1942d 100644
--- a/aio.html
+++ b/aio.html
@@ -310,7 +310,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-imaging-data-structure-and-formats"><p>Content from <a href="imaging-data-structure-and-formats.html">Imaging Data: Structure And Formats</a></p>
 <hr>
-<p>Last updated on 2025-01-07 |
+<p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/imaging-data-structure-and-formats.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -1432,7 +1432,7 @@ <h3 class="callout-title">Key Points</h3>
  -->
 </section></section><section id="aio-structural-mri"><p>Content from <a href="structural-mri.html">Structural MRI: Bias Correction, Segmentation and Image Registration</a></p>
 <hr>
-<p>Last updated on 2025-01-07 |
+<p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/structural-mri.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -1611,7 +1611,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Reproducing your work </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>When you are using these workflows for your actual research, we
 <strong>highly recommend</strong> that you save the SPM pipelines so
@@ -1727,7 +1727,7 @@ <h3 class="callout-title">Exercise 3</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>You should have an output that looks something like this. <img src="fig/aic_smri_tissue_seg_check.png" alt="Tissue segmentation check" class="figure"></p>
 </div>
@@ -1918,7 +1918,7 @@ <h3 class="callout-title">BONUS Exercise 1</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb12">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2121,7 +2121,7 @@ <h3 class="callout-title">Key Points</h3>
  -->
 </section></section><section id="aio-pet-imaging"><p>Content from <a href="pet-imaging.html">Processing and analysing PET brain images</a></p>
 <hr>
-<p>Last updated on 2025-01-07 |
+<p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/pet-imaging.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -3053,7 +3053,7 @@ <h3 class="callout-title">Key Points</h3>
  -->
 </section></section><section id="aio-diffusion-weighted-imaging"><p>Content from <a href="diffusion-weighted-imaging.html">Diffusion-weighted imaging (DWI)</a></p>
 <hr>
-<p>Last updated on 2025-01-07 |
+<p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/diffusion-weighted-imaging.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -3644,7 +3644,7 @@ <h3 class="callout-title">Key Points</h3>
  -->
 </section></section><section id="aio-functional-mri"><p>Content from <a href="functional-mri.html">Functional Magnetic Resonance Imaging (fMRI)</a></p>
 <hr>
-<p>Last updated on 2025-01-07 |
+<p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/functional-mri.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -4060,7 +4060,7 @@ <h3 class="callout-title">Key Points</h3>
  -->
 </section></section><section id="aio-command-line"><p>Content from <a href="command-line.html">Extra: Using the Command Line</a></p>
 <hr>
-<p>Last updated on 2025-01-07 |
+<p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/command-line.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -4421,7 +4421,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   That just flew off the screen!
   </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>Using <code>cat</code> on a large text file can end up looking
 impressive as text swarms all over your terminal, but it can be hard to
@@ -4884,8 +4884,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/aio.html",
   "identifier": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/aio.html",
   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
+  "dateModified": "2025-01-14",
+  "datePublished": "2025-01-14"
 }
 
   </script><script>
diff --git a/command-line.html b/command-line.html
index 7ae1c1f..2e982b0 100644
--- a/command-line.html
+++ b/command-line.html
@@ -279,7 +279,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Extra: Using the Command Line</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/command-line.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -623,7 +623,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   That just flew off the screen!
   </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <p>Using <code>cat</code> on a large text file can end up looking
 impressive as text swarms all over your terminal, but it can be hard to
@@ -1052,8 +1052,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/command-line.html",
   "identifier": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/command-line.html",
   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
+  "dateModified": "2025-01-14",
+  "datePublished": "2025-01-14"
 }
 
   </script><script>
diff --git a/diffusion-weighted-imaging.html b/diffusion-weighted-imaging.html
index 4db4ded..2e6e659 100644
--- a/diffusion-weighted-imaging.html
+++ b/diffusion-weighted-imaging.html
@@ -276,7 +276,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Diffusion-weighted imaging (DWI)</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/diffusion-weighted-imaging.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -893,8 +893,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/diffusion-weighted-imaging.html",
   "identifier": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/diffusion-weighted-imaging.html",
   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
+  "dateModified": "2025-01-14",
+  "datePublished": "2025-01-14"
 }
 
   </script><script>
diff --git a/functional-mri.html b/functional-mri.html
index 625141d..f516153 100644
--- a/functional-mri.html
+++ b/functional-mri.html
@@ -278,7 +278,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Functional Magnetic Resonance Imaging (fMRI)</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/functional-mri.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -722,8 +722,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/functional-mri.html",
   "identifier": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/functional-mri.html",
   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
+  "dateModified": "2025-01-14",
+  "datePublished": "2025-01-14"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index 2cd39f3..20bd0cf 100644
--- a/images.html
+++ b/images.html
@@ -804,8 +804,8 @@ <h3 id="command-line-figure-4">Figure 4</h3>
   "url": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/images.html",
   "identifier": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/images.html",
   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
+  "dateModified": "2025-01-14",
+  "datePublished": "2025-01-14"
 }
 
   </script><script>
diff --git a/imaging-data-structure-and-formats.html b/imaging-data-structure-and-formats.html
index 52fb28f..21e11a7 100644
--- a/imaging-data-structure-and-formats.html
+++ b/imaging-data-structure-and-formats.html
@@ -280,7 +280,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Imaging Data: Structure And Formats</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/imaging-data-structure-and-formats.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -1376,8 +1376,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/imaging-data-structure-and-formats.html",
   "identifier": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/imaging-data-structure-and-formats.html",
   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
+  "dateModified": "2025-01-14",
+  "datePublished": "2025-01-14"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index 9cbd686..81c76bb 100644
--- a/index.html
+++ b/index.html
@@ -514,8 +514,8 @@ <h3 id="acknowledgements">Acknowledgements<a class="anchor" aria-label="anchor"
   "url": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/index.html",
   "identifier": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/index.html",
   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
+  "dateModified": "2025-01-14",
+  "datePublished": "2025-01-14"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index b114b80..8a97e8c 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -364,8 +364,8 @@ <h1>Instructor Notes</h1>
   "url": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/instructor-notes.html",
   "identifier": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/instructor-notes.html",
   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
+  "dateModified": "2025-01-14",
+  "datePublished": "2025-01-14"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index a54ca6a..419414d 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -323,8 +323,8 @@ <h1>Page not found</h1>
   "url": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/instructor/404.html",
   "identifier": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/instructor/404.html",
   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
+  "dateModified": "2025-01-14",
+  "datePublished": "2025-01-14"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 6c1cb74..e1e6ca7 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -262,7 +262,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -347,8 +347,8 @@ <h1>Contributor Code of Conduct</h1>
   "url": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/instructor/CODE_OF_CONDUCT.html",
   "identifier": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
+  "dateModified": "2025-01-14",
+  "datePublished": "2025-01-14"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 3015852..5411a8c 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -262,7 +262,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -395,8 +395,8 @@ <h1>Licenses</h1>
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diff --git a/instructor/aio.html b/instructor/aio.html
index c3ad8a9..e2e833c 100644
--- a/instructor/aio.html
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@@ -312,7 +312,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-imaging-data-structure-and-formats"><p>Content from <a href="imaging-data-structure-and-formats.html">Imaging Data: Structure And Formats</a></p>
 <hr>
-<p>Last updated on 2025-01-07 |
+<p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/imaging-data-structure-and-formats.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 32 minutes</p>
@@ -1449,7 +1449,7 @@ <h3 class="callout-title">Key Points</h3>
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 <hr>
-<p>Last updated on 2025-01-07 |
+<p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/structural-mri.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 65 minutes</p>
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-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
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 <div class="accordion-body">
 <p>When you are using these workflows for your actual research, we
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 <div class="accordion-body">
 <p>You should have an output that looks something like this. <img src="../fig/aic_smri_tissue_seg_check.png" alt="Tissue segmentation check" class="figure"></p>
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 <hr>
-<p>Last updated on 2025-01-07 |
+<p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/pet-imaging.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 45 minutes</p>
@@ -3072,7 +3072,7 @@ <h3 class="callout-title">Key Points</h3>
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 </section></section><section id="aio-diffusion-weighted-imaging"><p>Content from <a href="diffusion-weighted-imaging.html">Diffusion-weighted imaging (DWI)</a></p>
 <hr>
-<p>Last updated on 2025-01-07 |
+<p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/diffusion-weighted-imaging.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 12 minutes</p>
@@ -3664,7 +3664,7 @@ <h3 class="callout-title">Key Points</h3>
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 </section></section><section id="aio-functional-mri"><p>Content from <a href="functional-mri.html">Functional Magnetic Resonance Imaging (fMRI)</a></p>
 <hr>
-<p>Last updated on 2025-01-07 |
+<p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/functional-mri.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 12 minutes</p>
@@ -4081,7 +4081,7 @@ <h3 class="callout-title">Key Points</h3>
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 </section></section><section id="aio-command-line"><p>Content from <a href="command-line.html">Extra: Using the Command Line</a></p>
 <hr>
-<p>Last updated on 2025-01-07 |
+<p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/command-line.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 12 minutes</p>
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 <div class="accordion-body">
 <p>Using <code>cat</code> on a large text file can end up looking
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       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Extra: Using the Command Line</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/command-line.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -625,7 +625,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
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 </button>
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 <div class="accordion-body">
 <p>Using <code>cat</code> on a large text file can end up looking
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         <h1>Diffusion-weighted imaging (DWI)</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/diffusion-weighted-imaging.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -895,8 +895,8 @@ <h3 class="callout-title">Key Points</h3>
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diff --git a/instructor/functional-mri.html b/instructor/functional-mri.html
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         <h1>Functional Magnetic Resonance Imaging (fMRI)</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/functional-mri.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -724,8 +724,8 @@ <h3 class="callout-title">Key Points</h3>
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diff --git a/instructor/images.html b/instructor/images.html
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-  "datePublished": "2025-01-07"
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diff --git a/instructor/imaging-data-structure-and-formats.html b/instructor/imaging-data-structure-and-formats.html
index 6e5a596..9a5b70e 100644
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@@ -280,7 +280,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Imaging Data: Structure And Formats</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/imaging-data-structure-and-formats.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -1392,8 +1392,8 @@ <h3 class="callout-title">Key Points</h3>
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-  "dateModified": "2025-01-07",
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index d3a0f64..a5030d8 100644
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   "dateCreated": "2024-08-16",
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diff --git a/instructor/key-points.html b/instructor/key-points.html
index 328758d..4f1d3bc 100644
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diff --git a/instructor/pet-imaging.html b/instructor/pet-imaging.html
index d4e93d5..9a60dd9 100644
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       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Processing and analysing PET brain images</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/pet-imaging.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -1180,8 +1180,8 @@ <h3 class="callout-title">Key Points</h3>
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   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
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 }
 
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diff --git a/instructor/profiles.html b/instructor/profiles.html
index 00a2f25..b601888 100644
--- a/instructor/profiles.html
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   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
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 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index e0e89bb..39a9825 100644
--- a/instructor/reference.html
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@@ -262,7 +262,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Reference</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/learners/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -339,8 +339,8 @@ <h1>Reference</h1>
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   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
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diff --git a/instructor/structural-mri.html b/instructor/structural-mri.html
index 2d94c85..be2f9f1 100644
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@@ -279,7 +279,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Structural MRI: Bias Correction, Segmentation and Image Registration</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/structural-mri.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -443,7 +443,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
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 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>When you are using these workflows for your actual research, we
 <strong>highly recommend</strong> that you save the SPM pipelines so
@@ -547,7 +547,7 @@ <h3 class="callout-title">Exercise 3</h3>
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+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>You should have an output that looks something like this. <img src="../fig/aic_smri_tissue_seg_check.png" alt="Tissue segmentation check" class="figure"></p>
 </div>
@@ -722,7 +722,7 @@ <h3 class="callout-title">BONUS Exercise 1</h3>
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diff --git a/key-points.html b/key-points.html
index 9bd955c..eeb6733 100644
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   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
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diff --git a/pet-imaging.html b/pet-imaging.html
index 9350058..7b32a00 100644
--- a/pet-imaging.html
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@@ -282,7 +282,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Processing and analysing PET brain images</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
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   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
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diff --git a/pkgdown.yml b/pkgdown.yml
index c87bf26..136f2c8 100644
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diff --git a/profiles.html b/profiles.html
index 29800bf..7ceca5a 100644
--- a/profiles.html
+++ b/profiles.html
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   "identifier": "https://davecash75.github.io/eu-mind2024-neuroimaging-workshop/profiles.html",
   "dateCreated": "2024-08-16",
-  "dateModified": "2025-01-07",
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diff --git a/reference.html b/reference.html
index bb15ae5..25923c5 100644
--- a/reference.html
+++ b/reference.html
@@ -262,7 +262,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Reference</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/learners/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -337,8 +337,8 @@ <h1>Reference</h1>
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   "dateCreated": "2024-08-16",
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diff --git a/structural-mri.html b/structural-mri.html
index bfb36b7..68ed432 100644
--- a/structural-mri.html
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         <h1>Structural MRI: Bias Correction, Segmentation and Image Registration</h1>
-        <p>Last updated on 2025-01-07 |
+        <p>Last updated on 2025-01-14 |
 
         <a href="https://github.com/davecash75/eu-mind2024-neuroimaging-workshop/edit/main/episodes/structural-mri.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
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+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>When you are using these workflows for your actual research, we
 <strong>highly recommend</strong> that you save the SPM pipelines so
@@ -545,7 +545,7 @@ <h3 class="callout-title">Exercise 3</h3>
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 <div class="accordion-body">
 <p>You should have an output that looks something like this. <img src="fig/aic_smri_tissue_seg_check.png" alt="Tissue segmentation check" class="figure"></p>
 </div>
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@@ -969,8 +969,8 @@ <h3 class="callout-title">Key Points</h3>
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-  "dateModified": "2025-01-07",
-  "datePublished": "2025-01-07"
+  "dateModified": "2025-01-14",
+  "datePublished": "2025-01-14"
 }
 
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