diff --git a/404.html b/404.html
index 9bff00e..ce83a07 100644
--- a/404.html
+++ b/404.html
@@ -315,9 +315,9 @@ <h1>Page not found</h1>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/404.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/404.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index deded97..8283fc4 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -334,9 +334,9 @@ <h1>Contributor Code of Conduct</h1>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/CODE_OF_CONDUCT.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/CODE_OF_CONDUCT.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 715e052..7b64902 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -385,9 +385,9 @@ <h1>Licenses</h1>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/LICENSE.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/LICENSE.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index b2e85cd..ea5d4ac 100644
--- a/aio.html
+++ b/aio.html
@@ -586,11 +586,11 @@ <h3 id="diffusion">Diffusion<a class="anchor" aria-label="anchor" href="#diffusi
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">wget</span> https://zenodo.org/record/3677090/files/0219191_mystudy-0219-1114.tar.gz <span class="at">-O</span> ../data/0219191_mystudy-0219-1114.tar.gz</span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples</span>
-<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">tar</span> <span class="at">-xvzf</span> ../data/0219191_mystudy-0219-1114.tar.gz <span class="at">-C</span> ../data/dicom_examples</span>
-<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">gzip</span> <span class="at">-d</span> ../data/dicom_examples/0219191_mystudy-0219-1114/dcm/<span class="pp">*</span>dcm.gz</span>
-<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">rm</span> ../data/0219191_mystudy-0219-1114.tar.gz</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">wget</span> https://zenodo.org/record/3677090/files/0219191_mystudy-0219-1114.tar.gz <span class="at">-O</span> ../data/0219191_mystudy-0219-1114.tar.gz</span>
+<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples</span>
+<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="fu">tar</span> <span class="at">-xvzf</span> ../data/0219191_mystudy-0219-1114.tar.gz <span class="at">-C</span> ../data/dicom_examples</span>
+<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="fu">gzip</span> <span class="at">-d</span> ../data/dicom_examples/0219191_mystudy-0219-1114/dcm/<span class="pp">*</span>dcm.gz</span>
+<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="fu">rm</span> ../data/0219191_mystudy-0219-1114.tar.gz</span></code></pre>
 </div>
 <figure><img src="fig/dicom_to_nifti.png" alt="dicom-to-nifti" class="figure mx-auto d-block"></figure><p>NIfTI is one of the most ubiquitous file formats for storing
 neuroimaging data. If you’re interested in learning more about NIfTI
@@ -602,7 +602,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-help</span></span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-help</span></span></code></pre>
 </div>
 <div id="converting-dicom-to-nifti" class="callout challenge">
 <div class="callout-square">
@@ -621,13 +621,13 @@ <h3 class="callout-title">Converting DICOM to NIfTI<a class="anchor" aria-label=
 <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">
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples/nii</span>
-<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-z</span> y <span class="at">-o</span> ../data/dicom_examples/nii ../data/dicom_examples/0219191_mystudy-0219-1114/</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples/nii</span>
+<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-z</span> y <span class="at">-o</span> ../data/dicom_examples/nii ../data/dicom_examples/0219191_mystudy-0219-1114/</span></code></pre>
 </div>
 </div>
 </div>
@@ -697,7 +697,7 @@ <h3 class="card-title">Objectives</h3>
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> nibabel <span class="im">as</span> nib</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="im">import</span> nibabel <span class="im">as</span> nib</span></code></pre>
 </div>
 <p>First, use the <code>load()</code> function to create a NiBabel image
 object from a NIfTI file. We’ll load in an example T1w image from the
@@ -705,7 +705,7 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>t1_img <span class="op">=</span> nib.load(<span class="st">"../data/dicom_examples/nii/0219191_mystudy-0219-1114_anat_ses-01_T1w_20190219111436_5.nii.gz"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>t1_img <span class="op">=</span> nib.load(<span class="st">"../data/dicom_examples/nii/0219191_mystudy-0219-1114_anat_ses-01_T1w_20190219111436_5.nii.gz"</span>)</span></code></pre>
 </div>
 <p>Loading in a NIfTI file with <code>NiBabel</code> gives us a special
 type of data object which encodes all the information in the file.Each
@@ -721,8 +721,8 @@ <h3 id="header-contains-metadata-about-the-image-such-as-image-dimensions-data-t
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>t1_hdr <span class="op">=</span> t1_img.header</span>
-<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(t1_hdr)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a>t1_hdr <span class="op">=</span> t1_img.header</span>
+<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="bu">print</span>(t1_hdr)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -783,7 +783,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb5">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>t1_hdr.keys()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a>t1_hdr.keys()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -850,7 +850,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>t1_hdr[<span class="st">'&lt;key_name&gt;'</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a>t1_hdr[<span class="st">'&lt;key_name&gt;'</span>]</span></code></pre>
 </div>
 <div id="extract-values-from-the-nifti-header" class="callout challenge">
 <div class="callout-square">
@@ -869,12 +869,12 @@ <h3 class="callout-title">Extract values from the NIfTI header<a class="anchor"
 <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" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>t1_hdr[<span class="st">'pixdim'</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a>t1_hdr[<span class="st">'pixdim'</span>]</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -897,8 +897,8 @@ <h3 id="data">2. Data<a class="anchor" aria-label="anchor" href="#data"></a>
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>t1_data <span class="op">=</span> t1_img.get_fdata()</span>
-<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a>t1_data</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a>t1_data <span class="op">=</span> t1_img.get_fdata()</span>
+<span id="cb10-2"><a href="#cb10-2" tabindex="-1"></a>t1_data</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -994,7 +994,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb12">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="bu">type</span>(t1_data)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1" tabindex="-1"></a><span class="bu">type</span>(t1_data)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1023,12 +1023,12 @@ <h3 class="callout-title">Check out attributes of the array<a class="anchor" ari
 <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a>t1_data.ndim</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb14-1"><a href="#cb14-1" tabindex="-1"></a>t1_data.ndim</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1061,12 +1061,12 @@ <h3 class="callout-title">Check out attributes of the array<em>(continued)</em><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb16">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a>t1_data.shape</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb16-1"><a href="#cb16-1" tabindex="-1"></a>t1_data.shape</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1086,7 +1086,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
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 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb18-1"><a href="#cb18-1" aria-hidden="true" tabindex="-1"></a>t1_data.dtype</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb18-1"><a href="#cb18-1" tabindex="-1"></a>t1_data.dtype</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1101,9 +1101,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb20">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> numpy <span class="im">as</span> np</span>
-<span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">min</span>(t1_data))</span>
-<span id="cb20-3"><a href="#cb20-3" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">max</span>(t1_data))</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb20-1"><a href="#cb20-1" tabindex="-1"></a><span class="im">import</span> numpy <span class="im">as</span> np</span>
+<span id="cb20-2"><a href="#cb20-2" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">min</span>(t1_data))</span>
+<span id="cb20-3"><a href="#cb20-3" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">max</span>(t1_data))</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1121,7 +1121,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb22">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a>t1_data[<span class="dv">9</span>, <span class="dv">19</span>, <span class="dv">2</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb22-1"><a href="#cb22-1" tabindex="-1"></a>t1_data[<span class="dv">9</span>, <span class="dv">19</span>, <span class="dv">2</span>]</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1147,7 +1147,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb24-1"><a href="#cb24-1" aria-hidden="true" tabindex="-1"></a>x_slice <span class="op">=</span> t1_data[<span class="dv">9</span>, :, :]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb24-1"><a href="#cb24-1" tabindex="-1"></a>x_slice <span class="op">=</span> t1_data[<span class="dv">9</span>, :, :]</span></code></pre>
 </div>
 <p>This is similar to the indexing we did before to pull out a single
 voxel. However, instead of providing a value for each axis, the
@@ -1170,12 +1170,12 @@ <h3 class="callout-title">Slicing MRI data<a class="anchor" aria-label="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a>y_slice <span class="op">=</span> t1_data[:, <span class="dv">19</span>, :]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb25-1"><a href="#cb25-1" tabindex="-1"></a>y_slice <span class="op">=</span> t1_data[:, <span class="dv">19</span>, :]</span></code></pre>
 </div>
 </div>
 </div>
@@ -1198,12 +1198,12 @@ <h3 class="callout-title">Slicing MRI data<em>(continued)</em><a class="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb26">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb26-1"><a href="#cb26-1" aria-hidden="true" tabindex="-1"></a>z_slice <span class="op">=</span> t1_data[:, :, <span class="dv">2</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb26-1"><a href="#cb26-1" tabindex="-1"></a>z_slice <span class="op">=</span> t1_data[:, :, <span class="dv">2</span>]</span></code></pre>
 </div>
 </div>
 </div>
@@ -1222,14 +1222,14 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb27">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> matplotlib.pyplot <span class="im">as</span> plt</span>
-<span id="cb27-2"><a href="#cb27-2" aria-hidden="true" tabindex="-1"></a><span class="op">%</span>matplotlib inline</span>
-<span id="cb27-3"><a href="#cb27-3" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb27-4"><a href="#cb27-4" aria-hidden="true" tabindex="-1"></a>slices <span class="op">=</span> [x_slice, y_slice, z_slice]</span>
-<span id="cb27-5"><a href="#cb27-5" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb27-6"><a href="#cb27-6" aria-hidden="true" tabindex="-1"></a>fig, axes <span class="op">=</span> plt.subplots(<span class="dv">1</span>, <span class="bu">len</span>(slices))</span>
-<span id="cb27-7"><a href="#cb27-7" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> i, <span class="bu">slice</span> <span class="kw">in</span> <span class="bu">enumerate</span>(slices):</span>
-<span id="cb27-8"><a href="#cb27-8" aria-hidden="true" tabindex="-1"></a>    axes[i].imshow(<span class="bu">slice</span>.T, cmap<span class="op">=</span><span class="st">"gray"</span>, origin<span class="op">=</span><span class="st">"lower"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb27-1"><a href="#cb27-1" tabindex="-1"></a><span class="im">import</span> matplotlib.pyplot <span class="im">as</span> plt</span>
+<span id="cb27-2"><a href="#cb27-2" tabindex="-1"></a><span class="op">%</span>matplotlib inline</span>
+<span id="cb27-3"><a href="#cb27-3" tabindex="-1"></a></span>
+<span id="cb27-4"><a href="#cb27-4" tabindex="-1"></a>slices <span class="op">=</span> [x_slice, y_slice, z_slice]</span>
+<span id="cb27-5"><a href="#cb27-5" tabindex="-1"></a></span>
+<span id="cb27-6"><a href="#cb27-6" tabindex="-1"></a>fig, axes <span class="op">=</span> plt.subplots(<span class="dv">1</span>, <span class="bu">len</span>(slices))</span>
+<span id="cb27-7"><a href="#cb27-7" tabindex="-1"></a><span class="cf">for</span> i, <span class="bu">slice</span> <span class="kw">in</span> <span class="bu">enumerate</span>(slices):</span>
+<span id="cb27-8"><a href="#cb27-8" tabindex="-1"></a>    axes[i].imshow(<span class="bu">slice</span>.T, cmap<span class="op">=</span><span class="st">"gray"</span>, origin<span class="op">=</span><span class="st">"lower"</span>)</span></code></pre>
 </div>
 <p>Now, we’re going to step away from discussing our data and talk about
 the final important attribute of a NIfTI.</p>
@@ -1243,8 +1243,8 @@ <h3 id="affine-tells-the-position-of-the-image-array-data-in-a-reference-space">
 <div class="codewrapper sourceCode" id="cb28">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb28-1"><a href="#cb28-1" aria-hidden="true" tabindex="-1"></a>t1_affine <span class="op">=</span> t1_img.affine</span>
-<span id="cb28-2"><a href="#cb28-2" aria-hidden="true" tabindex="-1"></a>t1_affine</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb28-1"><a href="#cb28-1" tabindex="-1"></a>t1_affine <span class="op">=</span> t1_img.affine</span>
+<span id="cb28-2"><a href="#cb28-2" tabindex="-1"></a>t1_affine</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1470,18 +1470,18 @@ <h3 id="datalad">DataLad<a class="anchor" aria-label="anchor" href="#datalad"></
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="ex">datalad</span> install ///openneuro/ds000030</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span>
+<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="ex">datalad</span> install ///openneuro/ds000030</span></code></pre>
 </div>
 <p>Let’s take a look at the <code>participants.tsv</code> file to see
 what the demographics for this dataset look like.</p>
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>participant_metadata <span class="op">=</span> pd.read_csv(<span class="st">'../data/ds000030/participants.tsv'</span>, sep<span class="op">=</span><span class="st">'</span><span class="ch">\t</span><span class="st">'</span>)</span>
-<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>participant_metadata</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
+<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a></span>
+<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a>participant_metadata <span class="op">=</span> pd.read_csv(<span class="st">'../data/ds000030/participants.tsv'</span>, sep<span class="op">=</span><span class="st">'</span><span class="ch">\t</span><span class="st">'</span>)</span>
+<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a>participant_metadata</span></code></pre>
 </div>
 <p><strong>OUTPUT:</strong></p>
 <table border="1" class="table dataframe">
@@ -1809,7 +1809,7 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1826,11 +1826,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb5">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>participant_metadata <span class="op">=</span> participant_metadata[(participant_metadata.diagnosis.isin([<span class="st">'CONTROL'</span>, <span class="st">'SCHZ'</span>])) <span class="op">&amp;</span></span>
-<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>                                            (participant_metadata.T1w <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
-<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>                                            (participant_metadata.rest <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
-<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>                                            (participant_metadata.ghost_NoGhost <span class="op">==</span> <span class="st">'No_ghost'</span>)]</span>
-<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a>participant_metadata <span class="op">=</span> participant_metadata[(participant_metadata.diagnosis.isin([<span class="st">'CONTROL'</span>, <span class="st">'SCHZ'</span>])) <span class="op">&amp;</span></span>
+<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a>                                            (participant_metadata.T1w <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
+<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a>                                            (participant_metadata.rest <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
+<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a>                                            (participant_metadata.ghost_NoGhost <span class="op">==</span> <span class="st">'No_ghost'</span>)]</span>
+<span id="cb5-5"><a href="#cb5-5" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1850,9 +1850,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> bids.layout <span class="im">import</span> BIDSLayout</span>
-<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="im">from</span> bids.layout <span class="im">import</span> BIDSLayout</span>
+<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a></span>
+<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>)</span></code></pre>
 </div>
 <p>The pybids layout object indexes the BIDS folder. Indexing can take a
 really long time, especially if you have several subjects, modalities,
@@ -1862,9 +1862,9 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>layout.save(<span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span>
-<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>, database_path<span class="op">=</span><span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a>layout.save(<span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span>
+<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a></span>
+<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>, database_path<span class="op">=</span><span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span></code></pre>
 </div>
 <p>The pybids layout object also lets you query your BIDS dataset
 according to a number of parameters by using a <code>get_*()</code>
@@ -1873,7 +1873,7 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb9">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>layout.get_subjects()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a>layout.get_subjects()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1894,7 +1894,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb11">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>layout.get_modalities()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a>layout.get_modalities()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1905,11 +1905,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb13">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="co">#Task fMRI</span></span>
-<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(layout.get_tasks())</span>
-<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb13-4"><a href="#cb13-4" aria-hidden="true" tabindex="-1"></a><span class="co">#Data types (bold, brainmask, confounds, smoothwm, probtissue, warp...)</span></span>
-<span id="cb13-5"><a href="#cb13-5" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(layout.get_types())</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb13-1"><a href="#cb13-1" tabindex="-1"></a><span class="co">#Task fMRI</span></span>
+<span id="cb13-2"><a href="#cb13-2" tabindex="-1"></a><span class="bu">print</span>(layout.get_tasks())</span>
+<span id="cb13-3"><a href="#cb13-3" tabindex="-1"></a></span>
+<span id="cb13-4"><a href="#cb13-4" tabindex="-1"></a><span class="co">#Data types (bold, brainmask, confounds, smoothwm, probtissue, warp...)</span></span>
+<span id="cb13-5"><a href="#cb13-5" tabindex="-1"></a><span class="bu">print</span>(layout.get_types())</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1935,7 +1935,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a>layout.get_types(modality<span class="op">=</span><span class="st">'func'</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb15-1"><a href="#cb15-1" tabindex="-1"></a>layout.get_types(modality<span class="op">=</span><span class="st">'func'</span>)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1946,7 +1946,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb17">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a>layout.get(task<span class="op">=</span><span class="st">'rest'</span>, <span class="bu">type</span><span class="op">=</span><span class="st">'bold'</span>, extensions<span class="op">=</span><span class="st">'nii.gz'</span>, return_type<span class="op">=</span><span class="st">'file'</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb17-1"><a href="#cb17-1" tabindex="-1"></a>layout.get(task<span class="op">=</span><span class="st">'rest'</span>, <span class="bu">type</span><span class="op">=</span><span class="st">'bold'</span>, extensions<span class="op">=</span><span class="st">'nii.gz'</span>, return_type<span class="op">=</span><span class="st">'file'</span>)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1958,8 +1958,8 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb19">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a>df <span class="op">=</span> layout.as_data_frame()</span>
-<span id="cb19-2"><a href="#cb19-2" aria-hidden="true" tabindex="-1"></a>df.head()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb19-1"><a href="#cb19-1" tabindex="-1"></a>df <span class="op">=</span> layout.as_data_frame()</span>
+<span id="cb19-2"><a href="#cb19-2" tabindex="-1"></a>df.head()</span></code></pre>
 </div>
 <p><strong>OUTPUT:</strong></p>
 <table border="1" class="table dataframe">
@@ -2104,7 +2104,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-bids-derivatives"><p>Content from <a href="bids-derivatives.html">BIDS derivatives</a></p>
 <hr>
-<p>Last updated on 2024-02-18 |
+<p>Last updated on 2024-02-28 |
         
         <a href="https://github.com/carpentries-incubator/SDC-BIDS-IntroMRI/edit/main/episodes/bids-derivatives.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -2117,8 +2117,10 @@ <h2 class="card-header">Overview</h2>
 <div class="card-body">
 <div class="inner">
 <h3 class="card-title">Questions</h3>
-<ul><li>
-</li></ul>
+<ul>
+<li>What are BIDS Apps?</li>
+<li>What are containers?</li>
+</ul>
 </div>
 </div>
 </div>
@@ -2126,8 +2128,11 @@ <h3 class="card-title">Questions</h3>
 <div class="card-body">
 <div class="inner bordered">
 <h3 class="card-title">Objectives</h3>
-<ul><li>
-</li></ul>
+<ul>
+<li>Learn about neuroimaging applications using BIDS data
+structures</li>
+<li>Use neuroimaging applications through containers</li>
+</ul>
 </div>
 </div>
 </div>
@@ -2164,16 +2169,16 @@ <h3 class="card-title">Objectives</h3>
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">singularity</span> build mriqc-0.16.1.simg docker://poldracklab/mriqc:0.16.1<span class="kw">`</span></span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">singularity</span> build mriqc-0.16.1.simg docker://poldracklab/mriqc:0.16.1<span class="kw">`</span></span></code></pre>
 </div>
 <p>To run the container:</p>
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">singularity</span> run <span class="at">--cleanenv</span> <span class="dt">\</span></span>
-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>  <span class="at">-B</span> bids_folder:/data <span class="dt">\</span></span>
-<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>  mriqc-0.16.1.simg <span class="dt">\</span></span>
-<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>  /data /data/derivatives participant</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="ex">singularity</span> run <span class="at">--cleanenv</span> <span class="dt">\</span></span>
+<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a>  <span class="at">-B</span> bids_folder:/data <span class="dt">\</span></span>
+<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a>  mriqc-0.16.1.simg <span class="dt">\</span></span>
+<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a>  /data /data/derivatives participant</span></code></pre>
 </div>
 <div id="keypoints1" class="callout keypoints">
 <div class="callout-square">
@@ -2234,9 +2239,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/aio.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/aio.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/anatomy-of-nifti.html b/anatomy-of-nifti.html
index bd5b87e..52726ca 100644
--- a/anatomy-of-nifti.html
+++ b/anatomy-of-nifti.html
@@ -319,7 +319,7 @@ <h3 class="card-title">Objectives</h3>
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> nibabel <span class="im">as</span> nib</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="im">import</span> nibabel <span class="im">as</span> nib</span></code></pre>
 </div>
 <p>First, use the <code>load()</code> function to create a NiBabel image
 object from a NIfTI file. We’ll load in an example T1w image from the
@@ -327,7 +327,7 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>t1_img <span class="op">=</span> nib.load(<span class="st">"../data/dicom_examples/nii/0219191_mystudy-0219-1114_anat_ses-01_T1w_20190219111436_5.nii.gz"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>t1_img <span class="op">=</span> nib.load(<span class="st">"../data/dicom_examples/nii/0219191_mystudy-0219-1114_anat_ses-01_T1w_20190219111436_5.nii.gz"</span>)</span></code></pre>
 </div>
 <p>Loading in a NIfTI file with <code>NiBabel</code> gives us a special
 type of data object which encodes all the information in the file.Each
@@ -342,8 +342,8 @@ <h3 id="header-contains-metadata-about-the-image-such-as-image-dimensions-data-t
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>t1_hdr <span class="op">=</span> t1_img.header</span>
-<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(t1_hdr)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a>t1_hdr <span class="op">=</span> t1_img.header</span>
+<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="bu">print</span>(t1_hdr)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -404,7 +404,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb5">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>t1_hdr.keys()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a>t1_hdr.keys()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -469,7 +469,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>t1_hdr[<span class="st">'&lt;key_name&gt;'</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a>t1_hdr[<span class="st">'&lt;key_name&gt;'</span>]</span></code></pre>
 </div>
 <div id="extract-values-from-the-nifti-header" class="callout challenge">
 <div class="callout-square">
@@ -488,12 +488,12 @@ <h3 class="callout-title">Extract values from the NIfTI header<a class="anchor"
 <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" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>t1_hdr[<span class="st">'pixdim'</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a>t1_hdr[<span class="st">'pixdim'</span>]</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -515,8 +515,8 @@ <h3 id="data">2. Data<a class="anchor" aria-label="anchor" href="#data"></a></h3
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>t1_data <span class="op">=</span> t1_img.get_fdata()</span>
-<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a>t1_data</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a>t1_data <span class="op">=</span> t1_img.get_fdata()</span>
+<span id="cb10-2"><a href="#cb10-2" tabindex="-1"></a>t1_data</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -612,7 +612,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb12">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="bu">type</span>(t1_data)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1" tabindex="-1"></a><span class="bu">type</span>(t1_data)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -641,12 +641,12 @@ <h3 class="callout-title">Check out attributes of the array<a class="anchor" ari
 <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a>t1_data.ndim</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb14-1"><a href="#cb14-1" tabindex="-1"></a>t1_data.ndim</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -679,12 +679,12 @@ <h3 class="callout-title">Check out attributes of the array<em>(continued)</em><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb16">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a>t1_data.shape</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb16-1"><a href="#cb16-1" tabindex="-1"></a>t1_data.shape</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -704,7 +704,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb18">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb18-1"><a href="#cb18-1" aria-hidden="true" tabindex="-1"></a>t1_data.dtype</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb18-1"><a href="#cb18-1" tabindex="-1"></a>t1_data.dtype</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -719,9 +719,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb20">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> numpy <span class="im">as</span> np</span>
-<span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">min</span>(t1_data))</span>
-<span id="cb20-3"><a href="#cb20-3" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">max</span>(t1_data))</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb20-1"><a href="#cb20-1" tabindex="-1"></a><span class="im">import</span> numpy <span class="im">as</span> np</span>
+<span id="cb20-2"><a href="#cb20-2" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">min</span>(t1_data))</span>
+<span id="cb20-3"><a href="#cb20-3" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">max</span>(t1_data))</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -739,7 +739,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb22">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a>t1_data[<span class="dv">9</span>, <span class="dv">19</span>, <span class="dv">2</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb22-1"><a href="#cb22-1" tabindex="-1"></a>t1_data[<span class="dv">9</span>, <span class="dv">19</span>, <span class="dv">2</span>]</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -764,7 +764,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb24-1"><a href="#cb24-1" aria-hidden="true" tabindex="-1"></a>x_slice <span class="op">=</span> t1_data[<span class="dv">9</span>, :, :]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb24-1"><a href="#cb24-1" tabindex="-1"></a>x_slice <span class="op">=</span> t1_data[<span class="dv">9</span>, :, :]</span></code></pre>
 </div>
 <p>This is similar to the indexing we did before to pull out a single
 voxel. However, instead of providing a value for each axis, the
@@ -787,12 +787,12 @@ <h3 class="callout-title">Slicing MRI data<a class="anchor" aria-label="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a>y_slice <span class="op">=</span> t1_data[:, <span class="dv">19</span>, :]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb25-1"><a href="#cb25-1" tabindex="-1"></a>y_slice <span class="op">=</span> t1_data[:, <span class="dv">19</span>, :]</span></code></pre>
 </div>
 </div>
 </div>
@@ -815,12 +815,12 @@ <h3 class="callout-title">Slicing MRI data<em>(continued)</em><a class="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb26">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb26-1"><a href="#cb26-1" aria-hidden="true" tabindex="-1"></a>z_slice <span class="op">=</span> t1_data[:, :, <span class="dv">2</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb26-1"><a href="#cb26-1" tabindex="-1"></a>z_slice <span class="op">=</span> t1_data[:, :, <span class="dv">2</span>]</span></code></pre>
 </div>
 </div>
 </div>
@@ -838,14 +838,14 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb27">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> matplotlib.pyplot <span class="im">as</span> plt</span>
-<span id="cb27-2"><a href="#cb27-2" aria-hidden="true" tabindex="-1"></a><span class="op">%</span>matplotlib inline</span>
-<span id="cb27-3"><a href="#cb27-3" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb27-4"><a href="#cb27-4" aria-hidden="true" tabindex="-1"></a>slices <span class="op">=</span> [x_slice, y_slice, z_slice]</span>
-<span id="cb27-5"><a href="#cb27-5" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb27-6"><a href="#cb27-6" aria-hidden="true" tabindex="-1"></a>fig, axes <span class="op">=</span> plt.subplots(<span class="dv">1</span>, <span class="bu">len</span>(slices))</span>
-<span id="cb27-7"><a href="#cb27-7" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> i, <span class="bu">slice</span> <span class="kw">in</span> <span class="bu">enumerate</span>(slices):</span>
-<span id="cb27-8"><a href="#cb27-8" aria-hidden="true" tabindex="-1"></a>    axes[i].imshow(<span class="bu">slice</span>.T, cmap<span class="op">=</span><span class="st">"gray"</span>, origin<span class="op">=</span><span class="st">"lower"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb27-1"><a href="#cb27-1" tabindex="-1"></a><span class="im">import</span> matplotlib.pyplot <span class="im">as</span> plt</span>
+<span id="cb27-2"><a href="#cb27-2" tabindex="-1"></a><span class="op">%</span>matplotlib inline</span>
+<span id="cb27-3"><a href="#cb27-3" tabindex="-1"></a></span>
+<span id="cb27-4"><a href="#cb27-4" tabindex="-1"></a>slices <span class="op">=</span> [x_slice, y_slice, z_slice]</span>
+<span id="cb27-5"><a href="#cb27-5" tabindex="-1"></a></span>
+<span id="cb27-6"><a href="#cb27-6" tabindex="-1"></a>fig, axes <span class="op">=</span> plt.subplots(<span class="dv">1</span>, <span class="bu">len</span>(slices))</span>
+<span id="cb27-7"><a href="#cb27-7" tabindex="-1"></a><span class="cf">for</span> i, <span class="bu">slice</span> <span class="kw">in</span> <span class="bu">enumerate</span>(slices):</span>
+<span id="cb27-8"><a href="#cb27-8" tabindex="-1"></a>    axes[i].imshow(<span class="bu">slice</span>.T, cmap<span class="op">=</span><span class="st">"gray"</span>, origin<span class="op">=</span><span class="st">"lower"</span>)</span></code></pre>
 </div>
 <p>Now, we’re going to step away from discussing our data and talk about
 the final important attribute of a NIfTI.</p>
@@ -858,8 +858,8 @@ <h3 id="affine-tells-the-position-of-the-image-array-data-in-a-reference-space">
 <div class="codewrapper sourceCode" id="cb28">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb28-1"><a href="#cb28-1" aria-hidden="true" tabindex="-1"></a>t1_affine <span class="op">=</span> t1_img.affine</span>
-<span id="cb28-2"><a href="#cb28-2" aria-hidden="true" tabindex="-1"></a>t1_affine</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb28-1"><a href="#cb28-1" tabindex="-1"></a>t1_affine <span class="op">=</span> t1_img.affine</span>
+<span id="cb28-2"><a href="#cb28-2" tabindex="-1"></a>t1_affine</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -991,9 +991,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/anatomy-of-nifti.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/anatomy-of-nifti.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/before-we-start.html b/before-we-start.html
index b4d368c..64bca43 100644
--- a/before-we-start.html
+++ b/before-we-start.html
@@ -476,9 +476,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/before-we-start.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/before-we-start.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/bids-derivatives.html b/bids-derivatives.html
index 5ec5c18..fafe5de 100644
--- a/bids-derivatives.html
+++ b/bids-derivatives.html
@@ -260,7 +260,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>BIDS derivatives</h1>
-        <p>Last updated on 2024-02-18 |
+        <p>Last updated on 2024-02-28 |
         
         <a href="https://github.com/carpentries-incubator/SDC-BIDS-IntroMRI/edit/main/episodes/bids-derivatives.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -279,16 +279,19 @@ <h2 class="card-header">Overview</h2>
 <div class="card-body">
 <div class="inner">
 <h3 class="card-title">Questions</h3>
-<ul><li>
-</li></ul></div>
+<ul><li>What are BIDS Apps?</li>
+<li>What are containers?</li>
+</ul></div>
 </div>
 </div>
 <div class="col-md-8">
 <div class="card-body">
 <div class="inner bordered">
 <h3 class="card-title">Objectives</h3>
-<ul><li>
-</li></ul></div>
+<ul><li>Learn about neuroimaging applications using BIDS data
+structures</li>
+<li>Use neuroimaging applications through containers</li>
+</ul></div>
 </div>
 </div>
 </div>
@@ -316,16 +319,16 @@ <h3 class="card-title">Objectives</h3>
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">singularity</span> build mriqc-0.16.1.simg docker://poldracklab/mriqc:0.16.1<span class="kw">`</span></span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">singularity</span> build mriqc-0.16.1.simg docker://poldracklab/mriqc:0.16.1<span class="kw">`</span></span></code></pre>
 </div>
 <p>To run the container:</p>
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">singularity</span> run <span class="at">--cleanenv</span> <span class="dt">\</span></span>
-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>  <span class="at">-B</span> bids_folder:/data <span class="dt">\</span></span>
-<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>  mriqc-0.16.1.simg <span class="dt">\</span></span>
-<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>  /data /data/derivatives participant</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="ex">singularity</span> run <span class="at">--cleanenv</span> <span class="dt">\</span></span>
+<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a>  <span class="at">-B</span> bids_folder:/data <span class="dt">\</span></span>
+<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a>  mriqc-0.16.1.simg <span class="dt">\</span></span>
+<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a>  /data /data/derivatives participant</span></code></pre>
 </div>
 <div id="keypoints1" class="callout keypoints">
 <div class="callout-square">
@@ -399,9 +402,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/bids-derivatives.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/bids-derivatives.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/data-organization-bids.html b/data-organization-bids.html
index 80eb404..c4a22aa 100644
--- a/data-organization-bids.html
+++ b/data-organization-bids.html
@@ -401,9 +401,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/data-organization-bids.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/data-organization-bids.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/discuss.html b/discuss.html
index 419b2c7..5f89304 100644
--- a/discuss.html
+++ b/discuss.html
@@ -327,9 +327,9 @@ <h1>Discussion</h1>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/discuss.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/discuss.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index 0b76d67..9e4b50a 100644
--- a/images.html
+++ b/images.html
@@ -388,9 +388,9 @@ <h3 id="bids-derivatives-figure-1">Figure 1</h3>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/images.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/images.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index 50ebb87..bd72ce2 100644
--- a/index.html
+++ b/index.html
@@ -311,18 +311,17 @@ <h3 id="getting-started">Getting Started<a class="anchor" aria-label="anchor" hr
 </h2>
 <hr class="half-width"><p>The Binder webpage for this lesson can be accessed by clicking the
 button below.</p>
-<p><a href="https://mybinder.org/v2/gh/carpentries-incubator/SDC-BIDS-IntroMRI/gh-pages?filepath=code%2F" class="external-link"><img src="https://mybinder.org/badge_logo.svg" class="figure">{alt=‘Binder’}</a></p>
+<p><a href="https://mybinder.org/v2/gh/carpentries-incubator/SDC-BIDS-IntroMRI/gh-pages?filepath=code%2F" class="external-link"><img src="https://mybinder.org/badge_logo.svg" alt="Binder" class="figure"></a></p>
 <p>Binder enables you to run the collection of Python notebooks found in
 the <code>code</code> folder. All of the software and data used in the
 lesson are pre-installed in a custom computational environment and no
 additional software needs to be installed locally.</p>
-<div id="binder-tips" class="callout callout">
+<div id="callout1" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div id="binder-tips" class="callout-inner">
-<h3 class="callout-title">Binder Tips<a class="anchor" aria-label="anchor" href="#binder-tips"></a>
-</h3>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="binder-tips">Binder Tips<a class="anchor" aria-label="anchor" href="#binder-tips"></a></h3>
 <div class="callout-content">
 <p>If using Binder, please be aware that startup can take anywhere from
 30 seconds to 10 minutes, depending on your internet connection and how
@@ -356,7 +355,7 @@ <h3 id="install-python-packages">Install Python Packages<a class="anchor" aria-l
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pip</span> install nibabel nilearn pybids</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">pip</span> install nibabel nilearn pybids</span></code></pre>
 </div>
 </div>
 <div class="section level3">
@@ -371,7 +370,7 @@ <h3 id="install-dcm2niix">Install dcm2niix<a class="anchor" aria-label="anchor"
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">conda</span> install <span class="at">-c</span> conda-forge dcm2niix</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="ex">conda</span> install <span class="at">-c</span> conda-forge dcm2niix</span></code></pre>
 </div>
 </div>
 <div class="section level3">
@@ -385,7 +384,7 @@ <h3 id="install-datalad">Install DataLad<a class="anchor" aria-label="anchor" hr
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="ex">conda</span> install <span class="at">-c</span> conda-forge datalad</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="ex">conda</span> install <span class="at">-c</span> conda-forge datalad</span></code></pre>
 </div>
 </div>
 <div class="section level3">
@@ -396,9 +395,9 @@ <h3 id="obtain-lesson-materials">Obtain lesson materials<a class="anchor" aria-l
 <div class="codewrapper sourceCode" id="cb4">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> ~/Desktop/dc-mri/data</span>
-<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span>
-<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a><span class="ex">datalad</span> clone https://github.com/OpenNeuroDatasets/ds000030.git</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="fu">mkdir</span> ~/Desktop/dc-mri/data</span>
+<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span>
+<span id="cb4-3"><a href="#cb4-3" tabindex="-1"></a><span class="ex">datalad</span> clone https://github.com/OpenNeuroDatasets/ds000030.git</span></code></pre>
 </div>
 </div>
 </section><section id="launch-python-interface"><h2 class="section-heading">Launch Python interface<a class="anchor" aria-label="anchor" href="#launch-python-interface"></a>
@@ -456,7 +455,7 @@ <h4 class="accordion-header" id="headingSolution2">Unix shell</h4>
 <div class="codewrapper sourceCode" id="cb5">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span></code></pre>
 </div>
 </div>
 </div>
@@ -477,7 +476,7 @@ <h4 class="accordion-header" id="headingSolution3">Command Prompt (Windows)</h4>
 <div class="codewrapper sourceCode" id="cb6">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> /D %userprofile%<span class="dt">\D</span>esktop<span class="dt">\d</span>c-mri<span class="dt">\d</span>ata</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="bu">cd</span> /D %userprofile%<span class="dt">\D</span>esktop<span class="dt">\d</span>c-mri<span class="dt">\d</span>ata</span></code></pre>
 </div>
 </div>
 </div>
@@ -494,7 +493,7 @@ <h4 class="accordion-header" id="headingSolution4">Unix shell</h4>
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="ex">jupyter</span> notebook</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="ex">jupyter</span> notebook</span></code></pre>
 </div>
 </div>
 </div>
@@ -510,7 +509,7 @@ <h4 class="accordion-header" id="headingSolution5">Command Prompt (Windows)</h4>
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="ex">python</span> <span class="at">-m</span> notebook</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="ex">python</span> <span class="at">-m</span> notebook</span></code></pre>
 </div>
 </div>
 </div>
@@ -535,7 +534,7 @@ <h3 id="option-b-ipython-interpreter">Option B: IPython interpreter<a class="anc
 <div class="codewrapper sourceCode" id="cb9">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="ex">ipython</span></span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a><span class="ex">ipython</span></span></code></pre>
 </div>
 <p>  <!-- vertical spacer --></p>
 </div>
@@ -545,7 +544,7 @@ <h3 id="option-c-plain-vanilla-python-interpreter">Option C: plain-vanilla Pytho
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="ex">python</span></span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a><span class="ex">python</span></span></code></pre>
 </div>
 <p>If you are using <a href="https://gitforwindows.org" class="external-link">Git Bash on
 Windows</a>, you have to call Python <em>via</em>
@@ -553,7 +552,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <div class="codewrapper sourceCode" id="cb11">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="ex">winpty</span> python</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a><span class="ex">winpty</span> python</span></code></pre>
 </div>
 </div>
 </section></section></main><nav class="bottom-pagination mx-md-4" aria-label="Next Chapter"><!-- content for small screens --><div class="d-block d-sm-block d-md-none">
@@ -604,9 +603,9 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/index.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/index.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index fc0e7d8..ed5bb47 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -355,9 +355,9 @@ <h1>Instructor Notes</h1>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor-notes.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor-notes.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 60f7e05..66f83a9 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -315,9 +315,9 @@ <h1>Page not found</h1>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/404.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/404.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 2e39462..812fc0b 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -336,9 +336,9 @@ <h1>Contributor Code of Conduct</h1>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/CODE_OF_CONDUCT.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/CODE_OF_CONDUCT.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index ebcda05..5e67d8f 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -387,9 +387,9 @@ <h1>Licenses</h1>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/LICENSE.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/LICENSE.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index 101e23e..c0eff06 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -590,11 +590,11 @@ <h3 id="diffusion">Diffusion<a class="anchor" aria-label="anchor" href="#diffusi
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">wget</span> https://zenodo.org/record/3677090/files/0219191_mystudy-0219-1114.tar.gz <span class="at">-O</span> ../data/0219191_mystudy-0219-1114.tar.gz</span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples</span>
-<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">tar</span> <span class="at">-xvzf</span> ../data/0219191_mystudy-0219-1114.tar.gz <span class="at">-C</span> ../data/dicom_examples</span>
-<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">gzip</span> <span class="at">-d</span> ../data/dicom_examples/0219191_mystudy-0219-1114/dcm/<span class="pp">*</span>dcm.gz</span>
-<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">rm</span> ../data/0219191_mystudy-0219-1114.tar.gz</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">wget</span> https://zenodo.org/record/3677090/files/0219191_mystudy-0219-1114.tar.gz <span class="at">-O</span> ../data/0219191_mystudy-0219-1114.tar.gz</span>
+<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples</span>
+<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="fu">tar</span> <span class="at">-xvzf</span> ../data/0219191_mystudy-0219-1114.tar.gz <span class="at">-C</span> ../data/dicom_examples</span>
+<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="fu">gzip</span> <span class="at">-d</span> ../data/dicom_examples/0219191_mystudy-0219-1114/dcm/<span class="pp">*</span>dcm.gz</span>
+<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="fu">rm</span> ../data/0219191_mystudy-0219-1114.tar.gz</span></code></pre>
 </div>
 <figure><img src="../fig/dicom_to_nifti.png" alt="dicom-to-nifti" class="figure mx-auto d-block"></figure><p>NIfTI is one of the most ubiquitous file formats for storing
 neuroimaging data. If you’re interested in learning more about NIfTI
@@ -606,7 +606,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-help</span></span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-help</span></span></code></pre>
 </div>
 <div id="converting-dicom-to-nifti" class="callout challenge">
 <div class="callout-square">
@@ -625,13 +625,13 @@ <h3 class="callout-title">Converting DICOM to NIfTI<a class="anchor" aria-label=
 <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">
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples/nii</span>
-<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-z</span> y <span class="at">-o</span> ../data/dicom_examples/nii ../data/dicom_examples/0219191_mystudy-0219-1114/</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples/nii</span>
+<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-z</span> y <span class="at">-o</span> ../data/dicom_examples/nii ../data/dicom_examples/0219191_mystudy-0219-1114/</span></code></pre>
 </div>
 </div>
 </div>
@@ -702,7 +702,7 @@ <h3 class="card-title">Objectives</h3>
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> nibabel <span class="im">as</span> nib</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="im">import</span> nibabel <span class="im">as</span> nib</span></code></pre>
 </div>
 <p>First, use the <code>load()</code> function to create a NiBabel image
 object from a NIfTI file. We’ll load in an example T1w image from the
@@ -710,7 +710,7 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>t1_img <span class="op">=</span> nib.load(<span class="st">"../data/dicom_examples/nii/0219191_mystudy-0219-1114_anat_ses-01_T1w_20190219111436_5.nii.gz"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>t1_img <span class="op">=</span> nib.load(<span class="st">"../data/dicom_examples/nii/0219191_mystudy-0219-1114_anat_ses-01_T1w_20190219111436_5.nii.gz"</span>)</span></code></pre>
 </div>
 <p>Loading in a NIfTI file with <code>NiBabel</code> gives us a special
 type of data object which encodes all the information in the file.Each
@@ -726,8 +726,8 @@ <h3 id="header-contains-metadata-about-the-image-such-as-image-dimensions-data-t
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>t1_hdr <span class="op">=</span> t1_img.header</span>
-<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(t1_hdr)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a>t1_hdr <span class="op">=</span> t1_img.header</span>
+<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="bu">print</span>(t1_hdr)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -788,7 +788,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb5">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>t1_hdr.keys()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a>t1_hdr.keys()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -855,7 +855,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>t1_hdr[<span class="st">'&lt;key_name&gt;'</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a>t1_hdr[<span class="st">'&lt;key_name&gt;'</span>]</span></code></pre>
 </div>
 <div id="extract-values-from-the-nifti-header" class="callout challenge">
 <div class="callout-square">
@@ -874,12 +874,12 @@ <h3 class="callout-title">Extract values from the NIfTI header<a class="anchor"
 <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" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>t1_hdr[<span class="st">'pixdim'</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a>t1_hdr[<span class="st">'pixdim'</span>]</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -902,8 +902,8 @@ <h3 id="data">2. Data<a class="anchor" aria-label="anchor" href="#data"></a>
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>t1_data <span class="op">=</span> t1_img.get_fdata()</span>
-<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a>t1_data</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a>t1_data <span class="op">=</span> t1_img.get_fdata()</span>
+<span id="cb10-2"><a href="#cb10-2" tabindex="-1"></a>t1_data</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -999,7 +999,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb12">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="bu">type</span>(t1_data)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1" tabindex="-1"></a><span class="bu">type</span>(t1_data)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1028,12 +1028,12 @@ <h3 class="callout-title">Check out attributes of the array<a class="anchor" ari
 <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a>t1_data.ndim</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb14-1"><a href="#cb14-1" tabindex="-1"></a>t1_data.ndim</span></code></pre>
 </div>
 <div class="codewrapper">
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@@ -1066,12 +1066,12 @@ <h3 class="callout-title">Check out attributes of the array<em>(continued)</em><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb16">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a>t1_data.shape</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb16-1"><a href="#cb16-1" tabindex="-1"></a>t1_data.shape</span></code></pre>
 </div>
 <div class="codewrapper">
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@@ -1091,7 +1091,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb18">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb18-1"><a href="#cb18-1" aria-hidden="true" tabindex="-1"></a>t1_data.dtype</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb18-1"><a href="#cb18-1" tabindex="-1"></a>t1_data.dtype</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1106,9 +1106,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb20">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> numpy <span class="im">as</span> np</span>
-<span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">min</span>(t1_data))</span>
-<span id="cb20-3"><a href="#cb20-3" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">max</span>(t1_data))</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb20-1"><a href="#cb20-1" tabindex="-1"></a><span class="im">import</span> numpy <span class="im">as</span> np</span>
+<span id="cb20-2"><a href="#cb20-2" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">min</span>(t1_data))</span>
+<span id="cb20-3"><a href="#cb20-3" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">max</span>(t1_data))</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1126,7 +1126,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb22">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a>t1_data[<span class="dv">9</span>, <span class="dv">19</span>, <span class="dv">2</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb22-1"><a href="#cb22-1" tabindex="-1"></a>t1_data[<span class="dv">9</span>, <span class="dv">19</span>, <span class="dv">2</span>]</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1152,7 +1152,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
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 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb24-1"><a href="#cb24-1" aria-hidden="true" tabindex="-1"></a>x_slice <span class="op">=</span> t1_data[<span class="dv">9</span>, :, :]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb24-1"><a href="#cb24-1" tabindex="-1"></a>x_slice <span class="op">=</span> t1_data[<span class="dv">9</span>, :, :]</span></code></pre>
 </div>
 <p>This is similar to the indexing we did before to pull out a single
 voxel. However, instead of providing a value for each axis, the
@@ -1175,12 +1175,12 @@ <h3 class="callout-title">Slicing MRI data<a class="anchor" aria-label="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
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 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a>y_slice <span class="op">=</span> t1_data[:, <span class="dv">19</span>, :]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb25-1"><a href="#cb25-1" tabindex="-1"></a>y_slice <span class="op">=</span> t1_data[:, <span class="dv">19</span>, :]</span></code></pre>
 </div>
 </div>
 </div>
@@ -1203,12 +1203,12 @@ <h3 class="callout-title">Slicing MRI data<em>(continued)</em><a class="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
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 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb26-1"><a href="#cb26-1" aria-hidden="true" tabindex="-1"></a>z_slice <span class="op">=</span> t1_data[:, :, <span class="dv">2</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb26-1"><a href="#cb26-1" tabindex="-1"></a>z_slice <span class="op">=</span> t1_data[:, :, <span class="dv">2</span>]</span></code></pre>
 </div>
 </div>
 </div>
@@ -1227,14 +1227,14 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
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 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> matplotlib.pyplot <span class="im">as</span> plt</span>
-<span id="cb27-2"><a href="#cb27-2" aria-hidden="true" tabindex="-1"></a><span class="op">%</span>matplotlib inline</span>
-<span id="cb27-3"><a href="#cb27-3" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb27-4"><a href="#cb27-4" aria-hidden="true" tabindex="-1"></a>slices <span class="op">=</span> [x_slice, y_slice, z_slice]</span>
-<span id="cb27-5"><a href="#cb27-5" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb27-6"><a href="#cb27-6" aria-hidden="true" tabindex="-1"></a>fig, axes <span class="op">=</span> plt.subplots(<span class="dv">1</span>, <span class="bu">len</span>(slices))</span>
-<span id="cb27-7"><a href="#cb27-7" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> i, <span class="bu">slice</span> <span class="kw">in</span> <span class="bu">enumerate</span>(slices):</span>
-<span id="cb27-8"><a href="#cb27-8" aria-hidden="true" tabindex="-1"></a>    axes[i].imshow(<span class="bu">slice</span>.T, cmap<span class="op">=</span><span class="st">"gray"</span>, origin<span class="op">=</span><span class="st">"lower"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb27-1"><a href="#cb27-1" tabindex="-1"></a><span class="im">import</span> matplotlib.pyplot <span class="im">as</span> plt</span>
+<span id="cb27-2"><a href="#cb27-2" tabindex="-1"></a><span class="op">%</span>matplotlib inline</span>
+<span id="cb27-3"><a href="#cb27-3" tabindex="-1"></a></span>
+<span id="cb27-4"><a href="#cb27-4" tabindex="-1"></a>slices <span class="op">=</span> [x_slice, y_slice, z_slice]</span>
+<span id="cb27-5"><a href="#cb27-5" tabindex="-1"></a></span>
+<span id="cb27-6"><a href="#cb27-6" tabindex="-1"></a>fig, axes <span class="op">=</span> plt.subplots(<span class="dv">1</span>, <span class="bu">len</span>(slices))</span>
+<span id="cb27-7"><a href="#cb27-7" tabindex="-1"></a><span class="cf">for</span> i, <span class="bu">slice</span> <span class="kw">in</span> <span class="bu">enumerate</span>(slices):</span>
+<span id="cb27-8"><a href="#cb27-8" tabindex="-1"></a>    axes[i].imshow(<span class="bu">slice</span>.T, cmap<span class="op">=</span><span class="st">"gray"</span>, origin<span class="op">=</span><span class="st">"lower"</span>)</span></code></pre>
 </div>
 <p>Now, we’re going to step away from discussing our data and talk about
 the final important attribute of a NIfTI.</p>
@@ -1248,8 +1248,8 @@ <h3 id="affine-tells-the-position-of-the-image-array-data-in-a-reference-space">
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 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb28-1"><a href="#cb28-1" aria-hidden="true" tabindex="-1"></a>t1_affine <span class="op">=</span> t1_img.affine</span>
-<span id="cb28-2"><a href="#cb28-2" aria-hidden="true" tabindex="-1"></a>t1_affine</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb28-1"><a href="#cb28-1" tabindex="-1"></a>t1_affine <span class="op">=</span> t1_img.affine</span>
+<span id="cb28-2"><a href="#cb28-2" tabindex="-1"></a>t1_affine</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1477,18 +1477,18 @@ <h3 id="datalad">DataLad<a class="anchor" aria-label="anchor" href="#datalad"></
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="ex">datalad</span> install ///openneuro/ds000030</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span>
+<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="ex">datalad</span> install ///openneuro/ds000030</span></code></pre>
 </div>
 <p>Let’s take a look at the <code>participants.tsv</code> file to see
 what the demographics for this dataset look like.</p>
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>participant_metadata <span class="op">=</span> pd.read_csv(<span class="st">'../data/ds000030/participants.tsv'</span>, sep<span class="op">=</span><span class="st">'</span><span class="ch">\t</span><span class="st">'</span>)</span>
-<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>participant_metadata</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
+<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a></span>
+<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a>participant_metadata <span class="op">=</span> pd.read_csv(<span class="st">'../data/ds000030/participants.tsv'</span>, sep<span class="op">=</span><span class="st">'</span><span class="ch">\t</span><span class="st">'</span>)</span>
+<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a>participant_metadata</span></code></pre>
 </div>
 <p><strong>OUTPUT:</strong></p>
 <table border="1" class="table dataframe">
@@ -1816,7 +1816,7 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1833,11 +1833,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb5">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>participant_metadata <span class="op">=</span> participant_metadata[(participant_metadata.diagnosis.isin([<span class="st">'CONTROL'</span>, <span class="st">'SCHZ'</span>])) <span class="op">&amp;</span></span>
-<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>                                            (participant_metadata.T1w <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
-<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>                                            (participant_metadata.rest <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
-<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>                                            (participant_metadata.ghost_NoGhost <span class="op">==</span> <span class="st">'No_ghost'</span>)]</span>
-<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a>participant_metadata <span class="op">=</span> participant_metadata[(participant_metadata.diagnosis.isin([<span class="st">'CONTROL'</span>, <span class="st">'SCHZ'</span>])) <span class="op">&amp;</span></span>
+<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a>                                            (participant_metadata.T1w <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
+<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a>                                            (participant_metadata.rest <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
+<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a>                                            (participant_metadata.ghost_NoGhost <span class="op">==</span> <span class="st">'No_ghost'</span>)]</span>
+<span id="cb5-5"><a href="#cb5-5" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1857,9 +1857,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> bids.layout <span class="im">import</span> BIDSLayout</span>
-<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="im">from</span> bids.layout <span class="im">import</span> BIDSLayout</span>
+<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a></span>
+<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>)</span></code></pre>
 </div>
 <p>The pybids layout object indexes the BIDS folder. Indexing can take a
 really long time, especially if you have several subjects, modalities,
@@ -1869,9 +1869,9 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>layout.save(<span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span>
-<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>, database_path<span class="op">=</span><span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a>layout.save(<span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span>
+<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a></span>
+<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>, database_path<span class="op">=</span><span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span></code></pre>
 </div>
 <p>The pybids layout object also lets you query your BIDS dataset
 according to a number of parameters by using a <code>get_*()</code>
@@ -1880,7 +1880,7 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb9">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>layout.get_subjects()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a>layout.get_subjects()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1901,7 +1901,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb11">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>layout.get_modalities()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a>layout.get_modalities()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1912,11 +1912,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb13">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="co">#Task fMRI</span></span>
-<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(layout.get_tasks())</span>
-<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb13-4"><a href="#cb13-4" aria-hidden="true" tabindex="-1"></a><span class="co">#Data types (bold, brainmask, confounds, smoothwm, probtissue, warp...)</span></span>
-<span id="cb13-5"><a href="#cb13-5" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(layout.get_types())</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb13-1"><a href="#cb13-1" tabindex="-1"></a><span class="co">#Task fMRI</span></span>
+<span id="cb13-2"><a href="#cb13-2" tabindex="-1"></a><span class="bu">print</span>(layout.get_tasks())</span>
+<span id="cb13-3"><a href="#cb13-3" tabindex="-1"></a></span>
+<span id="cb13-4"><a href="#cb13-4" tabindex="-1"></a><span class="co">#Data types (bold, brainmask, confounds, smoothwm, probtissue, warp...)</span></span>
+<span id="cb13-5"><a href="#cb13-5" tabindex="-1"></a><span class="bu">print</span>(layout.get_types())</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1942,7 +1942,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a>layout.get_types(modality<span class="op">=</span><span class="st">'func'</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb15-1"><a href="#cb15-1" tabindex="-1"></a>layout.get_types(modality<span class="op">=</span><span class="st">'func'</span>)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1953,7 +1953,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb17">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a>layout.get(task<span class="op">=</span><span class="st">'rest'</span>, <span class="bu">type</span><span class="op">=</span><span class="st">'bold'</span>, extensions<span class="op">=</span><span class="st">'nii.gz'</span>, return_type<span class="op">=</span><span class="st">'file'</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb17-1"><a href="#cb17-1" tabindex="-1"></a>layout.get(task<span class="op">=</span><span class="st">'rest'</span>, <span class="bu">type</span><span class="op">=</span><span class="st">'bold'</span>, extensions<span class="op">=</span><span class="st">'nii.gz'</span>, return_type<span class="op">=</span><span class="st">'file'</span>)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1965,8 +1965,8 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb19">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a>df <span class="op">=</span> layout.as_data_frame()</span>
-<span id="cb19-2"><a href="#cb19-2" aria-hidden="true" tabindex="-1"></a>df.head()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb19-1"><a href="#cb19-1" tabindex="-1"></a>df <span class="op">=</span> layout.as_data_frame()</span>
+<span id="cb19-2"><a href="#cb19-2" tabindex="-1"></a>df.head()</span></code></pre>
 </div>
 <p><strong>OUTPUT:</strong></p>
 <table border="1" class="table dataframe">
@@ -2111,7 +2111,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-bids-derivatives"><p>Content from <a href="bids-derivatives.html">BIDS derivatives</a></p>
 <hr>
-<p>Last updated on 2024-02-18 |
+<p>Last updated on 2024-02-28 |
         
         <a href="https://github.com/carpentries-incubator/SDC-BIDS-IntroMRI/edit/main/episodes/bids-derivatives.md" 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>
@@ -2125,8 +2125,10 @@ <h2 class="card-header">Overview</h2>
 <div class="card-body">
 <div class="inner">
 <h3 class="card-title">Questions</h3>
-<ul><li>
-</li></ul>
+<ul>
+<li>What are BIDS Apps?</li>
+<li>What are containers?</li>
+</ul>
 </div>
 </div>
 </div>
@@ -2134,8 +2136,11 @@ <h3 class="card-title">Questions</h3>
 <div class="card-body">
 <div class="inner bordered">
 <h3 class="card-title">Objectives</h3>
-<ul><li>
-</li></ul>
+<ul>
+<li>Learn about neuroimaging applications using BIDS data
+structures</li>
+<li>Use neuroimaging applications through containers</li>
+</ul>
 </div>
 </div>
 </div>
@@ -2172,16 +2177,16 @@ <h3 class="card-title">Objectives</h3>
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">singularity</span> build mriqc-0.16.1.simg docker://poldracklab/mriqc:0.16.1<span class="kw">`</span></span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">singularity</span> build mriqc-0.16.1.simg docker://poldracklab/mriqc:0.16.1<span class="kw">`</span></span></code></pre>
 </div>
 <p>To run the container:</p>
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">singularity</span> run <span class="at">--cleanenv</span> <span class="dt">\</span></span>
-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>  <span class="at">-B</span> bids_folder:/data <span class="dt">\</span></span>
-<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>  mriqc-0.16.1.simg <span class="dt">\</span></span>
-<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>  /data /data/derivatives participant</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="ex">singularity</span> run <span class="at">--cleanenv</span> <span class="dt">\</span></span>
+<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a>  <span class="at">-B</span> bids_folder:/data <span class="dt">\</span></span>
+<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a>  mriqc-0.16.1.simg <span class="dt">\</span></span>
+<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a>  /data /data/derivatives participant</span></code></pre>
 </div>
 <div id="keypoints1" class="callout keypoints">
 <div class="callout-square">
@@ -2242,9 +2247,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/aio.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/aio.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/anatomy-of-nifti.html b/instructor/anatomy-of-nifti.html
index 4ed39da..122a45c 100644
--- a/instructor/anatomy-of-nifti.html
+++ b/instructor/anatomy-of-nifti.html
@@ -321,7 +321,7 @@ <h3 class="card-title">Objectives</h3>
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> nibabel <span class="im">as</span> nib</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="im">import</span> nibabel <span class="im">as</span> nib</span></code></pre>
 </div>
 <p>First, use the <code>load()</code> function to create a NiBabel image
 object from a NIfTI file. We’ll load in an example T1w image from the
@@ -329,7 +329,7 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>t1_img <span class="op">=</span> nib.load(<span class="st">"../data/dicom_examples/nii/0219191_mystudy-0219-1114_anat_ses-01_T1w_20190219111436_5.nii.gz"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>t1_img <span class="op">=</span> nib.load(<span class="st">"../data/dicom_examples/nii/0219191_mystudy-0219-1114_anat_ses-01_T1w_20190219111436_5.nii.gz"</span>)</span></code></pre>
 </div>
 <p>Loading in a NIfTI file with <code>NiBabel</code> gives us a special
 type of data object which encodes all the information in the file.Each
@@ -344,8 +344,8 @@ <h3 id="header-contains-metadata-about-the-image-such-as-image-dimensions-data-t
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>t1_hdr <span class="op">=</span> t1_img.header</span>
-<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(t1_hdr)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a>t1_hdr <span class="op">=</span> t1_img.header</span>
+<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="bu">print</span>(t1_hdr)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -406,7 +406,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb5">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>t1_hdr.keys()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a>t1_hdr.keys()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -471,7 +471,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>t1_hdr[<span class="st">'&lt;key_name&gt;'</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a>t1_hdr[<span class="st">'&lt;key_name&gt;'</span>]</span></code></pre>
 </div>
 <div id="extract-values-from-the-nifti-header" class="callout challenge">
 <div class="callout-square">
@@ -490,12 +490,12 @@ <h3 class="callout-title">Extract values from the NIfTI header<a class="anchor"
 <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" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>t1_hdr[<span class="st">'pixdim'</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a>t1_hdr[<span class="st">'pixdim'</span>]</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -517,8 +517,8 @@ <h3 id="data">2. Data<a class="anchor" aria-label="anchor" href="#data"></a></h3
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>t1_data <span class="op">=</span> t1_img.get_fdata()</span>
-<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a>t1_data</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a>t1_data <span class="op">=</span> t1_img.get_fdata()</span>
+<span id="cb10-2"><a href="#cb10-2" tabindex="-1"></a>t1_data</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -614,7 +614,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb12">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="bu">type</span>(t1_data)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1" tabindex="-1"></a><span class="bu">type</span>(t1_data)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -643,12 +643,12 @@ <h3 class="callout-title">Check out attributes of the array<a class="anchor" ari
 <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a>t1_data.ndim</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb14-1"><a href="#cb14-1" tabindex="-1"></a>t1_data.ndim</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -681,12 +681,12 @@ <h3 class="callout-title">Check out attributes of the array<em>(continued)</em><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb16">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a>t1_data.shape</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb16-1"><a href="#cb16-1" tabindex="-1"></a>t1_data.shape</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -706,7 +706,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb18">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb18-1"><a href="#cb18-1" aria-hidden="true" tabindex="-1"></a>t1_data.dtype</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb18-1"><a href="#cb18-1" tabindex="-1"></a>t1_data.dtype</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -721,9 +721,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb20">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> numpy <span class="im">as</span> np</span>
-<span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">min</span>(t1_data))</span>
-<span id="cb20-3"><a href="#cb20-3" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">max</span>(t1_data))</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb20-1"><a href="#cb20-1" tabindex="-1"></a><span class="im">import</span> numpy <span class="im">as</span> np</span>
+<span id="cb20-2"><a href="#cb20-2" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">min</span>(t1_data))</span>
+<span id="cb20-3"><a href="#cb20-3" tabindex="-1"></a><span class="bu">print</span>(np.<span class="bu">max</span>(t1_data))</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -741,7 +741,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb22">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a>t1_data[<span class="dv">9</span>, <span class="dv">19</span>, <span class="dv">2</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb22-1"><a href="#cb22-1" tabindex="-1"></a>t1_data[<span class="dv">9</span>, <span class="dv">19</span>, <span class="dv">2</span>]</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -766,7 +766,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb24-1"><a href="#cb24-1" aria-hidden="true" tabindex="-1"></a>x_slice <span class="op">=</span> t1_data[<span class="dv">9</span>, :, :]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb24-1"><a href="#cb24-1" tabindex="-1"></a>x_slice <span class="op">=</span> t1_data[<span class="dv">9</span>, :, :]</span></code></pre>
 </div>
 <p>This is similar to the indexing we did before to pull out a single
 voxel. However, instead of providing a value for each axis, the
@@ -789,12 +789,12 @@ <h3 class="callout-title">Slicing MRI data<a class="anchor" aria-label="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a>y_slice <span class="op">=</span> t1_data[:, <span class="dv">19</span>, :]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb25-1"><a href="#cb25-1" tabindex="-1"></a>y_slice <span class="op">=</span> t1_data[:, <span class="dv">19</span>, :]</span></code></pre>
 </div>
 </div>
 </div>
@@ -817,12 +817,12 @@ <h3 class="callout-title">Slicing MRI data<em>(continued)</em><a class="anchor"
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5">Show me the solution</h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb26">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb26-1"><a href="#cb26-1" aria-hidden="true" tabindex="-1"></a>z_slice <span class="op">=</span> t1_data[:, :, <span class="dv">2</span>]</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb26-1"><a href="#cb26-1" tabindex="-1"></a>z_slice <span class="op">=</span> t1_data[:, :, <span class="dv">2</span>]</span></code></pre>
 </div>
 </div>
 </div>
@@ -840,14 +840,14 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb27">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> matplotlib.pyplot <span class="im">as</span> plt</span>
-<span id="cb27-2"><a href="#cb27-2" aria-hidden="true" tabindex="-1"></a><span class="op">%</span>matplotlib inline</span>
-<span id="cb27-3"><a href="#cb27-3" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb27-4"><a href="#cb27-4" aria-hidden="true" tabindex="-1"></a>slices <span class="op">=</span> [x_slice, y_slice, z_slice]</span>
-<span id="cb27-5"><a href="#cb27-5" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb27-6"><a href="#cb27-6" aria-hidden="true" tabindex="-1"></a>fig, axes <span class="op">=</span> plt.subplots(<span class="dv">1</span>, <span class="bu">len</span>(slices))</span>
-<span id="cb27-7"><a href="#cb27-7" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> i, <span class="bu">slice</span> <span class="kw">in</span> <span class="bu">enumerate</span>(slices):</span>
-<span id="cb27-8"><a href="#cb27-8" aria-hidden="true" tabindex="-1"></a>    axes[i].imshow(<span class="bu">slice</span>.T, cmap<span class="op">=</span><span class="st">"gray"</span>, origin<span class="op">=</span><span class="st">"lower"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb27-1"><a href="#cb27-1" tabindex="-1"></a><span class="im">import</span> matplotlib.pyplot <span class="im">as</span> plt</span>
+<span id="cb27-2"><a href="#cb27-2" tabindex="-1"></a><span class="op">%</span>matplotlib inline</span>
+<span id="cb27-3"><a href="#cb27-3" tabindex="-1"></a></span>
+<span id="cb27-4"><a href="#cb27-4" tabindex="-1"></a>slices <span class="op">=</span> [x_slice, y_slice, z_slice]</span>
+<span id="cb27-5"><a href="#cb27-5" tabindex="-1"></a></span>
+<span id="cb27-6"><a href="#cb27-6" tabindex="-1"></a>fig, axes <span class="op">=</span> plt.subplots(<span class="dv">1</span>, <span class="bu">len</span>(slices))</span>
+<span id="cb27-7"><a href="#cb27-7" tabindex="-1"></a><span class="cf">for</span> i, <span class="bu">slice</span> <span class="kw">in</span> <span class="bu">enumerate</span>(slices):</span>
+<span id="cb27-8"><a href="#cb27-8" tabindex="-1"></a>    axes[i].imshow(<span class="bu">slice</span>.T, cmap<span class="op">=</span><span class="st">"gray"</span>, origin<span class="op">=</span><span class="st">"lower"</span>)</span></code></pre>
 </div>
 <p>Now, we’re going to step away from discussing our data and talk about
 the final important attribute of a NIfTI.</p>
@@ -860,8 +860,8 @@ <h3 id="affine-tells-the-position-of-the-image-array-data-in-a-reference-space">
 <div class="codewrapper sourceCode" id="cb28">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb28-1"><a href="#cb28-1" aria-hidden="true" tabindex="-1"></a>t1_affine <span class="op">=</span> t1_img.affine</span>
-<span id="cb28-2"><a href="#cb28-2" aria-hidden="true" tabindex="-1"></a>t1_affine</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb28-1"><a href="#cb28-1" tabindex="-1"></a>t1_affine <span class="op">=</span> t1_img.affine</span>
+<span id="cb28-2"><a href="#cb28-2" tabindex="-1"></a>t1_affine</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -993,9 +993,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/anatomy-of-nifti.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/anatomy-of-nifti.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/before-we-start.html b/instructor/before-we-start.html
index a26d430..95b7615 100644
--- a/instructor/before-we-start.html
+++ b/instructor/before-we-start.html
@@ -478,9 +478,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/before-we-start.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/before-we-start.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/bids-derivatives.html b/instructor/bids-derivatives.html
index d8f112f..3d96da8 100644
--- a/instructor/bids-derivatives.html
+++ b/instructor/bids-derivatives.html
@@ -260,7 +260,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>BIDS derivatives</h1>
-        <p>Last updated on 2024-02-18 |
+        <p>Last updated on 2024-02-28 |
         
         <a href="https://github.com/carpentries-incubator/SDC-BIDS-IntroMRI/edit/main/episodes/bids-derivatives.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -281,16 +281,19 @@ <h2 class="card-header">Overview</h2>
 <div class="card-body">
 <div class="inner">
 <h3 class="card-title">Questions</h3>
-<ul><li>
-</li></ul></div>
+<ul><li>What are BIDS Apps?</li>
+<li>What are containers?</li>
+</ul></div>
 </div>
 </div>
 <div class="col-md-8">
 <div class="card-body">
 <div class="inner bordered">
 <h3 class="card-title">Objectives</h3>
-<ul><li>
-</li></ul></div>
+<ul><li>Learn about neuroimaging applications using BIDS data
+structures</li>
+<li>Use neuroimaging applications through containers</li>
+</ul></div>
 </div>
 </div>
 </div>
@@ -318,16 +321,16 @@ <h3 class="card-title">Objectives</h3>
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">singularity</span> build mriqc-0.16.1.simg docker://poldracklab/mriqc:0.16.1<span class="kw">`</span></span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">singularity</span> build mriqc-0.16.1.simg docker://poldracklab/mriqc:0.16.1<span class="kw">`</span></span></code></pre>
 </div>
 <p>To run the container:</p>
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">singularity</span> run <span class="at">--cleanenv</span> <span class="dt">\</span></span>
-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>  <span class="at">-B</span> bids_folder:/data <span class="dt">\</span></span>
-<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>  mriqc-0.16.1.simg <span class="dt">\</span></span>
-<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>  /data /data/derivatives participant</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="ex">singularity</span> run <span class="at">--cleanenv</span> <span class="dt">\</span></span>
+<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a>  <span class="at">-B</span> bids_folder:/data <span class="dt">\</span></span>
+<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a>  mriqc-0.16.1.simg <span class="dt">\</span></span>
+<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a>  /data /data/derivatives participant</span></code></pre>
 </div>
 <div id="keypoints1" class="callout keypoints">
 <div class="callout-square">
@@ -401,9 +404,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/bids-derivatives.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/bids-derivatives.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/data-organization-bids.html b/instructor/data-organization-bids.html
index 606aa32..5ca06f8 100644
--- a/instructor/data-organization-bids.html
+++ b/instructor/data-organization-bids.html
@@ -403,9 +403,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/data-organization-bids.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/data-organization-bids.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/discuss.html b/instructor/discuss.html
index 70d797a..f10f00e 100644
--- a/instructor/discuss.html
+++ b/instructor/discuss.html
@@ -329,9 +329,9 @@ <h1>Discussion</h1>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/discuss.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/discuss.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/images.html b/instructor/images.html
index d8f33ce..10d67e8 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -390,9 +390,9 @@ <h3 id="bids-derivatives-figure-1">Figure 1</h3>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/images.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/images.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index b67b811..dbf53d6 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -349,6 +349,7 @@ <h3 id="getting-started">Getting Started<a class="anchor" aria-label="anchor" hr
  6. <a href="bids-derivatives.html">BIDS derivatives</a>
 </td>
 <td>
+What are BIDS Apps?<br>What are containers?
 </td>
 </tr><tr><td>
 <span class="visually-hidden">Duration: </span>03h 40m
@@ -369,18 +370,17 @@ <h3 id="getting-started">Getting Started<a class="anchor" aria-label="anchor" hr
 </h2>
 <hr class="half-width"><p>The Binder webpage for this lesson can be accessed by clicking the
 button below.</p>
-<p><a href="https://mybinder.org/v2/gh/carpentries-incubator/SDC-BIDS-IntroMRI/gh-pages?filepath=code%2F" class="external-link"><img src="https://mybinder.org/badge_logo.svg" class="figure">{alt=‘Binder’}</a></p>
+<p><a href="https://mybinder.org/v2/gh/carpentries-incubator/SDC-BIDS-IntroMRI/gh-pages?filepath=code%2F" class="external-link"><img src="https://mybinder.org/badge_logo.svg" alt="Binder" class="figure"></a></p>
 <p>Binder enables you to run the collection of Python notebooks found in
 the <code>code</code> folder. All of the software and data used in the
 lesson are pre-installed in a custom computational environment and no
 additional software needs to be installed locally.</p>
-<div id="binder-tips" class="callout callout">
+<div id="callout1" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
 </div>
-<div id="binder-tips" class="callout-inner">
-<h3 class="callout-title">Binder Tips<a class="anchor" aria-label="anchor" href="#binder-tips"></a>
-</h3>
+<div class="section level3 callout-title callout-inner">
+<h3 class="callout-title" id="binder-tips">Binder Tips<a class="anchor" aria-label="anchor" href="#binder-tips"></a></h3>
 <div class="callout-content">
 <p>If using Binder, please be aware that startup can take anywhere from
 30 seconds to 10 minutes, depending on your internet connection and how
@@ -414,7 +414,7 @@ <h3 id="install-python-packages">Install Python Packages<a class="anchor" aria-l
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pip</span> install nibabel nilearn pybids</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">pip</span> install nibabel nilearn pybids</span></code></pre>
 </div>
 </div>
 <div class="section level3">
@@ -429,7 +429,7 @@ <h3 id="install-dcm2niix">Install dcm2niix<a class="anchor" aria-label="anchor"
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">conda</span> install <span class="at">-c</span> conda-forge dcm2niix</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="ex">conda</span> install <span class="at">-c</span> conda-forge dcm2niix</span></code></pre>
 </div>
 </div>
 <div class="section level3">
@@ -443,7 +443,7 @@ <h3 id="install-datalad">Install DataLad<a class="anchor" aria-label="anchor" hr
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="ex">conda</span> install <span class="at">-c</span> conda-forge datalad</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="ex">conda</span> install <span class="at">-c</span> conda-forge datalad</span></code></pre>
 </div>
 </div>
 <div class="section level3">
@@ -454,9 +454,9 @@ <h3 id="obtain-lesson-materials">Obtain lesson materials<a class="anchor" aria-l
 <div class="codewrapper sourceCode" id="cb4">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> ~/Desktop/dc-mri/data</span>
-<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span>
-<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a><span class="ex">datalad</span> clone https://github.com/OpenNeuroDatasets/ds000030.git</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="fu">mkdir</span> ~/Desktop/dc-mri/data</span>
+<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span>
+<span id="cb4-3"><a href="#cb4-3" tabindex="-1"></a><span class="ex">datalad</span> clone https://github.com/OpenNeuroDatasets/ds000030.git</span></code></pre>
 </div>
 </div>
 </section><section id="launch-python-interface"><h2 class="section-heading">Launch Python interface<a class="anchor" aria-label="anchor" href="#launch-python-interface"></a>
@@ -514,7 +514,7 @@ <h4 class="accordion-header" id="headingSolution2">Unix shell</h4>
 <div class="codewrapper sourceCode" id="cb5">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span></code></pre>
 </div>
 </div>
 </div>
@@ -535,7 +535,7 @@ <h4 class="accordion-header" id="headingSolution3">Command Prompt (Windows)</h4>
 <div class="codewrapper sourceCode" id="cb6">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> /D %userprofile%<span class="dt">\D</span>esktop<span class="dt">\d</span>c-mri<span class="dt">\d</span>ata</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="bu">cd</span> /D %userprofile%<span class="dt">\D</span>esktop<span class="dt">\d</span>c-mri<span class="dt">\d</span>ata</span></code></pre>
 </div>
 </div>
 </div>
@@ -552,7 +552,7 @@ <h4 class="accordion-header" id="headingSolution4">Unix shell</h4>
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="ex">jupyter</span> notebook</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="ex">jupyter</span> notebook</span></code></pre>
 </div>
 </div>
 </div>
@@ -568,7 +568,7 @@ <h4 class="accordion-header" id="headingSolution5">Command Prompt (Windows)</h4>
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="ex">python</span> <span class="at">-m</span> notebook</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="ex">python</span> <span class="at">-m</span> notebook</span></code></pre>
 </div>
 </div>
 </div>
@@ -593,7 +593,7 @@ <h3 id="option-b-ipython-interpreter">Option B: IPython interpreter<a class="anc
 <div class="codewrapper sourceCode" id="cb9">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="ex">ipython</span></span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a><span class="ex">ipython</span></span></code></pre>
 </div>
 <p>  <!-- vertical spacer --></p>
 </div>
@@ -603,7 +603,7 @@ <h3 id="option-c-plain-vanilla-python-interpreter">Option C: plain-vanilla Pytho
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="ex">python</span></span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a><span class="ex">python</span></span></code></pre>
 </div>
 <p>If you are using <a href="https://gitforwindows.org" class="external-link">Git Bash on
 Windows</a>, you have to call Python <em>via</em>
@@ -611,7 +611,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <div class="codewrapper sourceCode" id="cb11">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="ex">winpty</span> python</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a><span class="ex">winpty</span> python</span></code></pre>
 </div>
 </div>
 </section></section></main><nav class="bottom-pagination mx-md-4" aria-label="Next Chapter"><!-- content for small screens --><div class="d-block d-sm-block d-md-none">
@@ -662,9 +662,9 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/index.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/index.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index 48936cf..cede477 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -363,9 +363,9 @@ <h1>Instructor Notes</h1>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/instructor-notes.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/instructor-notes.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/key-points.html b/instructor/key-points.html
index de8a5a6..0ae4aa3 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -382,9 +382,9 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/key-points.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/key-points.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/open-mri-datasets.html b/instructor/open-mri-datasets.html
index badc440..12b0c59 100644
--- a/instructor/open-mri-datasets.html
+++ b/instructor/open-mri-datasets.html
@@ -323,18 +323,18 @@ <h3 id="datalad">DataLad<a class="anchor" aria-label="anchor" href="#datalad"></
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="ex">datalad</span> install ///openneuro/ds000030</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span>
+<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="ex">datalad</span> install ///openneuro/ds000030</span></code></pre>
 </div>
 <p>Let’s take a look at the <code>participants.tsv</code> file to see
 what the demographics for this dataset look like.</p>
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>participant_metadata <span class="op">=</span> pd.read_csv(<span class="st">'../data/ds000030/participants.tsv'</span>, sep<span class="op">=</span><span class="st">'</span><span class="ch">\t</span><span class="st">'</span>)</span>
-<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>participant_metadata</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
+<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a></span>
+<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a>participant_metadata <span class="op">=</span> pd.read_csv(<span class="st">'../data/ds000030/participants.tsv'</span>, sep<span class="op">=</span><span class="st">'</span><span class="ch">\t</span><span class="st">'</span>)</span>
+<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a>participant_metadata</span></code></pre>
 </div>
 <p><strong>OUTPUT:</strong></p>
 <table border="1" class="table dataframe"><thead><tr style="text-align: right;"><th>
@@ -646,7 +646,7 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -663,11 +663,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb5">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>participant_metadata <span class="op">=</span> participant_metadata[(participant_metadata.diagnosis.isin([<span class="st">'CONTROL'</span>, <span class="st">'SCHZ'</span>])) <span class="op">&amp;</span></span>
-<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>                                            (participant_metadata.T1w <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
-<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>                                            (participant_metadata.rest <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
-<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>                                            (participant_metadata.ghost_NoGhost <span class="op">==</span> <span class="st">'No_ghost'</span>)]</span>
-<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a>participant_metadata <span class="op">=</span> participant_metadata[(participant_metadata.diagnosis.isin([<span class="st">'CONTROL'</span>, <span class="st">'SCHZ'</span>])) <span class="op">&amp;</span></span>
+<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a>                                            (participant_metadata.T1w <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
+<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a>                                            (participant_metadata.rest <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
+<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a>                                            (participant_metadata.ghost_NoGhost <span class="op">==</span> <span class="st">'No_ghost'</span>)]</span>
+<span id="cb5-5"><a href="#cb5-5" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -687,9 +687,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> bids.layout <span class="im">import</span> BIDSLayout</span>
-<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="im">from</span> bids.layout <span class="im">import</span> BIDSLayout</span>
+<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a></span>
+<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>)</span></code></pre>
 </div>
 <p>The pybids layout object indexes the BIDS folder. Indexing can take a
 really long time, especially if you have several subjects, modalities,
@@ -699,9 +699,9 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>layout.save(<span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span>
-<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>, database_path<span class="op">=</span><span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a>layout.save(<span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span>
+<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a></span>
+<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>, database_path<span class="op">=</span><span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span></code></pre>
 </div>
 <p>The pybids layout object also lets you query your BIDS dataset
 according to a number of parameters by using a <code>get_*()</code>
@@ -710,7 +710,7 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb9">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>layout.get_subjects()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a>layout.get_subjects()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -731,7 +731,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb11">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>layout.get_modalities()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a>layout.get_modalities()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -742,11 +742,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb13">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="co">#Task fMRI</span></span>
-<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(layout.get_tasks())</span>
-<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb13-4"><a href="#cb13-4" aria-hidden="true" tabindex="-1"></a><span class="co">#Data types (bold, brainmask, confounds, smoothwm, probtissue, warp...)</span></span>
-<span id="cb13-5"><a href="#cb13-5" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(layout.get_types())</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb13-1"><a href="#cb13-1" tabindex="-1"></a><span class="co">#Task fMRI</span></span>
+<span id="cb13-2"><a href="#cb13-2" tabindex="-1"></a><span class="bu">print</span>(layout.get_tasks())</span>
+<span id="cb13-3"><a href="#cb13-3" tabindex="-1"></a></span>
+<span id="cb13-4"><a href="#cb13-4" tabindex="-1"></a><span class="co">#Data types (bold, brainmask, confounds, smoothwm, probtissue, warp...)</span></span>
+<span id="cb13-5"><a href="#cb13-5" tabindex="-1"></a><span class="bu">print</span>(layout.get_types())</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -772,7 +772,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a>layout.get_types(modality<span class="op">=</span><span class="st">'func'</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb15-1"><a href="#cb15-1" tabindex="-1"></a>layout.get_types(modality<span class="op">=</span><span class="st">'func'</span>)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -783,7 +783,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb17">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a>layout.get(task<span class="op">=</span><span class="st">'rest'</span>, <span class="bu">type</span><span class="op">=</span><span class="st">'bold'</span>, extensions<span class="op">=</span><span class="st">'nii.gz'</span>, return_type<span class="op">=</span><span class="st">'file'</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb17-1"><a href="#cb17-1" tabindex="-1"></a>layout.get(task<span class="op">=</span><span class="st">'rest'</span>, <span class="bu">type</span><span class="op">=</span><span class="st">'bold'</span>, extensions<span class="op">=</span><span class="st">'nii.gz'</span>, return_type<span class="op">=</span><span class="st">'file'</span>)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -795,8 +795,8 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb19">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a>df <span class="op">=</span> layout.as_data_frame()</span>
-<span id="cb19-2"><a href="#cb19-2" aria-hidden="true" tabindex="-1"></a>df.head()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb19-1"><a href="#cb19-1" tabindex="-1"></a>df <span class="op">=</span> layout.as_data_frame()</span>
+<span id="cb19-2"><a href="#cb19-2" tabindex="-1"></a>df.head()</span></code></pre>
 </div>
 <p><strong>OUTPUT:</strong></p>
 <table border="1" class="table dataframe"><thead><tr style="text-align: right;"><th>
@@ -978,9 +978,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/open-mri-datasets.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/open-mri-datasets.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index f6fd36a..765294d 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -286,9 +286,9 @@ <h1>Learner Profiles</h1>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/profiles.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/profiles.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index 09ca017..18368e3 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -329,9 +329,9 @@ <h1>Glossary</h1>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/reference.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/reference.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/instructor/scanner-to-computer.html b/instructor/scanner-to-computer.html
index 7fe3fa4..fa0d984 100644
--- a/instructor/scanner-to-computer.html
+++ b/instructor/scanner-to-computer.html
@@ -360,11 +360,11 @@ <h3 id="diffusion">Diffusion<a class="anchor" aria-label="anchor" href="#diffusi
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">wget</span> https://zenodo.org/record/3677090/files/0219191_mystudy-0219-1114.tar.gz <span class="at">-O</span> ../data/0219191_mystudy-0219-1114.tar.gz</span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples</span>
-<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">tar</span> <span class="at">-xvzf</span> ../data/0219191_mystudy-0219-1114.tar.gz <span class="at">-C</span> ../data/dicom_examples</span>
-<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">gzip</span> <span class="at">-d</span> ../data/dicom_examples/0219191_mystudy-0219-1114/dcm/<span class="pp">*</span>dcm.gz</span>
-<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">rm</span> ../data/0219191_mystudy-0219-1114.tar.gz</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">wget</span> https://zenodo.org/record/3677090/files/0219191_mystudy-0219-1114.tar.gz <span class="at">-O</span> ../data/0219191_mystudy-0219-1114.tar.gz</span>
+<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples</span>
+<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="fu">tar</span> <span class="at">-xvzf</span> ../data/0219191_mystudy-0219-1114.tar.gz <span class="at">-C</span> ../data/dicom_examples</span>
+<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="fu">gzip</span> <span class="at">-d</span> ../data/dicom_examples/0219191_mystudy-0219-1114/dcm/<span class="pp">*</span>dcm.gz</span>
+<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="fu">rm</span> ../data/0219191_mystudy-0219-1114.tar.gz</span></code></pre>
 </div>
 <figure><img src="../fig/dicom_to_nifti.png" alt="dicom-to-nifti" class="figure mx-auto d-block"></figure><p>NIfTI is one of the most ubiquitous file formats for storing
 neuroimaging data. If you’re interested in learning more about NIfTI
@@ -376,7 +376,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-help</span></span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-help</span></span></code></pre>
 </div>
 <div id="converting-dicom-to-nifti" class="callout challenge">
 <div class="callout-square">
@@ -395,13 +395,13 @@ <h3 class="callout-title">Converting DICOM to NIfTI<a class="anchor" aria-label=
 <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">
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples/nii</span>
-<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-z</span> y <span class="at">-o</span> ../data/dicom_examples/nii ../data/dicom_examples/0219191_mystudy-0219-1114/</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples/nii</span>
+<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-z</span> y <span class="at">-o</span> ../data/dicom_examples/nii ../data/dicom_examples/0219191_mystudy-0219-1114/</span></code></pre>
 </div>
 </div>
 </div>
@@ -476,9 +476,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/scanner-to-computer.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/instructor/scanner-to-computer.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index 3451d03..d8e7094 100644
--- a/key-points.html
+++ b/key-points.html
@@ -380,9 +380,9 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/key-points.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/key-points.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/md5sum.txt b/md5sum.txt
index 866f359..c167c55 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -8,7 +8,7 @@
 "episodes/anatomy-of-nifti.md" "b305edc5b76d6aa7697c2046894c7a4e" "site/built/anatomy-of-nifti.md" "2024-02-18"
 "episodes/data-organization-bids.md" "3c6204f70909b4a8b759d1b425b7ae33" "site/built/data-organization-bids.md" "2024-02-18"
 "episodes/open-mri-datasets.md" "d1328f9baba7d4b77437580c9de91a33" "site/built/open-mri-datasets.md" "2024-02-18"
-"episodes/bids-derivatives.md" "62c106f26adc9e9584f418ed3b869854" "site/built/bids-derivatives.md" "2024-02-18"
+"episodes/bids-derivatives.md" "3d6954c0364237d1adbd1b64b489e9b0" "site/built/bids-derivatives.md" "2024-02-28"
 "instructors/instructor-notes.md" "a59fd3b94c07c3fe3218c054a0f03277" "site/built/instructor-notes.md" "2024-02-18"
 "learners/discuss.md" "2758e2e5abd231d82d25c6453d8abbc6" "site/built/discuss.md" "2024-02-18"
 "learners/reference.md" "28853696c21dd22dfb883e9c241e95fb" "site/built/reference.md" "2024-02-18"
diff --git a/open-mri-datasets.html b/open-mri-datasets.html
index 7a609cc..85d7dc2 100644
--- a/open-mri-datasets.html
+++ b/open-mri-datasets.html
@@ -321,18 +321,18 @@ <h3 id="datalad">DataLad<a class="anchor" aria-label="anchor" href="#datalad"></
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="ex">datalad</span> install ///openneuro/ds000030</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="bu">cd</span> ~/Desktop/dc-mri/data</span>
+<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="ex">datalad</span> install ///openneuro/ds000030</span></code></pre>
 </div>
 <p>Let’s take a look at the <code>participants.tsv</code> file to see
 what the demographics for this dataset look like.</p>
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>participant_metadata <span class="op">=</span> pd.read_csv(<span class="st">'../data/ds000030/participants.tsv'</span>, sep<span class="op">=</span><span class="st">'</span><span class="ch">\t</span><span class="st">'</span>)</span>
-<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>participant_metadata</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
+<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a></span>
+<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a>participant_metadata <span class="op">=</span> pd.read_csv(<span class="st">'../data/ds000030/participants.tsv'</span>, sep<span class="op">=</span><span class="st">'</span><span class="ch">\t</span><span class="st">'</span>)</span>
+<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a>participant_metadata</span></code></pre>
 </div>
 <p><strong>OUTPUT:</strong></p>
 <table border="1" class="table dataframe"><thead><tr style="text-align: right;"><th>
@@ -644,7 +644,7 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -661,11 +661,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb5">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>participant_metadata <span class="op">=</span> participant_metadata[(participant_metadata.diagnosis.isin([<span class="st">'CONTROL'</span>, <span class="st">'SCHZ'</span>])) <span class="op">&amp;</span></span>
-<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>                                            (participant_metadata.T1w <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
-<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>                                            (participant_metadata.rest <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
-<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>                                            (participant_metadata.ghost_NoGhost <span class="op">==</span> <span class="st">'No_ghost'</span>)]</span>
-<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a>participant_metadata <span class="op">=</span> participant_metadata[(participant_metadata.diagnosis.isin([<span class="st">'CONTROL'</span>, <span class="st">'SCHZ'</span>])) <span class="op">&amp;</span></span>
+<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a>                                            (participant_metadata.T1w <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
+<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a>                                            (participant_metadata.rest <span class="op">==</span> <span class="dv">1</span>) <span class="op">&amp;</span></span>
+<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a>                                            (participant_metadata.ghost_NoGhost <span class="op">==</span> <span class="st">'No_ghost'</span>)]</span>
+<span id="cb5-5"><a href="#cb5-5" tabindex="-1"></a>participant_metadata[<span class="st">'diagnosis'</span>].unique()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -685,9 +685,9 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb7">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> bids.layout <span class="im">import</span> BIDSLayout</span>
-<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="im">from</span> bids.layout <span class="im">import</span> BIDSLayout</span>
+<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a></span>
+<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>)</span></code></pre>
 </div>
 <p>The pybids layout object indexes the BIDS folder. Indexing can take a
 really long time, especially if you have several subjects, modalities,
@@ -697,9 +697,9 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>layout.save(<span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span>
-<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>, database_path<span class="op">=</span><span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a>layout.save(<span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span>
+<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a></span>
+<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a>layout <span class="op">=</span> BIDSLayout(<span class="st">"~/Desktop/dc-mri/data/ds000030"</span>, database_path<span class="op">=</span><span class="st">"~/Desktop/dc-mri/data/ds000030/.db"</span>)</span></code></pre>
 </div>
 <p>The pybids layout object also lets you query your BIDS dataset
 according to a number of parameters by using a <code>get_*()</code>
@@ -708,7 +708,7 @@ <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb9">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>layout.get_subjects()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a>layout.get_subjects()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -729,7 +729,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb11">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>layout.get_modalities()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a>layout.get_modalities()</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -740,11 +740,11 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb13">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="co">#Task fMRI</span></span>
-<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(layout.get_tasks())</span>
-<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb13-4"><a href="#cb13-4" aria-hidden="true" tabindex="-1"></a><span class="co">#Data types (bold, brainmask, confounds, smoothwm, probtissue, warp...)</span></span>
-<span id="cb13-5"><a href="#cb13-5" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(layout.get_types())</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb13-1"><a href="#cb13-1" tabindex="-1"></a><span class="co">#Task fMRI</span></span>
+<span id="cb13-2"><a href="#cb13-2" tabindex="-1"></a><span class="bu">print</span>(layout.get_tasks())</span>
+<span id="cb13-3"><a href="#cb13-3" tabindex="-1"></a></span>
+<span id="cb13-4"><a href="#cb13-4" tabindex="-1"></a><span class="co">#Data types (bold, brainmask, confounds, smoothwm, probtissue, warp...)</span></span>
+<span id="cb13-5"><a href="#cb13-5" tabindex="-1"></a><span class="bu">print</span>(layout.get_types())</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -770,7 +770,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a>layout.get_types(modality<span class="op">=</span><span class="st">'func'</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb15-1"><a href="#cb15-1" tabindex="-1"></a>layout.get_types(modality<span class="op">=</span><span class="st">'func'</span>)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -781,7 +781,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb17">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a>layout.get(task<span class="op">=</span><span class="st">'rest'</span>, <span class="bu">type</span><span class="op">=</span><span class="st">'bold'</span>, extensions<span class="op">=</span><span class="st">'nii.gz'</span>, return_type<span class="op">=</span><span class="st">'file'</span>)</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb17-1"><a href="#cb17-1" tabindex="-1"></a>layout.get(task<span class="op">=</span><span class="st">'rest'</span>, <span class="bu">type</span><span class="op">=</span><span class="st">'bold'</span>, extensions<span class="op">=</span><span class="st">'nii.gz'</span>, return_type<span class="op">=</span><span class="st">'file'</span>)</span></code></pre>
 </div>
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -793,8 +793,8 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <div class="codewrapper sourceCode" id="cb19">
 <h3 class="code-label">PYTHON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a>df <span class="op">=</span> layout.as_data_frame()</span>
-<span id="cb19-2"><a href="#cb19-2" aria-hidden="true" tabindex="-1"></a>df.head()</span></code></pre>
+<pre class="sourceCode python" tabindex="0"><code class="sourceCode python"><span id="cb19-1"><a href="#cb19-1" tabindex="-1"></a>df <span class="op">=</span> layout.as_data_frame()</span>
+<span id="cb19-2"><a href="#cb19-2" tabindex="-1"></a>df.head()</span></code></pre>
 </div>
 <p><strong>OUTPUT:</strong></p>
 <table border="1" class="table dataframe"><thead><tr style="text-align: right;"><th>
@@ -976,9 +976,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/open-mri-datasets.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/open-mri-datasets.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index 5a93192..8606754 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,6 +1,6 @@
-pandoc: 2.19.2
+pandoc: 3.1.11
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-02-27T00:29Z
+last_built: 2024-02-28T23:14Z
 
diff --git a/profiles.html b/profiles.html
index a781e7d..b61be22 100644
--- a/profiles.html
+++ b/profiles.html
@@ -286,9 +286,9 @@ <h1>Learner Profiles</h1>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/profiles.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/profiles.html",
-  "dateCreated": "2024-02-18",
-  "dateModified": "2024-02-27",
-  "datePublished": "2024-02-27"
+  "dateCreated": "2024-02-28",
+  "dateModified": "2024-02-28",
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index 8532bed..c93d441 100644
--- a/reference.html
+++ b/reference.html
@@ -327,9 +327,9 @@ <h1>Glossary</h1>
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/reference.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/reference.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>
diff --git a/scanner-to-computer.html b/scanner-to-computer.html
index 320d73a..7ef9dfe 100644
--- a/scanner-to-computer.html
+++ b/scanner-to-computer.html
@@ -358,11 +358,11 @@ <h3 id="diffusion">Diffusion<a class="anchor" aria-label="anchor" href="#diffusi
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">wget</span> https://zenodo.org/record/3677090/files/0219191_mystudy-0219-1114.tar.gz <span class="at">-O</span> ../data/0219191_mystudy-0219-1114.tar.gz</span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples</span>
-<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">tar</span> <span class="at">-xvzf</span> ../data/0219191_mystudy-0219-1114.tar.gz <span class="at">-C</span> ../data/dicom_examples</span>
-<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">gzip</span> <span class="at">-d</span> ../data/dicom_examples/0219191_mystudy-0219-1114/dcm/<span class="pp">*</span>dcm.gz</span>
-<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">rm</span> ../data/0219191_mystudy-0219-1114.tar.gz</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">wget</span> https://zenodo.org/record/3677090/files/0219191_mystudy-0219-1114.tar.gz <span class="at">-O</span> ../data/0219191_mystudy-0219-1114.tar.gz</span>
+<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples</span>
+<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="fu">tar</span> <span class="at">-xvzf</span> ../data/0219191_mystudy-0219-1114.tar.gz <span class="at">-C</span> ../data/dicom_examples</span>
+<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="fu">gzip</span> <span class="at">-d</span> ../data/dicom_examples/0219191_mystudy-0219-1114/dcm/<span class="pp">*</span>dcm.gz</span>
+<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="fu">rm</span> ../data/0219191_mystudy-0219-1114.tar.gz</span></code></pre>
 </div>
 <figure><img src="fig/dicom_to_nifti.png" alt="dicom-to-nifti" class="figure mx-auto d-block"></figure><p>NIfTI is one of the most ubiquitous file formats for storing
 neuroimaging data. If you’re interested in learning more about NIfTI
@@ -374,7 +374,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-help</span></span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-help</span></span></code></pre>
 </div>
 <div id="converting-dicom-to-nifti" class="callout challenge">
 <div class="callout-square">
@@ -393,13 +393,13 @@ <h3 class="callout-title">Converting DICOM to NIfTI<a class="anchor" aria-label=
 <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">
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples/nii</span>
-<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-z</span> y <span class="at">-o</span> ../data/dicom_examples/nii ../data/dicom_examples/0219191_mystudy-0219-1114/</span></code></pre>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> ../data/dicom_examples/nii</span>
+<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="ex">dcm2niix</span> <span class="at">-z</span> y <span class="at">-o</span> ../data/dicom_examples/nii ../data/dicom_examples/0219191_mystudy-0219-1114/</span></code></pre>
 </div>
 </div>
 </div>
@@ -474,9 +474,9 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "creativeWorkStatus": "active",
   "url": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/scanner-to-computer.html",
   "identifier": "https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/scanner-to-computer.html",
-  "dateCreated": "2024-02-18",
+  "dateCreated": "2024-02-28",
   "dateModified": "2024-02-18",
-  "datePublished": "2024-02-27"
+  "datePublished": "2024-02-28"
 }
 
   </script><script>