deploy: 005e96a

Artifacts.html

@@ -418,6 +418,7 @@ <h2> Contents </h2>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#introduction">Introduction</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#artifact-comparison">Artifact Comparison</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#displacement-artifacts">Displacement Artifacts</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#motion-and-flow-artifacts">Motion and Flow Artifacts</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#simulations-of-artifacts">Simulations of Artifacts</a></li>
 </ul>
             </nav>
@@ -497,7 +498,7 @@ <h2>Artifact Comparison<a class="headerlink" href="#artifact-comparison" title="
 <td><p>Signal loss around magnetic suscpetibility differences (e.g. implants, air)</p></td>
 <td><p>N/A</p></td>
 </tr>
-<tr class="row-odd"><td><p>Slice Misregistration</p></td>
+<tr class="row-odd"><td><p>Slice Displacement</p></td>
 <td><p>Slice shifting due to chemical shift or off-resonance</p></td>
 <td><p>N/A</p></td>
 </tr>
@@ -532,6 +533,15 @@ <h2>Displacement Artifacts<a class="headerlink" href="#displacement-artifacts" t
 \[\Delta_{SS} = \frac{\Delta f}{BW_{rf}} \Delta_z\]</div>
 <p>where <span class="math notranslate nohighlight">\(BW_{rf}\)</span> is the slice select pulse bandwidth.</p>
 </section>
+<section id="motion-and-flow-artifacts">
+<h2>Motion and Flow Artifacts<a class="headerlink" href="#motion-and-flow-artifacts" title="Permalink to this heading">#</a></h2>
+<p>Motion, including flow, can result in artifacts in MRI if it leads to inconsistency in the data.</p>
+<p>Periodic motion such as breathing, heart beating, and pulsatile flow will lead to distinct ghosting artifacts in the phase encoding direction.  The location of ghosting artifacts in sequential phase encoding, will be at predictable intervals in the phase encoding direction:</p>
+<div class="math notranslate nohighlight">
+\[\Delta_{PE} = \frac{TR}{T_{motion}} FOV_{PE}\]</div>
+<p>where <span class="math notranslate nohighlight">\(T_{motion}\)</span> is the period of the motion (e.g. <span class="math notranslate nohighlight">\(T_{motion} = 1 s\)</span> for a heart rate of 60 beats per minute ).</p>
+<p>Incoherent or more random motion such as irregular breathing, arrhytthmias, coughing, bulk motion will lead to more diffuse ghosting artifacts.</p>
+</section>
 <section id="simulations-of-artifacts">
 <h2>Simulations of Artifacts<a class="headerlink" href="#simulations-of-artifacts" title="Permalink to this heading">#</a></h2>
 <div class="cell docutils container">
@@ -783,6 +793,7 @@ <h2>Simulations of Artifacts<a class="headerlink" href="#simulations-of-artifact
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#introduction">Introduction</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#artifact-comparison">Artifact Comparison</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#displacement-artifacts">Displacement Artifacts</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#motion-and-flow-artifacts">Motion and Flow Artifacts</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#simulations-of-artifacts">Simulations of Artifacts</a></li>
 </ul>
   </nav></div>

MRI Contrast.html

@@ -484,6 +484,7 @@ <h2>Learning Goals<a class="headerlink" href="#learning-goals" title="Permalink
 <li><p>Describe how T1, T2, and proton density weighted images are formed</p></li>
 <li><p>Describe how inversion recovery works</p></li>
 <li><p>Describe how Gd-based contrast agents work</p></li>
+<li><p>Describe how fat/water imaging works</p></li>
 <li><p>Identify various image contrasts</p></li>
 </ul>
 </li>
@@ -1143,9 +1144,9 @@ <h2>Fat/Water Imaging<a class="headerlink" href="#fat-water-imaging" title="Perm
 <div class="math notranslate nohighlight">
 \[ S(TE_{out-of-phase}) = S_{water} - S_{fat}\]</div>
 <div class="math notranslate nohighlight">
-\[ S_{water} = \frac{S(TE_{in-phase}) + S(TE_{out-of-phase})}{2}\]</div>
+\[ \hat S_{water} = S(TE_{in-phase}) + S(TE_{out-of-phase})\]</div>
 <div class="math notranslate nohighlight">
-\[ S_{fat} = \frac{S(TE_{in-phase}) - S(TE_{out-of-phase})}{2}\]</div>
+\[ \hat S_{fat} = S(TE_{in-phase}) - S(TE_{out-of-phase})\]</div>
 <p>In reality, additional corrections are required to account for off-resonance, <span class="math notranslate nohighlight">\(\Delta f_r(\vec r)\)</span>, and more advanced methods also use a multi-peak model accounting for the various chemical shifts in fatty tissue.</p>
 </section>
 <section id="image-contrast-examples">

_sources/Artifacts.ipynb

@@ -63,7 +63,7 @@
     "| Motion/Flow | Copies or \"Ghosts\" of image regions that are changing due to motion or flow | Phase encoding |\n",
     "| Displacement/Distortion | Shifts in location due to chemical shift (fat) and off-resonance (e.g. magnetic susceptibility differences) |  Frequency encoding (2DFT), Phase encoding (EPI) |\n",
     "| T2* | Signal loss around magnetic suscpetibility differences (e.g. implants, air) | N/A |\n",
-    "|  Slice Misregistration | Slice shifting due to chemical shift or off-resonance | N/A | \n",
+    "|  Slice Displacement | Slice shifting due to chemical shift or off-resonance | N/A | \n",
     "| Dielectric Shading | Shading across entire image, particularly large FOV, higher B0 | N/A |\n",
     "| Boundary Artifacts | Artificial dark lines at tissue boundaries due to inversion or chemical shift | N/A |\n",
     "| Gradient non-linearity | Distortion of subject, particularly near edges of large FOV | N/A |"
@@ -96,6 +96,23 @@
     "where $BW_{rf}$ is the slice select pulse bandwidth."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Motion and Flow Artifacts\n",
+    "\n",
+    "Motion, including flow, can result in artifacts in MRI if it leads to inconsistency in the data.\n",
+    "\n",
+    "Periodic motion such as breathing, heart beating, and pulsatile flow will lead to distinct ghosting artifacts in the phase encoding direction.  The location of ghosting artifacts in sequential phase encoding, will be at predictable intervals in the phase encoding direction:\n",
+    "\n",
+    "$$\\Delta_{PE} = \\frac{TR}{T_{motion}} FOV_{PE}$$\n",
+    "\n",
+    "where $T_{motion}$ is the period of the motion (e.g. $T_{motion} = 1 s$ for a heart rate of 60 beats per minute ).\n",
+    "\n",
+    "Incoherent or more random motion such as irregular breathing, arrhytthmias, coughing, bulk motion will lead to more diffuse ghosting artifacts."
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

_sources/MRI Contrast.ipynb

@@ -47,6 +47,7 @@
     "    * Describe how T1, T2, and proton density weighted images are formed\n",
     "    * Describe how inversion recovery works\n",
     "    * Describe how Gd-based contrast agents work\n",
+    "    * Describe how fat/water imaging works\n",
     "    * Identify various image contrasts\n",
     "1. Manipulate MRI sequence parameters to improve performance\n",
     "    * Choose flip angle, TE, TR, and TI for desired contrast"
@@ -826,9 +827,9 @@
     "\n",
     "$$ S(TE_{out-of-phase}) = S_{water} - S_{fat}$$\n",
     "\n",
-    "$$ S_{water} = \\frac{S(TE_{in-phase}) + S(TE_{out-of-phase})}{2}$$\n",
+    "$$ \\hat S_{water} = S(TE_{in-phase}) + S(TE_{out-of-phase})$$\n",
     "\n",
-    "$$ S_{fat} = \\frac{S(TE_{in-phase}) - S(TE_{out-of-phase})}{2}$$\n",
+    "$$ \\hat S_{fat} = S(TE_{in-phase}) - S(TE_{out-of-phase})$$\n",
     "\n",
     "In reality, additional corrections are required to account for off-resonance, $\\Delta f_r(\\vec r)$, and more advanced methods also use a multi-peak model accounting for the various chemical shifts in fatty tissue."
    ]