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Advanced/advanced.html

@@ -114,6 +114,14 @@
             <li class="nav-item" data-level="2"><a href="#manual-subvolume" class="nav-link">Manual Subvolume</a>
               <ul class="nav flex-column">
               </ul>
+            </li>
+            <li class="nav-item" data-level="2"><a href="#invert-zte" class="nav-link">Invert ZTE</a>
+              <ul class="nav flex-column">
+              </ul>
+            </li>
+            <li class="nav-item" data-level="2"><a href="#petra-conversion" class="nav-link">PETRA conversion</a>
+              <ul class="nav flex-column">
+              </ul>
             </li>
               </ul>
             </li>
@@ -145,6 +153,10 @@ <h2 id="force-using-blender-for-constructive-solid-geometry">Force using Blender
 <p>While pycork seems to do a great replacement, we identified that in some instances when using the subvolume feature there was a crash in the low pycork library. Forcing using Blender instead can help to run those special cases.</p>
 <h2 id="manual-subvolume">Manual Subvolume</h2>
 <p>This feature is intended to give a bit more control for scenarios where the trajectory is regions where the skin mask may cause some issues, especially in targets near the back of the head. For most targets, there is no need to make any adjustments, but we have spotted a few cases (i.e., EEG-P7 location) in which the skin mask of the back of the head was pushing the whole domain and causing issues to place correctly the transducer. For these scenarios, adjusting a subvolume to extract for the simulations can mitigate these issues. This can also help to reduce image size for high-resolution cases.</p>
+<h2 id="invert-zte">Invert ZTE</h2>
+<p>In GE scanners, the oZTEo produces inverted MR images and can't be disabled. While we recommend using 3dRadial-based sequences for ZTE scans, 3dRadial may not be available in all scanners. If oZTEo is used, please activate this new option, otherwise an error will occur during the processing.</p>
+<h2 id="petra-conversion">PETRA conversion</h2>
+<p>The number of bins (default of 2) and minimal distance of bins (default to 50) are now configurable. This helps to match the functionality of the UCL's <a href="https://github.com/ucl-bug/petra-to-ct" target="_blank">petra-to-ct</a> tool. Adjust this if the PETRA conversion is not selecting correctly the bone region. There is also an option to create the histogram as done in the UCL's tool.</p>
 <h1 id="transcranial-ultrasound">Transcranial Ultrasound</h1>
 <p><img src="advanced-3.png" height=250px></p>
 <h2 id="ctx-500-correction">CTX-500 Correction</h2>

index.html

@@ -252,5 +252,5 @@ <h4 class="modal-title" id="keyboardModalLabel">Keyboard Shortcuts</h4>
 
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 MkDocs version : 1.4.2
-Build Date UTC : 2024-08-24 18:33:02.425713+00:00
+Build Date UTC : 2024-08-31 04:08:14.919770+00:00
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pipeline/pipeline.html

@@ -423,7 +423,7 @@ <h3 id="3ci-ctx_250-ctx_500-and-dpx_500">3.c.i - CTX_250, CTX_500 and DPX_500</h
 <p>The results window will show two orthogonal views of normalized acoustic intensity. The intensity in the skin and skull regions is masked out (it can be visualized later in those regions in step 3). In this step, the main goal is to ensure a correct spatial focusing on the target. In the example, a shift of 5 mm of the focal spot towards the transducer can be observed. This shift can be corrected by adding 5 mm in the TPO Distance input (in the example, we adjust to 52.5 mm). </p>
 <p>Also, there is a small lateral shift in the negative "Y" direction. This can be corrected with the "Mechanical" adjustment controls (in this example we adjust +1mm in the Y direction). </p>
 <p>After running a first pass of simulations in Step 2, a button action is available to calculate the distance from the target to the center of mass of the focal spot at -3dB and suggest applying the required mechanical corrections in X and Y directions. This action should help to minimize the number of iterations in simulations looking to ensure the focal spot is aligned in the X and Y directions to the intended target.</p>
-<p>The GUI shows a label with the "Distance target to FLHM center [X, Y, Z] (mm)" that helps to perform adjustments with mechanical  and steering adjustements.</p>
+<p>The GUI shows a label with the "Distance target to FLHM center [X, Y, Z] (mm)" that helps to perform adjustments with mechanical  and steering corrections.</p>
 <p>Please note that in the simulation domain, X, Y and Z are not mapped to subject coordinates. However, at the end of the simulations, there will be a report in which direction in the T1W space this adjustment translates. </p>
 <p>After making the adjustments, the simulation can be repeated.</p>
 <h3 id="3cii-h246">3.c.ii - H246</h3>
@@ -446,7 +446,7 @@ <h2 id="3d-thermal-simulation">3.d - Thermal simulation</h2>
 <p><img src="nsclc3-V2.svg" height=250px></p>
 <p>The thermal simulation solves the Bio-heat thermal equation (BHTE) for all the combinations of duty cycle, timing and ultrasound exposure indicated in the thermal profile definition file. </p>
 <p><img src="Simulation-12.png" height=450px></p>
-<p>The selection of spatial-peak pulse-average intensity (<span class="arithmatex"><span class="MathJax_Preview">I_{\text{SPPA}}</span><script type="math/tex">I_{\text{SPPA}}</script></span>) indicates the desired intensity at the target. The spatial-peak time-average intensity (<span class="arithmatex"><span class="MathJax_Preview">I_{\text{SPTA}}</span><script type="math/tex">I_{\text{SPTA}}</script></span>) is calculated based on the selected timing conditions.  Based on the selections of timing and desired <span class="arithmatex"><span class="MathJax_Preview">I_{\text{SPPA}}</span><script type="math/tex">I_{\text{SPPA}}</script></span> in tissue, the <span class="arithmatex"><span class="MathJax_Preview">I_{\text{SPPA}}</span><script type="math/tex">I_{\text{SPPA}}</script></span> in water conditions is calculated after taking into account all the losses. Thermal safety parameters (maximal temperature and thermal doses) in the skin, skull bone and brain tissue are calculated at the locations showing the highest temperature elevation in the whole 3D volume. The <code>MTB</code>, <code>MTS</code> and <code>MTC</code> push buttons in the lower region of the interface select the slice corresponding to the the maximal temperature in brain, skin and skull, respectively.</p>
+<p>The selection of spatial-peak pulse-average intensity (<span class="arithmatex"><span class="MathJax_Preview">I_{\text{SPPA}}</span><script type="math/tex">I_{\text{SPPA}}</script></span>) indicates the desired intensity at the target. The spatial-peak time-average intensity (<span class="arithmatex"><span class="MathJax_Preview">I_{\text{SPTA}}</span><script type="math/tex">I_{\text{SPTA}}</script></span>) is calculated based on the selected timing conditions.  Based on the selections of timing and desired <span class="arithmatex"><span class="MathJax_Preview">I_{\text{SPPA}}</span><script type="math/tex">I_{\text{SPPA}}</script></span> in tissue, the <span class="arithmatex"><span class="MathJax_Preview">I_{\text{SPPA}}</span><script type="math/tex">I_{\text{SPPA}}</script></span> in water conditions is calculated after taking into account all the losses. Thermal safety parameters (maximal temperature and thermal doses) in the skin, skull bone and brain tissue are calculated at the locations showing the highest temperature elevation in the whole 3D volume. The <code>MTB</code>, <code>MTS</code> and <code>MTC</code> push buttons in the lower region of the interface select the slice corresponding to the maximal temperature in brain, skin and skull, respectively.</p>
 <p>The <code>Update Profile and Calculate</code> action can be used to load an updated version of the thermal profile file. This will force the recalculation of thermal results.</p>
 <p>The <code>Show</code> dropdown menu can be used to select the 2D intensity and thermal <code>Maps</code> or <code>Profiles</code> that shows the temporal evolution of temperature at the target and locations of maximal temperature at skin, skull and brain tissue.</p>
 <p><img src="Simulation-15.png" height=450px></p>
@@ -553,7 +553,7 @@ <h2 id="3d-thermal-simulation">3.d - Thermal simulation</h2>
 </tr>
 </tbody>
 </table>
-<p>The <code>Export Current Thermal map (.nii.gz)</code> action exports the current thermal simulation on display in Nifti format for inspection in neuronavigation and visualization software</p></div>
+<p>The <code>Export maps (.nii.gz)</code> action exports the thermal, pressure and intensity fields in Nifti format based on the selected Isppa at target. This can be used for inspection in neuronavigation and visualization software</p></div>
             </div>
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sitemap.xml

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