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                     <div class="col-md-9" role="main">
 
 <h1 id="babelbrain">BabelBrain</h1>
-<p><strong>v0.2.9</strong></p>
+<p><strong>v0.2.9-b</strong><br />
+October 14th, 2023.</p>
 <p>Samuel Pichardo, Ph.D<br />
 Associate Professor<br />
 Radiology and Clinical Neurosciences, Hotchkiss Brain Institute<br />
 Cumming School of Medicine,<br />
 University of Calgary <br />
 [email protected]<br />
-www.neurofus.ca</p>
+<a href="https://www.neurofus.ca">www.neurofus.ca</a></p>
 <p><strong>GUI application for the modeling of transcranial ultrasound for neuromodulation applications</strong></p>
 <p><img src="intro.png"></p>
 <p><img src="Target-demo.png"></p>
@@ -132,7 +133,7 @@ <h1 id="disclaimer">Disclaimer</h1>
 <p>This software is provided "as is" and it is intended exclusively for research purposes.</p>
 <h2 id="licensing">Licensing</h2>
 <p>BSD 3-Clause License</p>
-<p>Copyright (c) 2022, Samuel Pichardo
+<p>Copyright (c) 2022,2023 Samuel Pichardo
 All rights reserved.</p>
 <p>Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:</p>
@@ -244,5 +245,5 @@ <h4 class="modal-title" id="keyboardModalLabel">Keyboard Shortcuts</h4>
 
 <!--
 MkDocs version : 1.4.2
-Build Date UTC : 2023-09-29 16:39:31.217380+00:00
+Build Date UTC : 2023-10-17 14:38:21.886766+00:00
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installation.html

@@ -96,6 +96,10 @@
             <li class="nav-item" data-level="2"><a href="#os" class="nav-link">OS</a>
               <ul class="nav flex-column">
               </ul>
+            </li>
+            <li class="nav-item" data-level="2"><a href="#extra-software-required-to-run-babelbrain" class="nav-link">Extra software required to run BabelBrain</a>
+              <ul class="nav flex-column">
+              </ul>
             </li>
               </ul>
             </li>
@@ -140,6 +144,7 @@ <h3 id="gpu">GPU</h3>
 <p>BabelBrain supports GPUs enabled via CUDA, OpenCL or Metal. High-end GPUs (8 GPU RAM or more) are recommended. ARM64 processors (M1, M2) in Mac systems with 24GB or more RAM are highly recommended. BabelBrain was designed with Mac systems based on M1 and M2 processors as primary targets. </p>
 <h4 id="note-for-intel-based-mac-systems">Note for Intel-based Mac systems</h4>
 <p>Intel-based systems need to have a dedicated AMD GPU (internal or external via Thunderbolt). Intel-based iMac Pro and MacPro systems have internal GPUs suitable for sub 500 kHz simulations (i.e., Vega 56, Vega 64). An external GPU (i.e., AMD W6800 Pro) offers excellent performance and capability for high-frequency simulations.</p>
+<h2 id="extra-software-required-to-run-babelbrain">Extra software required to run BabelBrain</h2>
 <h3 id="blender">Blender</h3>
 <p><a href="https://www.blender.org">Blender</a> is required for constructive solid geometry operations. Install with default options.</p>
 <h3 id="simnibs">SimNIBS</h3>
@@ -149,8 +154,8 @@ <h3 id="optional-fsl">Optional -FSL</h3>
 <h3 id="navigation-planning-software">Navigation-planning software</h3>
 <p>While not strictly required, it is highly recommended to use planning software to establish the target localization and orientation, called <strong>trajectory</strong> in the following documentation, of the ultrasound transducer for the simulation of transcranial ultrasound. The trajectory is just a transformation matrix in the T1W space that represents the translation-rotation of a vector describing the target and direction of ultrasound. BabelBrain can import trajectories defined in proprietary software (<a href="https://www.rogue-research.com/">Rogue Research's</a> Brainsight) or open-source visualization software (<a href="https://www.slicer.org/">3DSlicer</a>). Instructions are detailed in the pipeline section of this documentation. </p>
 <h1 id="standalone-application">Standalone application</h1>
-<p>Ready-to-use applications (no need for Python installation) for macOS and Windows are available in the <a href="https://github.com/ProteusMRIgHIFU/BabelBrain/releases">Releases</a> section. </p>
-<p>For MacOS, download the installer and drag "BabelBrain" into the Applications folder. </p>
+<p>Ready-to-use applications (no need for Python installation) for macOS and Windows are available in the <a href="https://github.com/ProteusMRIgHIFU/BabelBrain/releases">Releases</a> section. Please note that for macOS there are installers for ARM64 (M1 and newer Apple Silicon processors) and Intel X64, so be sure of picking the correct version matching your hardware. </p>
+<p>For MacOS, open the DMG file and double-click on the package installer. </p>
 <p><img src="install1.png" height=300px></p>
 <p>The first time you will use you may be prompted to authorize it to run and access directories. You may also need to authorize it in the Security settings of macOS.</p>
 <p>For Windows, download the MSI installer file and run to install BabelBrain. Shortcuts will be created in the Desktop and Start menu. <strong>Note</strong>: CUDA 11.7+ must be installed.</p>
@@ -167,8 +172,7 @@ <h2 id="manual-execution">Manual execution</h2>
 <h1 id="building-standalone-application">Building standalone application</h1>
 <p>A pyinstaller specification file is provided to build the macOS and Windows applications. In the <code>BabelBrain/BabelBrain</code> directory run</p>
 <p><code>pyinstaller BabelBrain.spec --noconfirm</code> </p>
-<p>A new application will be created at <code>BabelBrain/BabelBrain/dist/</code></p>
-<p>For macOS, a DMG image installer can be created with the <code>BabelBrain/BabelBrain/create_dmg.sh</code> script. You need to install <code>create-dmg</code> tool with homebrew. </p></div>
+<p>A new application will be created at <code>BabelBrain/BabelBrain/dist/</code></p></div>
             </div>
         </div>
 

pipeline/pipeline.html

@@ -157,8 +157,9 @@ <h1 id="1-preliminary-steps">1 - Preliminary steps</h1>
 <p><strong>Mandatory</strong>: Execute  SimNIBS 3.x <code>headreco</code> or SimNIBS 4.x <code>charm</code> processing tool:</p>
 <p><code>headreco all &lt;ID&gt; &lt;Path to T1W Nifti file&gt; &lt;Path to T2W Nifti file&gt;</code></p>
 <p>or</p>
-<p><code>charm &lt;ID&gt; &lt;Path to T1W Nifti file&gt; &lt;Path to T2W Nifti file&gt; --forceqform</code></p>
-<p><code>&lt;ID&gt;</code> is a string for identification. A subdirectory <code>m2m_&lt;ID&gt;</code> will be created. Take note of this directory, this will be referred to as the <strong>SimNIBS output</strong> directory in the following of this manual. The <code>--forceqform</code> parameter is required as often Nifti files are not 100% strict on how qform and sform matrices are saved. </p>
+<p><code>charm &lt;ID&gt; &lt;Path to T1W Nifti file&gt; &lt;Path to T2W Nifti file&gt;</code></p>
+<p><code>&lt;ID&gt;</code> is a string for identification. A subdirectory <code>m2m_&lt;ID&gt;</code> will be created. Take note of this directory, this will be referred to as the <strong>SimNIBS output</strong> directory in the following of this manual.</p>
+<p><strong>Note</strong>: Sometimes, <code>charm</code> may complain that the qform and sform matrices are inconsistent. We have observed this when converting DICOM datasets with <code>dcm2niix</code>. If <code>charm</code> complains, you can try passing the  <code>--forceqform</code> parameter when executing <code>charm</code>.  </p>
 </li>
 <li>
 <p><strong>Mandatory</strong>: Identify the coordinates of the target of focus ultrasound in T1W space. If you need to start in standardized space (e.g. MNI), there are many tools (FSL, SPM12, etc) that can be used to convert from standardized space to T1W space. </p>

sitemap.xml

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