Merge pull request #1462 from ashishsingh18/ppca_docs

perfusion pca documentation update
CBICA · Dec 13, 2021 · f1acb91 · f1acb91
2 parents 29fc9c2 + bf65594
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diff --git a/3_HowToGuides.txt b/3_HowToGuides.txt
@@ -35,7 +35,7 @@ This section provides step-by-step guidance to apply the CaPTk functionalities:
   - [Miscellaneous: Directionality Estimator](Glioblastoma_Directionality.html)
   - [Miscellaneous: Diffusion Derivatives](Diffusion_Derivatives.html)
   - [Miscellaneous: Perfusion Derivatives](Perfusion_Derivatives.html)
-  - [Miscellaneous: Principal Component Images Extraction](PCA_Extraction.html)
+  - [Miscellaneous: Perfusion PCA Parameter Extractor](PCA_Extraction.html)
 - \subpage ht_utilities "Utilities (CLI only)": Collection of helper utilities such as resampling, thresholding, image information, casting, label statistics, and more.
 	- [BraTS Metrics Computation](BraTS_Metrics.html)
 
@@ -1067,26 +1067,50 @@ ${CaPTk_InstallDir}/bin/PerfusionDerivatives.exe -i C:/InputImage/convertedNIfTI
 */
 
 /**
-\page PCA_Extraction Miscellaneous: Perfusion PCA Volume Extraction
+\page PCA_Extraction Miscellaneous: Perfusion PCA Parameter Extractor
 
 This application extracts the principal components from DSC-MRI scans as mentioned in [1].
 
 <b> REQUIREMENTS:</b>
-  -# A single DSC-MRI image 
-  -# Its corresponding mask for which the measurements need to be extracted
-
+Directory containing the following images in a sub-folder:
+  -# A single DSC-MRI image (filename must contain the text 'perf' or 'PERF' or 'DSC' to be correctly detected e.g. AAAA_perf.nii.gz )
+  -# Its corresponding mask for which the measurements need to be extracted (filename must contain the text 'label' or 'segmentation'
+   to be correctly detected e.g. AAA_label.nii.gz)
+  -# An example directory structure for the input data is as follows:
+  \verbatim
+	- RootFolder
+		- Subject_AAAA
+			- AAAA_perf.nii.gz
+			- AAAA_label.nii.gz
+	\endverbatim
+
 <b> USAGE:</b>
-	-# Load a DSC-MRI in CaPTk and the mask (Label:1) defining the voxels to extract the measurements.
-  -# Launch the application from "Applications" -> "Perfusion PCA".
-  -# Specify the number of principal components required and the output directory.
+	-# Launch the application from "Applications" -> "Perfusion PCA".
+	-# Specify the input directory containing a DSC-MRI and the mask (Label:1) defining the voxels to extract the measurements.
+	-# Specify the output directory to save results.
+	-# Select <U>Extract new parameters</U> to extract parameters or <U>Apply extracted parameters</U> to apply the extracted parameters.
+	-# Specify the number of PCA images to produce [default value = 0] (optional) or
+	-# Specify the variance threshold (optional)
+	-# Specify the 'Extracted parameters directory' (if in <U>Apply extracted parameters</U> mode)
 	-# Press the "Confirm" button.
-	-# The principal components will be extracted at the specified location and also loaded in CaPTk (~5 minutes).
+	-# The principal components will be extracted/applied and the results will be saved at the specified location.
+
+	<b>Note:</b>
+	-# In <U>extract new parameters</U> mode
+		- If none of the optional parameters are specified, default value of 0 is used for the number of PCA images to produce.
+
+	-# In <U>apply extracted parameters</U> mode
+		- In this mode one of the optional parameters is required.
 
 - This application is also available as with a stand-alone CLI for data analysts to build pipelines around, using the following example commands:
   - The following command will train a new model based on the samples in the inputDir using 5 principal components:
 	\verbatim
 ${CaPTk_InstallDir}/bin/PerfusionPCA.exe -t 0 -i C:/properly/formatted/inputDir -o C:/outputDir -n 5
 	\endverbatim
+  - The following command will train a new model based on the samples in the inputDir for a variance threshold of 99:
+	\verbatim
+${CaPTk_InstallDir}/bin/PerfusionPCA.exe -t 0 -i C:/properly/formatted/inputDir -o C:/outputDir -vt 99
+	\endverbatim
   - The following command will perform inference using an existing model for inputs in C:/input based on C:/modelDir using 5 principal components:
 	\verbatim
 ${CaPTk_InstallDir}/bin/PerfusionPCA.exe -t 1 -i C:/properly/formatted/inputDir -m C:/inputModelDir -o C:/outputDir -n 5

diff --git a/docs/How_To_Guides.html b/docs/How_To_Guides.html
@@ -3,7 +3,7 @@
 <head>
 <meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
 <meta http-equiv="X-UA-Compatible" content="IE=9"/>
-<meta name="generator" content="Doxygen 1.8.18"/>
+<meta name="generator" content="Doxygen 1.8.15"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
 <title>Cancer Imaging Phenomics Toolkit (CaPTk): How To Guides</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
@@ -13,13 +13,16 @@
 <script type="text/javascript" src="resize.js"></script>
 <script type="text/javascript" src="navtreedata.js"></script>
 <script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
+  $(document).ready(initResizable);
+/* @license-end */</script>
 <script type="text/x-mathjax-config">
   MathJax.Hub.Config({
     extensions: ["tex2jax.js"],
     jax: ["input/TeX","output/HTML-CSS"],
 });
-</script>
-<script type="text/javascript" async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"></script>
+</script><script type="text/javascript" async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"></script>
 <link href="doxygen.css" rel="stylesheet" type="text/css" />
 </head>
 <body>
@@ -38,7 +41,7 @@
 </table>
 </div>
 <!-- end header part -->
-<!-- Generated by Doxygen 1.8.18 -->
+<!-- Generated by Doxygen 1.8.15 -->
 </div><!-- top -->
 <div id="side-nav" class="ui-resizable side-nav-resizable">
   <div id="nav-tree">
@@ -52,7 +55,7 @@
 </div>
 <script type="text/javascript">
 /* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
-$(document).ready(function(){initNavTree('How_To_Guides.html',''); initResizable(); });
+$(document).ready(function(){initNavTree('How_To_Guides.html','');});
 /* @license-end */
 </script>
 <div id="doc-content">
@@ -98,7 +101,7 @@
 <li><a href="Glioblastoma_Directionality.html">Miscellaneous: Directionality Estimator</a></li>
 <li><a href="Diffusion_Derivatives.html">Miscellaneous: Diffusion Derivatives</a></li>
 <li><a href="Perfusion_Derivatives.html">Miscellaneous: Perfusion Derivatives</a></li>
-<li><a href="PCA_Extraction.html">Miscellaneous: Principal Component Images Extraction</a></li>
+<li><a href="PCA_Extraction.html">Miscellaneous: Perfusion PCA Parameter Extractor</a></li>
 </ul>
 </li>
 <li><a class="el" href="ht_utilities.html">Utilities (CLI only)</a>: Collection of helper utilities such as resampling, thresholding, image information, casting, label statistics, and more.<ul>
@@ -111,9 +114,9 @@
 <li>Training videos can be accessed in our <a href="https://www.youtube.com/channel/UC69N7TN5bH2onj4dHcPLxxA"><b>YouTube Channel</b></a>, specifically in the <a href="https://www.youtube.com/playlist?list=PLXdcXDD5czvjFFQGX9Jm3KouP0H9cWowu" target="_blank" rel="noopener noreferrer"><b>original</b></a> and <a href="https://www.youtube.com/playlist?list=PLXdcXDD5czvgCOfo_LLhAwFRNlpsBfjFx" target="_blank" rel="noopener noreferrer"><b>ITCR 2020</b></a> CaPTk Playlists.</li>
 <li>All applications are available as command-line applications (use parameter "-h" for detailed help messages).</li>
 </ul>
-<hr  />
- </div></div><!-- contents -->
-</div><!-- PageDoc -->
+<hr/>
+ </div></div><!-- PageDoc -->
+</div><!-- contents -->
 </div><!-- doc-content -->
 <!-- start footer part -->
 		<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->

diff --git a/docs/PCA_Extraction.html b/docs/PCA_Extraction.html
@@ -3,23 +3,26 @@
 <head>
 <meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
 <meta http-equiv="X-UA-Compatible" content="IE=9"/>
-<meta name="generator" content="Doxygen 1.8.18"/>
+<meta name="generator" content="Doxygen 1.8.15"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>Cancer Imaging Phenomics Toolkit (CaPTk): Miscellaneous: Perfusion PCA Volume Extraction</title>
+<title>Cancer Imaging Phenomics Toolkit (CaPTk): Miscellaneous: Perfusion PCA Parameter Extractor</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>
 <link href="navtree.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="resize.js"></script>
 <script type="text/javascript" src="navtreedata.js"></script>
 <script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
+  $(document).ready(initResizable);
+/* @license-end */</script>
 <script type="text/x-mathjax-config">
   MathJax.Hub.Config({
     extensions: ["tex2jax.js"],
     jax: ["input/TeX","output/HTML-CSS"],
 });
-</script>
-<script type="text/javascript" async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"></script>
+</script><script type="text/javascript" async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"></script>
 <link href="doxygen.css" rel="stylesheet" type="text/css" />
 </head>
 <body>
@@ -38,7 +41,7 @@
 </table>
 </div>
 <!-- end header part -->
-<!-- Generated by Doxygen 1.8.18 -->
+<!-- Generated by Doxygen 1.8.15 -->
 </div><!-- top -->
 <div id="side-nav" class="ui-resizable side-nav-resizable">
   <div id="nav-tree">
@@ -52,39 +55,58 @@
 </div>
 <script type="text/javascript">
 /* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
-$(document).ready(function(){initNavTree('PCA_Extraction.html',''); initResizable(); });
+$(document).ready(function(){initNavTree('PCA_Extraction.html','');});
 /* @license-end */
 </script>
 <div id="doc-content">
 <div class="PageDoc"><div class="header">
   <div class="headertitle">
-<div class="title">Miscellaneous: Perfusion PCA Volume Extraction </div>  </div>
+<div class="title">Miscellaneous: Perfusion PCA Parameter Extractor </div>  </div>
 </div><!--header-->
 <div class="contents">
 <div class="textblock"><p>This application extracts the principal components from DSC-MRI scans as mentioned in [1].</p>
-<p><b> REQUIREMENTS:</b></p><ol type="1">
-<li>A single DSC-MRI image</li>
-<li>Its corresponding mask for which the measurements need to be extracted</li>
+<p><b> REQUIREMENTS:</b> Directory containing the following images in a sub-folder:</p><ol type="1">
+<li>A single DSC-MRI image (filename must contain the text 'perf' or 'PERF' or 'DSC' to be correctly detected e.g. AAAA_perf.nii.gz )</li>
+<li>Its corresponding mask for which the measurements need to be extracted (filename must contain the text 'label' or 'segmentation' to be correctly detected e.g. AAA_label.nii.gz)</li>
+<li>An example directory structure for the input data is as follows: <pre class="fragment">  - RootFolder
+    - Subject_AAAA
+      - AAAA_perf.nii.gz
+      - AAAA_label.nii.gz</pre></li>
 </ol>
 <p><b> USAGE:</b></p><ol type="1">
-<li>Load a DSC-MRI in CaPTk and the mask (Label:1) defining the voxels to extract the measurements.</li>
 <li>Launch the application from "Applications" -&gt; "Perfusion PCA".</li>
-<li>Specify the number of principal components required and the output directory.</li>
+<li>Specify the input directory containing a DSC-MRI and the mask (Label:1) defining the voxels to extract the measurements.</li>
+<li>Specify the output directory to save results.</li>
+<li>Select <u>Extract new parameters</u> to extract parameters or <u>Apply extracted parameters</u> to apply the extracted parameters.</li>
+<li>Specify the number of PCA images to produce [default value = 0] (optional) or</li>
+<li>Specify the variance threshold (optional)</li>
+<li>Specify the 'Extracted parameters directory' (if in <u>Apply extracted parameters</u> mode)</li>
 <li>Press the "Confirm" button.</li>
-<li>The principal components will be extracted at the specified location and also loaded in CaPTk (~5 minutes).</li>
+<li>The principal components will be extracted/applied and the results will be saved at the specified location.</li>
+</ol>
+<p><b>Note:</b></p><ol type="1">
+<li>In <u>extract new parameters</u> mode<ul>
+<li>If none of the optional parameters are specified, default value of 0 is used for the number of PCA images to produce.</li>
+</ul>
+</li>
+<li>In <u>apply extracted parameters</u> mode<ul>
+<li>In this mode one of the optional parameters is required.</li>
+</ul>
+</li>
 </ol>
 <p>This application is also available as with a stand-alone CLI for data analysts to build pipelines around, using the following example commands:</p><ul>
 <li>The following command will train a new model based on the samples in the inputDir using 5 principal components: <pre class="fragment">${CaPTk_InstallDir}/bin/PerfusionPCA.exe -t 0 -i C:/properly/formatted/inputDir -o C:/outputDir -n 5</pre></li>
+<li>The following command will train a new model based on the samples in the inputDir for a variance threshold of 99: <pre class="fragment">${CaPTk_InstallDir}/bin/PerfusionPCA.exe -t 0 -i C:/properly/formatted/inputDir -o C:/outputDir -vt 99</pre></li>
 <li>The following command will perform inference using an existing model for inputs in C:/input based on C:/modelDir using 5 principal components: <pre class="fragment">${CaPTk_InstallDir}/bin/PerfusionPCA.exe -t 1 -i C:/properly/formatted/inputDir -m C:/inputModelDir -o C:/outputDir -n 5</pre></li>
 </ul>
-<hr  />
+<hr/>
 <p>References:</p>
 <ol type="1">
 <li>H.Akbari, L.Macyszyn, X.Da, R.L.Wolf, M.Bilello, R.Verma, D.M.O'Rourke, C.Davatzikos, "Pattern analysis of dynamic susceptibility contrast-enhanced MR imaging demonstrates peritumoral tissue heterogeneity", Radiology. 273(2):502-10, 2014, DOI:10.1148/radiol.14132458</li>
 </ol>
-<hr  />
- </div></div><!-- contents -->
-</div><!-- PageDoc -->
+<hr/>
+ </div></div><!-- PageDoc -->
+</div><!-- contents -->
 </div><!-- doc-content -->
 <!-- start footer part -->
 		<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->