Merge pull request #1485 from AlexanderGetka-cbica/1.9.0.Beta-version…

…-change 1.9.0.beta version change
CBICA · Mar 15, 2022 · 8351d11 · 8351d11
2 parents 853e8e2 + f584641
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diff --git a/6.1_Download.txt b/6.1_Download.txt
@@ -4,7 +4,8 @@
 
 Visit our <b>Download Page</b> hosted in NIH-supported NITRC (https://www.nitrc.org/frs/?group_id=1059), to download the CaPTk <b>binaries</b> and our GitHub page (https://github.com/CBICA/CaPTk) for the <b>source code</b>.
 
-CaPTk is currently distributed in the form of pre-compiled (executable) Windows, Linux (compiled on Ubuntu 16.04) and macOS (compiled on 10.13) installers with all dependencies integrated in the package.
+CaPTk is currently distributed in the form of pre-compiled (executable) Windows and Linux (compiled on Ubuntu 16.04) installers with all dependencies integrated in the package.
+<b>macOS</b> support, as of the 1.9.0 version Beta, is provided via Docker image, available via Docker Hub at https://hub.docker.com/r/cbica/captk. This image contains the Linux version.
 
 Check the [Installation](Installation.html) guide for details on installation.
 

diff --git a/6.2_Installation.txt b/6.2_Installation.txt
@@ -29,12 +29,26 @@ chmod +x CaPTk_${Version}.bin
 
 \subsection macOS
 
+<b>For CaPTk Versions prior to 1.9.0:</b>
 - Users will download the ".pkg" file from NITRC; double-click the file. 
 - If there is a window saying that this is an "unidentified developer", hit "OK" and then go to "System Preferences > Security and Privacy" and you need to click on "Open Anyway" beside the "CaPTk_$version.pkg" (this will prompt for your password).
 - Double click on the pkg file and click on "Open". This will guide you through the installation screen with licensing information.
 - Before installation begins, you may be prompted for your password again.
 - You will find CaPTk under your "Applications" folder and you can delete the disk image.
 
+<b>For CaPTk versions 1.9.0 and greater:</b>
+- macOS users will need to download Docker (https://docs.docker.com/get-docker/)
+- Then pull the container from Docker Hub (https://hub.docker.com/r/cbica/captk), example command: 
+\verbatim
+docker pull cbica/captk
+\endverbatim
+- The container can be run with:
+\verbatim
+ docker run -it cbica/captk [args go here]
+ \endverbatim
+- The above is sufficient for command line use. To enable the graphical user interface, you will need to set up graphical sharing. We cannot provide technical support for Docker, but this article contains an example: https://cntnr.io/running-guis-with-docker-on-mac-os-x-a14df6a76efc
+- In order to process your files with CaPTk, you will need to mount your input directory into Docker. Please see the Docker documentation for examples on how to do this. The "docker run" command can do this at startup, example: https://docs.docker.com/engine/reference/commandline/run/#mount-volume--v---read-only
+
 --------------------------------------------------------------------
 
 --------------------------------------------------------------------

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -13,7 +13,7 @@ SET( ${PROJECT_NAME}_Variant "Full" ) # the particular variant of CaPTk (Full/Ne
 
 SET( PROJECT_VERSION_MAJOR 1 )
 SET( PROJECT_VERSION_MINOR 9 )
-SET( PROJECT_VERSION_PATCH 0.Alpha )
+SET( PROJECT_VERSION_PATCH 0.Beta )
 SET( PROJECT_VERSION_TWEAK ) 
 
 # check for the string "nonRelease" in the PROJECT_VERSION_PATCH variable

diff --git a/docs/1_credits.html b/docs/1_credits.html
@@ -12,7 +12,7 @@
 		<br>
 		<img src="functionalityRepresentation.png"></center>
 		<br>
-		Cancer Imaging Phenomics Toolkit (CaPTk) v.1.9.0.Alpha &emsp;|&emsp;<b>Contact:</b> [email protected]
+		Cancer Imaging Phenomics Toolkit (CaPTk) v.1.9.0.Beta &emsp;|&emsp;<b>Contact:</b> [email protected]
 		<br>
 		<b>Disclaimer:</b> CaPTk has been designed for non-commercial research purposes only and has not been reviewed or approved by the Food and Drug Administration (FDA). It is not intended or recommended for clinical application.
 		<br>

diff --git a/docs/BraTS_Metrics.html b/docs/BraTS_Metrics.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/BreastCancer_LIBRA.html b/docs/BreastCancer_LIBRA.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/BreastCancer_breastSegmentation.html b/docs/BreastCancer_breastSegmentation.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/BreastCancer_texture.html b/docs/BreastCancer_texture.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Diffusion_Derivatives.html b/docs/Diffusion_Derivatives.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Download.html b/docs/Download.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>
@@ -62,7 +62,7 @@
 </div><!--header-->
 <div class="contents">
 <div class="textblock"><p>Visit our <b>Download Page</b> hosted in NIH-supported NITRC (<a href="https://www.nitrc.org/frs/?group_id=1059">https://www.nitrc.org/frs/?group_id=1059</a>), to download the CaPTk <b>binaries</b> and our GitHub page (<a href="https://github.com/CBICA/CaPTk">https://github.com/CBICA/CaPTk</a>) for the <b>source code</b>.</p>
-<p>CaPTk is currently distributed in the form of pre-compiled (executable) Windows, Linux (compiled on Ubuntu 16.04) and macOS (compiled on 10.13) installers with all dependencies integrated in the package.</p>
+<p>CaPTk is currently distributed in the form of pre-compiled (executable) Windows and Linux (compiled on Ubuntu 16.04) installers with all dependencies integrated in the package. <b>macOS</b> support, as of the 1.9.0 version Beta, is provided via Docker image, available via Docker Hub at <a href="https://hub.docker.com/r/cbica/captk">https://hub.docker.com/r/cbica/captk</a>. This image contains the Linux version.</p>
 <p>Check the <a href="Installation.html">Installation</a> guide for details on installation.</p>
 <hr  />
 <p> <b>Note:</b> Please make sure that whenever you use and/or refer to CaPTk in your research, you should always cite the following papers:</p>

diff --git a/docs/FAQ.html b/docs/FAQ.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Getting_Started.html b/docs/Getting_Started.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Glioblastoma_Atlas.html b/docs/Glioblastoma_Atlas.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Glioblastoma_Confetti.html b/docs/Glioblastoma_Confetti.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Glioblastoma_Directionality.html b/docs/Glioblastoma_Directionality.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Glioblastoma_EGFRvIII.html b/docs/Glioblastoma_EGFRvIII.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Glioblastoma_PHI.html b/docs/Glioblastoma_PHI.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>
@@ -76,6 +76,8 @@
 <ul>
 <li>This application is also available as with a stand-alone CLI for data analysts to build pipelines around, using the following example command: <pre class="fragment">${CaPTk_InstallDir}/bin/EGFRvIIISurrogateIndex.exe -i C:/inputDSCImage.nii.gz -m C:/maskWithNearAndFarLabels.nii.gz
 </pre></li>
+<li>Additionally, you can process a batch directory (subdirectories are subjects, and each must have a perfusion and mask image). Pass "--help" to the CLI application for more details. <pre class="fragment">${CaPTk_InstallDir}/bin/EGFRvIIISurrogateIndex.exe -b C:/inputDirectory/ -o C:/output.csv
+</pre></li>
 </ul>
 <p><b>RULES FOR ROI ANNOTATION</b>:</p><ul>
 <li>These two ROIs are used to sample tissue located on the two boundaries of the peritumoaral edema/invasion area: near to and far from the tumor, respectively, and hence to evaluate the heterogeneity or spatial gradient of perfusion signals [1-3].</li>

diff --git a/docs/Glioblastoma_Pseudoprogression.html b/docs/Glioblastoma_Pseudoprogression.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Glioblastoma_Recurrence.html b/docs/Glioblastoma_Recurrence.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Glioblastoma_Survival.html b/docs/Glioblastoma_Survival.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Glioblastoma_WhiteStripe.html b/docs/Glioblastoma_WhiteStripe.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/How_To_Guides.html b/docs/How_To_Guides.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/ITCR_Connectivity.html b/docs/ITCR_Connectivity.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Installation.html b/docs/Installation.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>
@@ -84,13 +84,21 @@ <h2><a class="anchor" id="Linux"></a>
 </ul>
 <h2><a class="anchor" id="macOS"></a>
 macOS</h2>
-<ul>
+<p><b>For CaPTk Versions prior to 1.9.0:</b></p><ul>
 <li>Users will download the ".pkg" file from NITRC; double-click the file.</li>
 <li>If there is a window saying that this is an "unidentified developer", hit "OK" and then go to "System Preferences &gt; Security and Privacy" and you need to click on "Open Anyway" beside the "CaPTk_$version.pkg" (this will prompt for your password).</li>
 <li>Double click on the pkg file and click on "Open". This will guide you through the installation screen with licensing information.</li>
 <li>Before installation begins, you may be prompted for your password again.</li>
 <li>You will find CaPTk under your "Applications" folder and you can delete the disk image.</li>
 </ul>
+<p><b>For CaPTk versions 1.9.0 and greater:</b></p><ul>
+<li>macOS users will need to download Docker (<a href="https://docs.docker.com/get-docker/">https://docs.docker.com/get-docker/</a>)</li>
+<li>Then pull the container from Docker Hub (<a href="https://hub.docker.com/r/cbica/captk">https://hub.docker.com/r/cbica/captk</a>), example command: <pre class="fragment">docker pull cbica/captk
+</pre></li>
+<li>The container can be run with: <pre class="fragment"> docker run -it cbica/captk [args go here]</pre></li>
+<li>The above is sufficient for command line use. To enable the graphical user interface, you will need to set up graphical sharing. We cannot provide technical support for Docker, but this article contains an example: <a href="https://cntnr.io/running-guis-with-docker-on-mac-os-x-a14df6a76efc">https://cntnr.io/running-guis-with-docker-on-mac-os-x-a14df6a76efc</a></li>
+<li>In order to process your files with CaPTk, you will need to mount your input directory into Docker. Please see the Docker documentation for examples on how to do this. The "docker run" command can do this at startup, example: <a href="https://docs.docker.com/engine/reference/commandline/run/#mount-volume&ndash;v&mdash;read-only">https://docs.docker.com/engine/reference/commandline/run/#mount-volume&amp;ndash;v&amp;mdash;read-only</a></li>
+</ul>
 <hr  />
 <hr  />
 <p> 

diff --git a/docs/LungCancer_SBRT.html b/docs/LungCancer_SBRT.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/PCA_Extraction.html b/docs/PCA_Extraction.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>
@@ -64,8 +64,8 @@
 <div class="textblock"><p>This application extracts the principal components from DSC-MRI scans as mentioned in [1].</p>
 <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
+<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 (this is the one you select for input)
     - Subject_AAAA
       - AAAA_perf.nii.gz
       - AAAA_label.nii.gz</pre></li>

diff --git a/docs/People.html b/docs/People.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Perfusion_Alignment.html b/docs/Perfusion_Alignment.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Perfusion_Derivatives.html b/docs/Perfusion_Derivatives.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/ReleaseNotes.html b/docs/ReleaseNotes.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Science.html b/docs/Science.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Technical_Reference.html b/docs/Technical_Reference.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Training_Module.html b/docs/Training_Module.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>

diff --git a/docs/ht_FeatureExtraction.html b/docs/ht_FeatureExtraction.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>
@@ -64,7 +64,7 @@
 <div class="textblock"><p><b>REQUIREMENTS:</b></p><ol type="1">
 <li>An image or a set of co-registered images.</li>
 <li>An ROI file containing various labels, for which features will be extracted.</li>
-<li>NOTE: CaPTk also extracts COLLAGE features [1] using the <a href="https://github.com/radxtools/collageradiomics/">Python implementation</a>.</li>
+<li>NOTE: CaPTk can also extract COLLAGE features [1] using the <a href="https://github.com/radxtools/collageradiomics/">Python implementation</a>, but this functionality must be invoked from the separate "CollageFeatures" executable.</li>
 </ol>
 <p><b>USAGE:</b></p><ol type="1">
 <li>Once image(s) and an ROI file are loaded, go to the "Feature Extraction" panel.</li>

diff --git a/docs/ht_Preprocessing.html b/docs/ht_Preprocessing.html
@@ -30,7 +30,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.9.0.Alpha</span>
+   &#160;<span id="projectnumber">1.9.0.Beta</span>
    </div>
   </td>
  </tr>