Merge pull request #1200 from sarthakpati/master

Initiating Alpha3 build
CBICA · Jul 21, 2020 · 250bcdf · 250bcdf
2 parents bdb669a + 19ed8be
commit 250bcdf
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diff --git a/5_TechReference.txt b/5_TechReference.txt
@@ -386,12 +386,6 @@ An example of the list of commands to run to compile CaPTk and its dependencies:
 \verbatim
 git clone https://github.com/CBICA/CaPTk.git
 cd CaPTk
-mkdir bin
-cd bin
-#git lfs fetch --all # downloads all the precompiled binaries for different applications and Qt with the required installation options
-# change ${platform} to either windows, linux or macos (case sensitive)
-wget https://github.com/CBICA/CaPTk/raw/master/binaries/precompiledApps/${platform}.zip -O precompiledApps.zip 
-wget https://github.com/CBICA/CaPTk/raw/master/binaries/qt_5.12.1/${platform}.zip -O qt.zip
 git submodule update --init --recursive # this ensures all submodules are initialized and up-to-date
 mkdir build # this is where we will build all the binaries
 cd build

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 8 )
-SET( PROJECT_VERSION_PATCH 0.nonRelease )
+SET( PROJECT_VERSION_PATCH 0.Alpha3 )
 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.1.8.0.Alpha2 &emsp;|&emsp;<b>Contact:</b> [email protected]
+ Cancer Imaging Phenomics Toolkit (CaPTk) v.1.8.0.Alpha3 &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/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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</span>
  </div>
  </td>
  </tr>
@@ -61,7 +61,7 @@
 <div class="title">Breast Cancer: Breast Segmentation </div> </div>
 </div><!--header-->
 <div class="contents">
-<div class="textblock"><p>This application uses LIBRA [1] to extract the breast region in the loaded image.</p>
+<div class="textblock"><p>This application uses LIBRA [1] to extract the breast region in the loaded image and is only availabe via the GUI (the <a href="BreastCancer_texture.html">Breast Texture Pipeline</a> can be used to generate a mask and perform radiomic analysis via the command line).</p>
 <p><b>REQUIREMENTS:</b></p><ul>
 <li>Raw (i.e., "FOR PROCESSING") or vendor post-processed (i.e., "FOR PRESENTATION") FFDM images.</li>
 <li>FFDM vendors currently supported: GE Healthcare and Hologic.</li>

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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</span>
  </div>
  </td>
  </tr>

diff --git a/docs/CaPTk.TAGFILE b/docs/CaPTk.TAGFILE
@@ -35,7 +35,7 @@
  <docanchor file="FAQ.html" title="Is there a minimum recommended screen resolution for running CaPTk?">gs_FAQ_6</docanchor>
  <docanchor file="FAQ.html" title="Where can I find the CaPTk Docker Image?">gs_FAQ_7</docanchor>
  <docanchor file="FAQ.html" title="How do I run the CaPTk Docker Image to show the interface?">gs_FAQ_8</docanchor>
- <docanchor file="FAQ.html" title="What if I am having an issue not listed here?">gs_FAQ_9</docanchor>
+ <docanchor file="FAQ.html" title="Is there something wrong with Feature Extraction?">gs_FAQ_9</docanchor>
  </compound>
  <compound kind="page">
  <name>How_To_Guides</name>

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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</span>
  </div>
  </td>
  </tr>

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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</span>
  </div>
  </td>
  </tr>
@@ -73,7 +73,7 @@
 <li class="level1"><a href="#gs_FAQ_6">Is there a minimum recommended screen resolution for running CaPTk?</a></li>
 <li class="level1"><a href="#gs_FAQ_7">Where can I find the CaPTk Docker Image?</a></li>
 <li class="level1"><a href="#gs_FAQ_8">How do I run the CaPTk Docker Image to show the interface?</a></li>
-<li class="level1"><a href="#gs_FAQ_9">What if I am having an issue not listed here?</a></li>
+<li class="level1"><a href="#gs_FAQ_9">Is there something wrong with Feature Extraction?</a></li>
 </ul>
 </div>
 <div class="textblock"><h1><a class="anchor" id="gs_FAQ_1"></a>
@@ -187,7 +187,10 @@ <h1><a class="anchor" id="gs_FAQ_8"></a>
  -u qtuser \
  cbica/captk
 </pre><h1><a class="anchor" id="gs_FAQ_9"></a>
-What if I am having an issue not listed here?</h1>
+Is there something wrong with Feature Extraction?</h1>
+<p>Please see the <a href="https://github.com/sarthakpati/CaPTk/tree/featureExtraction/src/applications/FeatureExtraction#frequently-asked-questions">Feature Extraction FAQ</a>.</p>
+<h1><a class="anchor" id="gs_FAQ_9"></a>
+Is there something wrong with Feature Extraction?</h1>
 <p>Please <a href="https://github.com/CBICA/CaPTk/issues/new?assignees=&amp;labels=&amp;template=bug-report.md&amp;title=">open a new issue</a> with us and we will do our best to resolve it. </p>
 </div></div><!-- contents -->
 </div><!-- PageDoc -->

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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</span>
  </div>
  </td>
  </tr>

diff --git a/docs/Glioblastoma_Molecular.html b/docs/Glioblastoma_Molecular.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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</span>
  </div>
  </td>
  </tr>

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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</span>
  </div>
  </td>
  </tr>

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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</span>
  </div>
  </td>
  </tr>

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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</span>
  </div>
  </td>
  </tr>

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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</span>
  </div>
  </td>
  </tr>

diff --git a/docs/ht_Segmentation.html b/docs/ht_Segmentation.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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</span>
  </div>
  </td>
  </tr>

diff --git a/docs/ht_SpecialApps.html b/docs/ht_SpecialApps.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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</span>
  </div>
  </td>
  </tr>

diff --git a/docs/ht_utilities.html b/docs/ht_utilities.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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</span>
  </div>
  </td>
  </tr>
@@ -73,7 +73,8 @@
 <li>Test 2 images <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.dcm -tb C:/test.nii.gz</pre></li>
 <li>Create mask from threshold <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.dcm -o C:/test.nii.gz -cm 50,1000</pre></li>
 <li>DICOM to NIfTI conversion <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.dcm -o C:/test.nii.gz -d2n</pre></li>
-<li>NIfTI to DICOM &amp; DICOM-Seg conversion <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/test_dicom/ -n2d C:/referenceDICOM/</pre></li>
+<li>NIfTI to DICOM conversion <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/imageToConvert.nii.gz -o C:/outputDicom/ -n2d C:/referenceDICOM/</pre></li>
+<li>NIfTI to DICOM-Seg conversion (using <a href="https://qiicr.gitbook.io/dcmqi-guide/">DCMQI</a>) <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/maskToConvert.nii.gz -o C:/outputDicom/ -ds C:/referenceDICOM/ -dsJ C:/dicomSeg.json</pre> Please see DCMQI's <a href="https://qiicr.gitbook.io/dcmqi-guide/faq">FAQ</a> and <a href="https://qiicr.gitbook.io/dcmqi-guide/use-cases/prostate#creating-the-meta-information-json-file">use case</a> for JSON-related information.</li>
 <li>Re-orient image <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output.nii.gz -or RAI</pre></li>
 <li>Cast image to another pixel type <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -o C:/test_int.nii.gz -c int</pre></li>
 <li>Thresholding:<ul>
@@ -84,14 +85,19 @@
 <li>Binary <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output.nii.gz -tAB 50,100 -tBn</pre></li>
 </ul>
 </li>
-<li>Convert file formats <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -o C:/test.mha</pre></li>
-<li>Extract Image Series from Joined stack and vice-versa (4D &lt;-&gt; 3D) <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output -j2e 1
+<li>Convert file formats <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -o C:/test.mha -cov</pre></li>
+<li>Extract Image Series from Joined stack and vice-versa (4D &lt;-&gt; 3D) <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output -j2e 1 # output images are written in the form C:/output_${slice}.nii.gz
+${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output/ -j2e 1 # output images are written in the form C:/output/extractedImage_${slice}.nii.gz
 ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/ -o C:/output.nii.gz -e2j 1.5</pre></li>
 <li>Transform coordinates from world to image and vice-versa <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -i2w 10,10,30
 ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -w2i 10.5,10.1,30.6</pre></li>
 <li>Label similarity Metrics between 2 label images: pure mathematical formulations are given as output <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/outputMask.nii.gz -l2s C:/referenceMask.nii.gz</pre></li>
 <li>BraTS similarity Metrics between 2 label images: special considerations for metrics are done in this mode because output needs to be BraTS-compliant. <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/outputMask.nii.gz -lsb C:/referenceMask.nii.gz</pre></li>
-<li>Collect information from all images in a directory and put it in CSV <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/inputDirectory -o C:/test/inputDirectoryProperties.csv -co 1 -cF volume -cFE .nii.gz -cP 0,1</pre></li>
+<li>Collect information from all images in a directory and put it in CSV <pre class="fragment">${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/inputDirectory -o C:/test/inputDirectoryProperties.csv \
+-co 1 \ # enable recursion
+-cF volume \ # only process files that contain this string pattern 
+-cFE .nii.gz \ # only process files with this extension 
+-cP 0,1 \ # which properties to read; see usage for all options</pre></li>
 </ul>
 <p>For a full list of available applications and examples, please use the command: </p><pre class="fragment">${CaPTk_InstallDir}/bin/Utilities -h
 </pre> </div></div><!-- contents -->

diff --git a/docs/index.html b/docs/index.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">1.8.0.Alpha2</span>
+ &#160;<span id="projectnumber">1.8.0.Alpha3</span>
  </div>
  </td>
  </tr>