Merge pull request #1461 from sarthakpati/master

Version update for alpha_2
CBICA · Dec 13, 2021 · 5087834 · 5087834
2 parents f1acb91 + a9c9a92
commit 5087834
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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 2.Alpha )
+SET( PROJECT_VERSION_PATCH 2.Alpha.2 )
 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.1.8.2.Alpha &emsp;|&emsp;<b>Contact:</b> [email protected]
+		Cancer Imaging Phenomics Toolkit (CaPTk) v.1.8.2.Alpha.2 &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 @@
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   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
    </div>
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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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
    </div>
   </td>
  </tr>
@@ -61,7 +61,7 @@
 <div class="title">Miscellaneous: Diffusion Derivatives </div>  </div>
 </div><!--header-->
 <div class="contents">
-<div class="textblock"><p>This application extracts various measurements from a Diffusion Weighted MRI scan. The exact measurements comprise i) fractional anisotropy (FA), ii) radial diffusivity (RAD), iii) axial diffusivity (AX), and iv) apparent diffusion coefficient (ADC).</p>
+<div class="textblock"><p>This application extracts various measurements from a Diffusion Weighted MRI scan. The exact measurements comprise i) fractional anisotropy (FA), ii) radial diffusivity (RAD), iii) axial diffusivity (AX), iv) apparent diffusion coefficient (ADC), and v) averaged b0 image (B0).</p>
 <p>This application is also available from the web on the <a href="https://ipp.cbica.upenn.edu/">CBICA Image Processing Portal</a>. Please see the experiment on the portal for details.</p>
 <p><b> REQUIREMENTS:</b></p><ol type="1">
 <li>A single DW-MRI image</li>
@@ -71,9 +71,10 @@
 <p><b> USAGE:</b></p><ol type="1">
 <li>Launch the application from "Applications" -&gt; "Diffusion Derivatives".</li>
 <li>Specify the paths to the input DW-MRI image, bval and bvec files with the gradient information, and the mask defining the voxels to extract the measurements.</li>
+<li>If desired, enable registration of outputs and select a fixed image to register to.</li>
 <li>Identify the diffusion measurements to be extracted, and the output directory.</li>
 <li>Press the "Confirm" button.</li>
-<li>The extracted measurements will be saved at the specified location (~5 minutes). <pre class="fragment">${CaPTk_InstallDir}/bin/ DiffusionDerivatives.exe -i C:/inputDWI.nii.gz -m C:/mask.nii.gz -b C:/input.bval -g C:/input.bvec -a 1 -f 1 -r 1 -t 1 -o C:/output
+<li>The extracted measurements will be saved at the specified location (~5 minutes). <pre class="fragment">${CaPTk_InstallDir}/bin/ DiffusionDerivatives.exe -i C:/inputDWI.nii.gz -m C:/mask.nii.gz -b C:/input.bval -g C:/input.bvec -a 1 -f 1 -r 1 -t 1 -z 1 -reg C:/template.nii.gz -o C:/output
 </pre></li>
 </ol>
 <hr  />

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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
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diff --git a/docs/Glioblastoma_Atlas.html b/docs/Glioblastoma_Atlas.html
@@ -30,7 +30,7 @@
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   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
    </div>
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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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
    </div>
   </td>
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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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
    </div>
   </td>
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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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
    </div>
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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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
    </div>
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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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
    </div>
   </td>
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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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
    </div>
   </td>
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diff --git a/docs/How_To_Guides.html b/docs/How_To_Guides.html
@@ -33,7 +33,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
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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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
    </div>
   </td>
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diff --git a/docs/LungCancer_SBRT.html b/docs/LungCancer_SBRT.html
@@ -30,7 +30,7 @@
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   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
    </div>
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diff --git a/docs/PCA_Extraction.html b/docs/PCA_Extraction.html
@@ -33,7 +33,7 @@
  <tr style="height: 56px;">
   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
    </div>
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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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
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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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
    </div>
   </td>
  </tr>
@@ -69,14 +69,14 @@
 </ol>
 <p><b> USAGE:</b></p><ol type="1">
 <li>Launch the application from "Applications" -&gt; "Perfusion Alignment".</li>
-<li>Specify the input DSC-MRI image, T1 post-contrast image, time-resolution of the DSC-MRI scan in seconds (2 seconds), number of time-points before (b) and after (a) drop of the perfusion curve, and the output directory.</li>
-<li>Specify the optional drop-scaling (-d in the command line) and standard-deviation threshold (-s in the command line) parameters</li>
+<li>Specify the input DSC-MRI image, T1 post-contrast image, time-resolution of the DSC-MRI scan in seconds (t1, ex. 2 seconds), number of time-points before (t3) and after (t4) drop of the perfusion curve, and the output directory.</li>
+<li>Optionally, specify the output repetition time (t2, default 1 second), intensity drop in mean curve inside the ROI (-s2 in the command line, default 100) and the maximum intensity before the drop in mean curve inside the ROI (-s1 in the command line, default 300) parameters</li>
 <li>Press "Confirm" button.</li>
-<li>The b+a+1 individual volumes of the aligned DSC-MRI image will be saved at the specified location (~5 minutes).</li>
-<li>Outupt folder will contain the alighned perfusion image along with CSV files containing the original, truncated, revised and interpolated perfusion curve signals.</li>
+<li>The individual volumes of the aligned DSC-MRI image will be saved at the specified location (~5 minutes).</li>
+<li>Output folder will contain the alighed perfusion image along with CSV files containing the original, truncated, revised and interpolated perfusion curve signals.</li>
 </ol>
 <ul>
-<li>This application is also available as a stand-alone CLI for data analysts to build pipelines around, using the following example command: <pre class="fragment">${CaPTk_InstallDir}/bin/PerfusionAlignment.exe -i C:/InputImage/convertedNIfTIPerf_image.nii.gz -b 15 -a 17 -t 2 -s 10 -d 1 -o C:/InputImage_output
+<li>This application is also available as a stand-alone CLI for data analysts to build pipelines around, using the following example command: <pre class="fragment">${CaPTk_InstallDir}/bin/PerfusionAlignment.exe -i C:/InputImage/convertedNIfTIPerf_image.nii.gz -m brainMask.nii.gz -t1 2 -t3 15 -t4 30 -o C:/testPerf
 </pre> </li>
 </ul>
 </div></div><!-- contents -->

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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
    </div>
   </td>
  </tr>

diff --git a/docs/ReleaseNotes.html b/docs/ReleaseNotes.html
@@ -30,7 +30,7 @@
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    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
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+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
    </div>
   </td>
  </tr>

diff --git a/docs/Science.html b/docs/Science.html
@@ -30,7 +30,7 @@
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    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
-   &#160;<span id="projectnumber">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</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)
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+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
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diff --git a/docs/Training_Module.html b/docs/Training_Module.html
@@ -30,7 +30,7 @@
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   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
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+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
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  </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">1.8.2.Alpha</span>
+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
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diff --git a/docs/ht_Preprocessing.html b/docs/ht_Preprocessing.html
@@ -30,7 +30,7 @@
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    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
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diff --git a/docs/ht_Segmentation.html b/docs/ht_Segmentation.html
@@ -30,7 +30,7 @@
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   <td id="projectalign" style="padding-left: 0.5em;">
    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
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+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
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diff --git a/docs/ht_SpecialApps.html b/docs/ht_SpecialApps.html
@@ -30,7 +30,7 @@
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    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
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diff --git a/docs/ht_utilities.html b/docs/ht_utilities.html
@@ -30,7 +30,7 @@
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    <div id="projectname">Cancer Imaging Phenomics Toolkit (CaPTk)
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+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
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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)
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+   &#160;<span id="projectnumber">1.8.2.Alpha.2</span>
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diff --git a/docs/index.qhp b/docs/index.qhp
@@ -5,7 +5,7 @@
   <filterSection>
     <filterAttribute>doxygen</filterAttribute>
     <toc>
-      <section title="Cancer Imaging Phenomics Toolkit (CaPTk) 1.8.2.Alpha" ref="index.html">
+      <section title="Cancer Imaging Phenomics Toolkit (CaPTk) 1.8.2.Alpha.2" ref="index.html">
         <section title="Overview" ref="index.html">
           <section title="Bug Tracker and Feature Request" ref="index.html#autotoc_md103" />
           <section title="Frequently Asked Questions (FAQ)" ref="index.html#autotoc_md104" />

diff --git a/docs/pages.html b/docs/pages.html
@@ -30,7 +30,7 @@
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