Documentation updates

6.1_Download.txt

@@ -9,7 +9,7 @@ CaPTk is currently distributed in the form of pre-compiled (executable) Windows,
 Check the [Installation](Installation.html) guide for details on installation.
 
 --------------------------------------------------------------------
-### Please make sure that whenever you use and/or refer to CaPTk in your research, you should always cite the following papers:
+<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:
 
 - C.Davatzikos, S.Rathore, S.Bakas, S.Pati, M.Bergman, R.Kalarot, P.Sridharan, A.Gastounioti, N.Jahani, E.Cohen, H.Akbari, B.Tunc, J.Doshi, D.Parker, M.Hsieh, A.Sotiras, H.Li, Y.Ou, R.K.Doot, M.Bilello, Y.Fan, R.T.Shinohara, P.Yushkevich, R.Verma, D.Kontos, "Cancer imaging phenomics toolkit: quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome", J Med Imaging, 5(1):011018, 2018, DOI:10.1117/1.JMI.5.1.011018
 - S.Pati, A.Singh, S.Rathore, A.Gastounioti, M.Bergman, P.Ngo, S.M.Ha, D.Bounias, J.Minock, G.Murphy, H.Li, A.Bhattarai, A.Wolf, P.Sridaran, R.Kalarot, H.Akbari, A.Sotiras, S.P.Thakur, R.Verma, R.T.Shinohara, P.Yushkevich, Y.Fan, D.Kontos, C.Davatzikos, S.Bakas, "The Cancer Imaging Phenomics Toolkit (CaPTk): Technical Overview", Springer - BrainLes 2019 - LNCS, Vol.11993, 380-394, 2020, DOI:10.1007/978-3-030-46643-5_38
@@ -24,7 +24,7 @@ In addition, if the journal/conference where you submit your paper does not rest
 
 
 --------------------------------------------------------------------
-## License
+\subsection lic License
 
 By installing the CaPTk, the user agrees to the following licenses, which pertain to the code and its different constituents:
 

6.2_Installation.txt

@@ -2,14 +2,14 @@
 
 \page Installation Installation Instructions
 
-## Windows
+\subsection Windows
 
 - Download the ".msi" installer file and double click to open.
 - On Windows 10, sometimes, Microsoft Edge does not let you download installers from unknown sources for security purposes (the warning comes up after the download finishes); you will need to select "Keep File" and follow prompts.
 - If a security prompt comes up after opening the installer, click on "Run Anyway".
 - Follow prompts for installation.
 
-## Linux
+\subsection Linux
 
 - Linux users have a CaPTk AppImage available called `CaPTk_${Version}.bin`. 
 - To run the AppImage, first open a terminal in the same directory as the .bin file.
@@ -27,7 +27,7 @@ chmod +x CaPTk_${Version}.bin
 \endverbatim
 - Follow prompts to install.
 
-## macOS
+\subsection macOS
 
 - 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).

7_ReleaseNotes.txt

@@ -2,6 +2,20 @@
 
 \page ReleaseNotes Changelog: Release Notes
 
+- New training module
+- Updated documentation
+- Miscellaneous bug fixes
+
+For a full list, please see https://github.com/CBICA/CaPTk/issues?q=is%3Aissue+is%3Aclosed
+
+\subsection Known Issues
+
+https://github.com/CBICA/CaPTk/issues
+
+\subsection Older Versions
+
+\subsubsection 1.8.0
+
 - Fixes to Preprocessing 
   - NIfTI to DICOM writing improvements
   - Registration improvements (rigid and deformable added to CLI and GUI)
@@ -26,51 +40,43 @@
 - Added Collage radiomic features to Feature Extraction module
 - Documentation updates
 
-For a full list, please see https://github.com/CBICA/CaPTk/issues?q=is%3Aissue+is%3Aclosed
-
-## Known Issues
-
-https://github.com/CBICA/CaPTk/issues
-
-## Older Versions
-
-### 1.7.6
+\subsubsection 1.7.6
 
 - New model and data for Pseudo-Progression Estimator
 - Generic bug fixes and improvements 
 - Documentation updates
 
-### 1.7.5
+\subsubsection 1.7.5
 
 - GUI improvements
 - Algorithmic fixes for Neuro applications
 - Better error handling added all around
 - Linux installation updates
 - Generic bug fixes and improvements 
 
-### 1.7.3
+\subsubsection 1.7.3
 
 - Light/Dark mode and font switcher
 - Lots of new Utilities (NIfTI to DICOM & DICOM-Seg object conversion, Orientation change, Thresholding, File format conversion)
 - New functions to deal with image "series" (extraction and joining)
 - Automated Docker builds
 - Generic bug fixes and improvements 
 
-### 1.7.2
+\subsubsection 1.7.2
 
 - Preferences dialog added (see File > Preferences)
 - DICOM reading updates on the GUI
 - DeepMedic runtime fixes
 - Comparison mode works on 2 images
 - Generic bug fixes and improvements 
 
-### 1.7.1 
+\subsubsection 1.7.1 
 
 - Better high DPI support for all supported platforms
 - Updated documentation for whole package
 - Generic bug fixes and improvements 
 
-### 1.7.0
+\subsubsection 1.7.0
 - New Applications and Tools
   - Perfusion Alignment
   - Deep Learning Inference Engine based on DeepMedic
@@ -86,19 +92,19 @@ https://github.com/CBICA/CaPTk/issues
   - Training Module improvements
   - Annotation visualization improvements (single/multiple label view)
 
-### 1.6.1
+\subsubsection 1.6.1
 - Generic bug fixes in several applications 
 - Feature Extraction fixes on par with IBSI
 - OpenGL rendering added to better handle scaling issues
 - New "Preprocessing" executable added which has a bunch of generic functionality
 
-### 1.6.0
+\subsubsection 1.6.0
 - New applications have been added: Lung Cancer Segmentation/Analysis, Pseudo-Progression, EGFRvIII-SVM, Training Module, DeepMedic Segmentation, Greedy Registration
 - Updates to Feature Extraction Panel (Lattice-based computation, new feature families)
 - macOS package has been added
 - Lots of bug-fixes and improvements
 
-### 1.5.0
+\subsubsection 1.5.0
 - New applications added: Perfusion derivatives (ap-rCBV, PSR, PH), Diffusion derivatives (FA, AX, RAD, TR), PCA Volume Extraction, GBM Molecular Subtype Prediction, GBM Population Atlas
 - Performance and UI improvements
 - New user-centric documentation & intro, based on NIH/ITCR guidelines
@@ -107,48 +113,48 @@ https://github.com/CBICA/CaPTk/issues
 - Updated implementation of Directionality Estimation  
 
 
-### 1.3.0
+\subsubsection 1.3.0
 - Labels updated to support GLISTR and GLISTRboost outputs
 - Added a way to invoke CaPTk from the command line to make QC of multiple subjects easier
 - Double click to add tissue points and tumor point centers
 - New applications added
 - Performance and UI improvements
 
-### 1.2.0
+\subsubsection 1.2.0
 - New applications added
 - Interactive functionality updated 
 - Added central core for statistical analyses
 - Bug fixes
 
-### 1.1.0
+\subsubsection 1.1.0
 - Added functionality to drawing 
 - Documentation updated with more illustrative screenshots
 
-### 1.0.1
+\subsubsection 1.0.1
 - Updated documentation outside and inside the application
 - Random bug-fixes 
 
-### 2017.02.01
+\subsubsection 2017.02.01
 - First public release of CaPTk_Full (version 1.0.0)
 - Applications populated using highlighted algorithms from CBICA
 - Feature Panel added to generate a comprehensive radiomic feature set for training
 - More optimizations and bug-fixes in interaction
 
-### 2016.10.14
+\subsubsection 2016.10.14
 - Release for MICCAI 2016
 - UI optimizations
 - Seed point selector updated
 
-### 2016.09.05
+\subsubsection 2016.09.05
 - Move to a date-based versioning system for more clarity and coherence
 - SeedSelector version for GLISTR, GLISTRboost, PORTR added to compilation
 - Major UI overhaul with more dynamic elements
 
-### 0.0.2
+\subsubsection 0.0.2
 - Bug fixes in the seed points are saved
 - Generic interactive improvements
 
-### 0.0.1
+\subsubsection 0.0.1
 - First (internal) release of CaPTk
 - Mostly a prototype at this stage
 - Interactive elements (seed-point initialization, ROI drawing) work properly

8_People.txt

@@ -3,7 +3,7 @@
 \page People People (Credits)
 
 
-## Advisors:
+\subsection advisors Advisors:
 
 - [Christos Davatzikos](https://www.med.upenn.edu/cbica/christos/)
 - [Despina Kontos](https://www.med.upenn.edu/cbica/cbig/despinak.html)
@@ -14,7 +14,7 @@
 - [Spyridon Bakas](https://www.med.upenn.edu/cbica/sbakas/)
 
 
-## Developers:
+\subsection devs Developers:
 
 - [Sarthak Pati](https://www.med.upenn.edu/cbica/aibil/spati.html): v.0.0.1 - present
 - [Saima Rathore](https://www.med.upenn.edu/sbia/srathore.html): v.0.0.1 - present
@@ -34,7 +34,7 @@
 
 More details are available from our repository's [Insights page](https://github.com/CBICA/CaPTk/graphs/contributors).
 
-## Collaborators:
+\subsection collabs Collaborators:
 
 - [Mark Bergman](https://www.med.upenn.edu/cbica/sbia/mbergman.html)
 - [Chiharu Sako](https://www.med.upenn.edu/cbica/aibil/sako.html)

9_ITCRCollaborations.txt

@@ -2,25 +2,29 @@
 
 \page ITCR_Connectivity ITCR Connectivity
 
+\tableofcontents
+
 This section includes a reference of all ongoing and existing connections between CaPTk and other projects funded under the [Informatics Technology for Cancer Research (ITCR)]() program.
 
 A connectivity map featuring all ITCR projects can be found [here](https://www.ndexbio.org/#/network/04c0a7e8-af92-11e7-94d3-0ac135e8bacf).
 
 \section itcr_existing Existing Connections
-\subsection itcr_dcmtk [DCMTK - DICOM ToolKit](https://dicom.offis.de/dcmtk.php.en)
-CaPTk uses DICOM ToolKit (DCMTK) for DICOM file handling. 
 
-\subsection itcr_dcmqi [DCMQI - DICOM for Quantitative Imaging](http://qiicr.org/dcmqi-guide/tutorials/intro.html)
-CaPTk leverages DCMQI for generating DICOM-Seg files from NIfTI file format. 
+\subsection itcr_dcmtk DCMT
+CaPTk uses [DCMTK - DICOM ToolKit (DCMTK)](https://dicom.offis.de/dcmtk.php.en) for DICOM file handling. 
+
+\subsection itcr_dcmqi DCMQI
+CaPTk leverages [DICOM for Quantitative Imaging (DCMQI)](http://qiicr.org/dcmqi-guide/tutorials/intro.html) for generating DICOM-Seg files from NIfTI files. 
 
-\subsection itcr_synapse [Synapse PACS](https://healthcaresolutions-us.fujifilm.com/enterprise-imaging/synapse-pacs)
-CaPTk’s performance evaluation metrics are used by Synapse.  
+\subsection itcr_synapse Synapse PACS
+CaPTk’s performance evaluation metrics are used by [Synapse PACS](https://healthcaresolutions-us.fujifilm.com/enterprise-imaging/synapse-pacs).  
 
-\subsection itr_tcia_idc [The Cancer Imaging Archive](https://www.cancerimagingarchive.net/)[/ Imaging Data Commons](https://datacommons.cancer.gov/repository/imaging-data-commons)
-Enriching TCIA data collections with segmentations and radiomic features. Robustness analysis on radiomic features on TCIA data. 
+\subsection itr_tcia_idc TCIA and IDC
+Enriching  [The Cancer Imaging Archive (TCIA)](https://www.cancerimagingarchive.net/) and [Imaging Data Commons (IDC)](https://datacommons.cancer.gov/repository/imaging-data-commons) data collections with segmentations and radiomic features. Robustness analysis on radiomic features on TCIA data has also been posted back to TCIA.
 
 \section itcr_ongoing Ongoing Development
-\subsection itcr_radxtools [RADxTools](https://radxtools.github.io/)
+
+\subsection itcr_radxtools RADxTools
 CaPTk provides the [CoLlAGe](https://github.com/radxtools/collageradiomics) features through its feature extraction functionality. 
 
 Contact [software [at] cbica.upenn.edu](mailto:software@cbica.upenn.edu) with any questions.

docs/CaPTk.TAGFILE

@@ -259,21 +259,42 @@
     <name>Download</name>
     <title>Download Instructions</title>
     <filename>Download.html</filename>
+    <docanchor file="Download.html" title="License">lic</docanchor>
   </compound>
   <compound kind="page">
     <name>Installation</name>
     <title>Installation Instructions</title>
     <filename>Installation.html</filename>
+    <docanchor file="Installation.html">Windows</docanchor>
+    <docanchor file="Installation.html">Linux</docanchor>
+    <docanchor file="Installation.html">macOS</docanchor>
   </compound>
   <compound kind="page">
     <name>ReleaseNotes</name>
     <title>Changelog: Release Notes</title>
     <filename>ReleaseNotes.html</filename>
+    <docanchor file="ReleaseNotes.html" title="Issues">Known</docanchor>
+    <docanchor file="ReleaseNotes.html" title="Versions">Older</docanchor>
   </compound>
   <compound kind="page">
     <name>People</name>
     <title>People (Credits)</title>
     <filename>People.html</filename>
+    <docanchor file="People.html" title="Advisors:">advisors</docanchor>
+    <docanchor file="People.html" title="Developers:">devs</docanchor>
+    <docanchor file="People.html" title="Collaborators:">collabs</docanchor>
+  </compound>
+  <compound kind="page">
+    <name>ITCR_Connectivity</name>
+    <title>ITCR Connectivity</title>
+    <filename>ITCR_Connectivity.html</filename>
+    <docanchor file="ITCR_Connectivity.html" title="Existing Connections">itcr_existing</docanchor>
+    <docanchor file="ITCR_Connectivity.html" title="DCMT">itcr_dcmtk</docanchor>
+    <docanchor file="ITCR_Connectivity.html" title="DCMQI">itcr_dcmqi</docanchor>
+    <docanchor file="ITCR_Connectivity.html" title="Synapse PACS">itcr_synapse</docanchor>
+    <docanchor file="ITCR_Connectivity.html" title="TCIA and IDC">itr_tcia_idc</docanchor>
+    <docanchor file="ITCR_Connectivity.html" title="Ongoing Development">itcr_ongoing</docanchor>
+    <docanchor file="ITCR_Connectivity.html" title="RADxTools">itcr_radxtools</docanchor>
   </compound>
   <compound kind="page">
     <name>index</name>

docs/Download.html

@@ -65,8 +65,7 @@
 <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>Check the <a href="Installation.html">Installation</a> guide for details on installation.</p>
 <hr  />
- <h3><a class="anchor" id="autotoc_md93"></a>
-Please make sure that whenever you use and/or refer to CaPTk in your research, you should always cite the following papers:</h3>
+<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>
 <ul>
 <li>C.Davatzikos, S.Rathore, S.Bakas, S.Pati, M.Bergman, R.Kalarot, P.Sridharan, A.Gastounioti, N.Jahani, E.Cohen, H.Akbari, B.Tunc, J.Doshi, D.Parker, M.Hsieh, A.Sotiras, H.Li, Y.Ou, R.K.Doot, M.Bilello, Y.Fan, R.T.Shinohara, P.Yushkevich, R.Verma, D.Kontos, "Cancer imaging phenomics toolkit: quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome", J Med Imaging, 5(1):011018, 2018, DOI:10.1117/1.JMI.5.1.011018</li>
 <li>S.Pati, A.Singh, S.Rathore, A.Gastounioti, M.Bergman, P.Ngo, S.M.Ha, D.Bounias, J.Minock, G.Murphy, H.Li, A.Bhattarai, A.Wolf, P.Sridaran, R.Kalarot, H.Akbari, A.Sotiras, S.P.Thakur, R.Verma, R.T.Shinohara, P.Yushkevich, Y.Fan, D.Kontos, C.Davatzikos, S.Bakas, "The Cancer Imaging Phenomics Toolkit (CaPTk): Technical Overview", Springer - BrainLes 2019 - LNCS, Vol.11993, 380-394, 2020, DOI:10.1007/978-3-030-46643-5_38</li>
@@ -79,7 +78,7 @@ <h3><a class="anchor" id="autotoc_md93"></a>
 <li>S.Pati, S.Rathore, R.Kalarot, P.Sridharan, M.Bergman, T.Shinohara, P.Yushkevich, Y.Fan, R.Verma, D.Kontos, C.Davatzikos. "Cancer and Phenomics Toolkit (CaPTk): A Software Suite for Computational Oncology and Radiomics", 102nd Scientific Assembly and Annual Meeting of the Radiological Society of North America (RSNA), Nov.27-Dec.2, 2016, Chicago IL. archive.rsna.org/2016/16014589.html</li>
 </ul>
 <hr  />
- <h2><a class="anchor" id="autotoc_md95"></a>
+ <h2><a class="anchor" id="lic"></a>
 License</h2>
 <p>By installing the CaPTk, the user agrees to the following licenses, which pertain to the code and its different constituents:</p>
 <ol type="1">