Cancer Imaging Phenomics Toolkit (CaPTk)  1.6.2.Alpha
Download Instructions


Visit our Download Page hosted in NIH-supported NITRC (https://www.nitrc.org/frs/?group_id=1059), to download the CaPTk source code and binaries.

CaPTk is currently distributed in the form of pre-compiled (executable) Windows installer, as well as in the form of its source code. We are actively working on producing pre-compiled binaries for Linux and macOS machines too. The Windows executable package contains all required dependencies and does not need administrative privileges for installation.

The Linux executable assumes Qt 4.8.x installed on the system and in the PATH and was built using GCC 4.8.6 (default with Ubuntu 14.04); the custom path for installation can be specified using the following command:

$package --target $desiredInstallDir

NOTE: For Linux users, the following packages are needed to install the binary: wget zip. As an example, the installation command on Ubuntu for these packages will be: 

sudo apt-get install wget zip



Please make sure that whenever you use and/or refer to CaPTk in your research, you should always cite the following paper:

  • 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


In addition, if the journal/conference where you submit your paper does not restrict you from citing abstracts you might also cite the following:

  • S.Rathore, S.Bakas, S.Pati, H.Akbari, R.Kalarot, P.Sridharan, M.Rozycki, M.Bergman, B.Tunc, R.Verma, M.Bilello, C.Davatzikos. "Brain Cancer Imaging Phenomics Toolkit (brain-CaPTk): An Interactive Platform for Quantitative Analysis of Glioblastoma", BrainLes 2017. LNCS Springer, 10670:133-145, 2017. DOI:10.1007/978-3-319-75238-9_12
  • S.Pati, S.Bakas, A.Sotiras, R.Kalarot, P.Sridharan, M.Bergman, S.Rathore, H.Akbari, P.Yushkevich, T.Shinohara, Y.Fan, D.Kontos, R.Verma, C.Davatzikos. "Cancer Imaging Phenomics Toolkit (CaPTk): A Radio(geno)mics Software Platform Leveraging Quantitative Imaging Analytics for Computational Oncology", 103rd Scientific Assembly and Annual Meeting of the Radiological Society of North America (RSNA), Nov.26-Dec.1, 2017, Chicago IL.
  • 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

License

By installing the CaPTk, the user agrees to the following licenses, which pertain to the code and its different constituents:

  1. SBIA Software License - https://www.med.upenn.edu/sbia/software-agreement.html
  2. SBIA Non-Commercial Software License - https://www.med.upenn.edu/sbia/software-agreement-non-commercial.html
  3. Insight Toolkit License - https://cmake.org/Wiki/ITK/License_Information
  4. Visualization Toolkit License - http://www.vtk.org/licensing/
  5. Qt Open Source License - https://doc.qt.io/qt-4.8/opensourceedition.html
  6. CC Attribution-ShareAlike for SRI24 data - https://creativecommons.org/licenses/by-sa/3.0/us/legalcode
  7. MRIcroGL License - BSD

The CaPTk software family (which includes the interactive framework and available applications) incorporates 3rd party libraries and toolkits. All rights to these components are subject to the terms and licenses of their respective owners. All trademarks are the property of their respective owners.

The incorporated packages include but are not limited to:

  1. Qt (https://www.qt.io/), The QT Company, Qt FOR APPLICATION DEVELOPMENT LICENSE (https://www.qt.io/terms-conditions/).
  2. ITK (https://www.itk.org/), Insight Software Consortium, Apache 2.0 License (https://itk.org/ITK/project/licenseversion1.html).
  3. VTK (http://www.vtk.org/), Kitware, BSD License (http://www.vtk.org/licensing/).
  4. OpenCV (http://www.opencv.org/), OpenCV, 3-Clause BSD License (http://opencv.org/license.html)
  5. KernelFit (https://github.com/glentner/KernelFit), Geoffrey Lentner, GPLv3 (https://www.gnu.org/licenses/gpl-3.0.en.html).
  6. MATLAB Runtime (https://www.mathworks.com/products/compiler/mcr.html), MathWorks, see MCR_license.txt within the Licenses folder of the CaPTk installation.
  7. ITK-SNAP (http://www.itksnap.org),Paul A. Yushkevich, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee, and Guido Gerig. User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability. Neuroimage 2006 Jul 1;31(3):1116-28, GPLv3 (https://www.gnu.org/licenses/gpl-3.0.en.html).

Changelog (Release notes)

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

  • 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

  • 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
  • DICOM to NIfTI conversion
  • Complete integration of WhiteStripe in the CaPTk UI (batch via CLI)
  • Updated implementation of Directionality Estimation

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

  • New applications added
  • Interactive functionality updated
  • Added central core for statistical analyses
  • Bug fixes

1.1.0

  • Added functionality to drawing
  • Documentation updated with more illustrative screenshots

1.0.1

  • Updated documentation outside and inside the application
  • Random bug-fixes

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

  • Release for MICCAI 2016
  • UI optimizations
  • Seed point selector updated

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

  • Bug fixes in the seed points are saved
  • Generic interactive improvements

0.0.1

  • First (internal) release of CaPTk
  • Mostly a prototype at this stage
  • Interactive elements (seed-point initialization, ROI drawing) work properly
  • Image loading for NIfTI and DICOM works
  • Some applications have been added to the compilation for testing

Next (People)