Cancer Imaging Phenomics Toolkit (CaPTk)  1.9.0
Frequently Asked Questions

Table of Contents

Which platforms are supported by CaPTk installers?

Platform (x64) Tested Unsupported
Windows 7, 8, 10 XP, Vista
Linux Ubuntu 16.04, 18.04; Debian 9, CentOS 7 (source build) Ubuntu 14.04; CentOS 6
macOS 10.13, 10.14 10.12
Docker N.A. N.A.

What DICOM images are currently supported by CaPTk?

CaPTk has limited DICOM support. It only supports a limited protocols for MR, CT and MG modalities. DICOM loading has only been tested for images from UPenn. If you are not able to load your DICOM images, please open a new issue and send some anonymized DICOM images for us to test.

How do I run CaPTk Applications from the Command Line?

  • The full list of command line applications available is shown by running the following command (pretty much every application is available via the command line): 
    ${CaPTk_InstallDir}/bin/CaPTk -h
  • An exemplary scenario to run Applications from the command line (the example shown is to get verbose help):
Platform (x64) Functionality Successful Installation Build From Source (after invoking "make install") FUSE Issues (after invoking "--appimage-extract")
Windows Generic ${CaPTk_InstallDir}/bin/${ApplicationName}.exe -h ${CaPTk_InstallDir}/bin/${ApplicationName}.exe -h N.A.
Linux Generic ${CaPTk_InstallDir}/bin/captk ${CaPTk_InstallDir}/bin/${ApplicationName}.cwl -h ${CaPTk_InstallDir}/bin/${ApplicationName} -h ~/CaPTk/${version}/${ApplicationName} -h
macOS Generic ~/Applications/CaPTk_${version}.app/Contents/Resources/bin/${ApplicationName} -h ${CaPTk_InstallDir}/bin/${ApplicationName} -h N.A.
Windows FeatureExtraction ${CaPTk_InstallDir}/bin/FeatureExtraction.exe -h ${CaPTk_InstallDir}/bin/FeatureExtraction.exe -h N.A.
Linux FeatureExtraction ${CaPTk_InstallDir}/bin/captk FeatureExtraction.cwl -h ${CaPTk_InstallDir}/bin/FeatureExtraction -h ~/CaPTk/${version}/FeatureExtraction -h
macOS FeatureExtraction ~/Applications/CaPTk_${version}.app/Contents/Resources/bin/FeatureExtraction -h ${CaPTk_InstallDir}/bin/FeatureExtraction -h N.A.
  • There are detailed examples of individual command line usage in the How To section of the documentation.

What are the OpenGL requirements to run CaPTk?

What if I am having issues with the Linux Installer?

This section highlights some of the common issues on Linux machines.

FUSE Issues

If the installer successfully finishes and you are not able to run CaPTk due to FUSE issues, please extract the installer using the following command to extract the contents of the AppImage onto the hard drive: 

user@pc:~# ~/CaPTk/${version}/captk --appimage-extract
  • This will extract the package to the path ~/CaPTk/${version}/squashfs-root/usr/ with the binaries present in ~/CaPTk/${version}/squashfs-root/usr/bin.
  • To run CaPTk from the command line in this manner, the user would need to make the following additions:
    • Add the path ~/CaPTk/${version}/squashfs-root/usr/lib to their environment variable PATH: export PATH=~/CaPTk/${version}/squashfs-root/usr/bin:$PATH
    • Add the path ~/CaPTk/${version}/squashfs-root/usr/lib to their environment variable LD_LIBRARY_PATH: export LD_LIBRARY_PATH=~/CaPTk/${version}/squashfs-root/usr/lib:$LD_LIBRARY_PATH
    • This will need to be present in the user's shell start up file .bashrc, .cshrc, .profile, .kshrc, etc.` for the settings to be persistent across login sessions.
    • All the command line applications should now be available for use. For example: 
      FeatureExtraction \ # the executable should already be in the $PATH
-n AAC0_timestamp \ # this is the subject ID for this run 
-i /usr/path/T1.nii.gz,/usr/path/T2.nii.gz -t T1,T2 \ # the co-registered input image(s) and their respective modalities
-m /user/path/mask.nii.gz \ # the mask file (co-registered with the input image(s)
-r 2,4,5 -l ED,EN,NE \ # the labels from the mask file from where features need to be extracted and their respective label identifier(s)
-p /usr/path/features.csv \ # the parameter file to use 
-o /usr/path/output.csv # the path to write the output

GLIBCXX or GLIBC Issues

  • This is happening because the Linux binaries are compiled using the GCC-4.8 package on Ubuntu 16.04; therefore you will need to update GCC 4.8.5 or newer in order to get CaPTk to work. Some examples are shown:
    • Ubuntu [ref]: 
      sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install gcc-4.9 g++-4.9
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9
    • CentOS [ref]: 
      sudo yum install centos-release-scl
sudo yum install devtoolset-6
  • You can still build CaPTk from source using the instructions in Technical Reference. Note that you will need a C++11 compliant compiler.

CXXABI issues

If you are running into mis-matched CXXABI behavior with a message similar to:

libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /lib/x86_64-linux-gnu/libGLU.so.1).

This means that you are running on a very new Linux distribution. Please see the discussion in https://github.com/CBICA/CaPTk/issues/1229 for details.

Is there a minimum recommended screen resolution for running CaPTk?

The minimum recommended resolution is 1200x1024. We have seen some visualization issues with high DPI (>2K) screens and bug reports related to it will be appreciated.

Where can I find the CaPTk Docker Image?

You can find all the builds in our Docker Hub repository: https://hub.docker.com/r/cbica/captk

How do I run the CaPTk Docker Image to show the interface?

docker run -it \
  -v /tmp/.X11-unix:/tmp/.X11-unix \
  -v $(pwd)/test:/app \
  -e DISPLAY=$DISPLAY \
  -u qtuser \
  cbica/captk

Is there something wrong with Feature Extraction?

Please see the Feature Extraction FAQ.

I am having issues running CaPTk on Ubuntu 20.04

This is a well-known problem, documented in the following GitHub issues:

A possible solution is to revert the default GCC to version 5 using the following steps [ref] 

echo "deb http://archive.ubuntu.com/ubuntu xenial main" | sudo tee /etc/apt/sources.list.d/xenial.list
sudo apt-get update
sudo update-alternatives --remove-all gcc
sudo update-alternatives --remove-all g++
sudo apt-get install gcc-5 g++-5
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 10
sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-5 10

I am having issues running CaPTk on Ubuntu 20.04

Please open a new issue with us and we will do our best to resolve it.