Cancer Imaging Phenomics Toolkit (CaPTk)  1.9.0
Miscellaneous: Perfusion Alignment

This application does perfusion alignment of the input Dynamic-Susceptibility Contrast-enhanced (DSC) MRI scan.


  1. A single DSC-MRI scan.
  2. The time-resolution (time-interval in seconds between the two volumes) of the given DSC-MRI scan.
  3. Number of time-points before and after the drop of the curve that we want our image to be aligned with.


  1. Launch the application from "Applications" -> "Perfusion Alignment".
  2. 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.
  3. 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
  4. Press "Confirm" button.
  5. The individual volumes of the aligned DSC-MRI image will be saved at the specified location (~5 minutes).
  6. Output folder will contain the alighed perfusion image along with CSV files containing the original, truncated, revised and interpolated perfusion curve signals.
  • This application is also available as a stand-alone CLI for data analysts to build pipelines around, using the following example command:
    ${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