Cancer Imaging Phenomics Toolkit (CaPTk)  1.8.0.Beta
Miscellaneous: PCA Volume Extraction

This application extracts the principal components from DSC-MRI scans as mentioned in [1].

REQUIREMENTS:

  1. A single DSC-MRI image
  2. Its corresponding mask for which the measurements need to be extracted

USAGE:

  1. Load a DSC-MRI in CaPTk and the mask (Label:1) defining the voxels to extract the measurements.
  2. Launch the application from "Applications" -> "PCA Volume Extraction".
  3. Specify the number of principal components required and the output directory.
  4. Press the "Confirm" button.
  5. The principal components will be extracted at the specified location and also loaded in CaPTk (~5 minutes).

This application is also available as with a stand-alone CLI for data analysts to build pipelines around, using the following example commands:

  • The following command will train a new model based on the samples in the inputDir using 5 principal components:
    ${CaPTk_InstallDir}/bin/PerfusionPCA.exe -t 0 -i C:/properly/formatted/inputDir -o C:/outputDir -n 5
  • The following command will perform inference using an existing model for inputs in C:/input based on C:/modelDir using 5 principal components:
    ${CaPTk_InstallDir}/bin/PerfusionPCA.exe -t 1 -i C:/properly/formatted/inputDir -m C:/inputModelDir -o C:/outputDir -n 5

References:

  1. H.Akbari, L.Macyszyn, X.Da, R.L.Wolf, M.Bilello, R.Verma, D.M.O'Rourke, C.Davatzikos, "Pattern analysis of dynamic susceptibility contrast-enhanced MR imaging demonstrates peritumoral tissue heterogeneity", Radiology. 273(2):502-10, 2014, DOI:10.1148/radiol.14132458