2014 Project Week:PkModeling user tool

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Key Investigators

  • BWH: Andrey Fedorov, Ron Kikinis
  • MGH: Jayashree Kalpathy-Cramer
  • GE: Jim Miller
  • Isomics: Steve Pieper

Project Description


  • Our goal is to develop an interactive module in 3D Slicer to help non-technical user do PK modeling. This module will wrap PkModeling extension CLI, possibly other pre-/post-processing tools, guide the user through the various choices that can be made, generate the maps and collect the summary statistics that will eventually be saved in a standard form.

Approach, Plan

  • discuss the desired capabilities of the module and its design
  • review the various components available in Slicer, or in the process of being integrated into Slicer that can be used by the module
  • test PkModeling functionality on the datasets from BWH and MGH


  • Design ideas: 3 modules of increasing complexity
    • one-click analysis: minimum interaction: fixed T1, population (model) AIF, produce maps and summary statistics
    • minimum user guidance: add manual AIF ROI definition for patient-specific AIF, allow direct ROI definition on the multivolume node
    • full analysis: choice of manual/auto/model AIF, T1 map based on FA/TR/IR
  • components to be added:
    • T1 modeling: FreeSurfer mri_ms_fitparams?
    • automatic AIF detection (MGH tool)
    • R2* correction from dual-echo sequence (MGH)
  • Features to be added to PkModeling
    • accept multivolume in concentration units (defined based on an attribute in the header, in the future need to consider adding units information to the Slicer volumes, on import?)
    • add population AIF
  • tested PkModeling on MGH brain DCE