PET Tracer Kinetic Modeling (methods, tools, etc.)

Models

In-House Software

Tools

The following are third party tools (some available free of charge, some not) which we've either found useful or have simply become aware of their existence. Where possible, we've included a brief introduction from their manuals to give a flavor of what they can be used for. All information reprinted without permission.

  1. ADAPT II (free/requires signed license agreement)
    1. "Mathematical Software for Pharmacokinetic/Pharmacodynamic Systems Analysis"; Developed and supported by the Biomedical Simulations Resource, University of Southern California, Los Angeles, California 90089-1415 phone/fax: (213)740-0839/(213)740-0343; braun@bmsrs.usc.edu
    2. 1992 ADAPT II User's Guide Introduction: ADAPT II consists of a set of high-level interactive programs, developed primarily for basic and clinical research modeling and data analysis applications involving pharmacokinetic and pharmacodynamic processes. The generality and flexibility of the package also make it a useful tool for dynamic system modeling applications involving other types of sparse data systems. Currently, ADAPT II contains programs for model simulation (SIM), parameter estimation (ID), and sample schedule design (SAMPLE). more to follow . . .
    3. COMMENT: This package is good for ROI based modeling (e.g. one tissue TAC and one blood TAC), but generation of functional images is not practical with this current version. Measured input TAC curves can be simulated in this software using an appropriate number of "mini" boluses trained together.
  2. MATLAB (The Mathworks, Inc.; commercial package)
    1. The MathWorks, Inc.; 24 Prime Park Way, Natick, Massachusetts 01760 phone/fax: (508)653-1414/(508)653-2997; info@mathworks.com
    2. COMMENT: A powerful programming environment based on a matrix manipulation paradigm. Also has many extension "toolboxes" for signal processing, modeling, etc., and has reasonable display-I/O capabilities. The SPM package from the Hammersmith group for analyzing PET and fMR images is written in Matlab.
  3. MATHEMATICA (Wolfram Research, Inc.; commercial package)
    1. Wolfram Research, Inc.; 100 Trade Center Drive, Champaign, IL 61820-7237 phone/fax: +1(217)398-0700/+1(217)398-0740; info@wri.com
    2. COMMENT: Symbolic Mathematics package
  4. IDL (Research Systems, Inc.; commercial package)
    1. Research Systems, Inc.; 2995 Wilderness Place, Boulder, CO 80301 phone/fax: (303)786-9900/(303)786-9930; info@rsinc.com
    2. COMMENT: Image display/manipulation package which frees you from having to worry about display I/O. Has a fairly powerful language which is interpretive, so you can explore data processing techniques and then write software to instantiate them in a form you like. Also has "Numerical Recipies in C" functions built in. The PV-WAVE software package started with the IDL core code a while back and is now developed independently. The ECAT 7.0 software will be in part based on IDL.
  5. AVS (Advanced Visual Systems, Inc., commercial package)
    1. Advanced Visual Systems, Inc.; 300 Fifth Avenue, Waltham, MA 02154 phone/fax: +1(617)890-4300/+1(617)890-8287; support@avs.com
    2. COMMENT: AVS is a very powerful 2D/3D display/programming enviroment for "Scientific Visualization". One of its real strengths is the way it allows you to create data manipulation "modules" which perform some arbitrary data manipulation task. These modules can then sit on a programmer's palate, and be drag/dropped into a computational network to perform whatever set of data manipulation tasks you wish. Although it comes with an extensive set of modules for input/fltering/manipulation/display, you can write your own too. The modules actualy become active processes that communicate with each other via RPC calls. You simply plop down the modules you want, link the data ports from the modules with your cursor, and presto, you have a complete program you can then save for future use. Somewhat expensive, requiring programming experience to develop your own modules, and a hardware hog, this was still my personal favorite display/programming environment back when we had the funds to support it ;-).
  6. Simulation, Analysis, and Modeling Software
    1. SAAM (Laboratory of Mathematical Biology, NIC/FCRDC NIH, freeware - DOS/Windows)
    2. SAMM II (expired-http://pharm.cpb.uokhsc.edu/pkin/saamii.html) (commercial package)
    3. COMMENT: None - haven't acquired it just yet.