TOPPCAT

TOPPCATlogo

T1-weighted perfusion imaging parameter calculation toolkit

Questions and answers:
What is TOPPCAT?

TOPPCAT stands for T-One weighted Perfusion imaging Parameter CAlculation Toolkit. Its purpose is to create quantitative maps of Ktrans (volume transfer constant between blood plasma and the extravascular extracellular space) and fV (fractional plasma volume) from dynamic T1-weighted (also known as dynamic contrast-enhanced or DCE) magnetic resonance perfusion images. This software is being offered as a research tool for individuals affiliated with industrial or academic institutions.

How do I download TOPPCAT?

TOPPCAT is available for download for individuals affiliated with industrial or academic institutions.

To get and use TOPPCAT:

  1. Fill out the Leave a Reply form on this page with your name and email address.
  2. In the Comment section, enter your institution name and mention that you would like to download TOPPCAT.
  3. Click the Post Comment button. Your comment will be submitted to us but will not be published on the website.
  4. You will receive an email with the link to where you can download the TOPPCAT software and related files.
  5. Read and abide by the software disclaimer:
Terms of Agreement:
Copyright ? 2004-2006 by Duke University. All rights reserved.

Permission to copy, use, and modify this software and accompanying documentation for educational and research purposes is hereby granted, without fee and without a signed licensing agreement, provided that the above copyright notice, this paragraph and the following two paragraphs appear in all copies including derivatives of the software. The copyright holder is free to make upgraded or improved versions of the software, provided that they are made readily available to others on these same terms without fee or any other charge. Contact the copyright holder at barbo013@mc.duke.edu for commercial licensing opportunities.

IN NO EVENT SHALL THE COPYRIGHT HOLDER BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, OF ANY KIND WHATSOEVER, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF HE HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

THE COPYRIGHT HOLDER SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING DOCUMENTATION IS PROVIDED “AS IS”. THE COPYRIGHT HOLDER HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS
6. In any publication using TOPPCAT software, cite the following reference:
Daniel P. Barboriak, James R. MacFall, Anthony O. Padua,Gerald E. York, Benjamin L. Viglianti, and Mark W. Dewhirst. Standardized software for calculation of Ktrans and vp from dynamic T1-weighted MR images. Presented at the International Society for Magnetic Resonance in Medicine Workshop on MR in Drug Development: From Discovery to Clinical Therapeutic Trials, McLean VA, April 2004.
How do I install TOPPCAT?

Make a directory called TOPPCAT in your ImageJ plugins folder and unzip the downloaded files (TOPPCAT_v1.6.zip and DBLAB.zip) into this subdirectory, and then restart ImageJ.

Important: If you have already installed DSCoMAN and/or JDTI, you do not need to download and install the DBLAB utility file again.

I am interested in TOPPCAT. What kind of documentation do you have available?
What kind of information could be gained from maps of Ktrans and fV?
Traditional MR imaging gives both structural and physiological information. For example, in a patient with a brain tumor, contrast-enhanced MR imaging can be used to specifically locate the position of the tumor in the brain. In addition, the presence of an area of contrast enhancement indicates a physiological change ? damage to the blood-brain barrier, with increased leakage of contrast agent from the plasma into the extravascular extracellular space. Taking advantage of recent advances in the quality and speed of MR image acquisition, dynamic contrast-enhanced MR imaging techniques have been developed to better quantify these kinds of physiological changes.
It may be helpful to conceptualize the presence of contrast enhancement in a tissue as having two components. The first component is due to the presence of blood vessels in the tissue. Intravenous contrast agents reach tissue via the blood stream, and, all other things being equal, tissues with a higher concentration of blood vessels demonstrate more contrast enhancement than those with less. The second component is that due to leakage of contrast agent across the capillary endothelium and into the extracellular extravascular space. Pathological processes such as tumors may alter the leakage rates of contrast agent.
Dynamic contrast-enhanced MR imaging techniques are used to separately measure these two components of the phenomenon of contrast enhancement. If measured accurately, changes in fV reflect changes in the vascularity of the underlying tissue, and changes in Ktrans reflect changes in capillary endothelial leakage. (It should be noted here that the two measurements are not completely independent ? Ktrans depends not only on the leakage rate of contrast agent across the capillary endothelium, but also on the surface area of capillary endothelium across which contrast agent can leak. Changes in fV can affect Ktrans because changes in tissue vascularity would likely change the surface area of leaking vessels in the tissue).
There has been increasing interest in DCE MR imaging because changes in these physiological tissue perfusion and leakage parameters may be useful as:
  • Prognostic indicators of malignancy in patients with cancer
  • Biomarkers of treatment efficacy in treatment of patients with cancer
  • Markers of disease activity in patients with multiple sclerosis
  • Measurements of myocardial perfusion in patients with coronary artery disease
  • Measurements of disease activity in animal models of experimental arthritis
  • Measurements of neovascularity and macrophage content in carotid plaques
  • Many other applications have been suggested ?
What kind of hardware / software is required to use TOPPCAT?

TOPPCAT is designed as modular plugins to the ImageJ software package, a well-known public domain open source Java-based image processing program authored and maintained by Wayne Rasband at the National Institute of Mental Health (rsb.info.nih.gov/ij/). The software is written in Java, and can be run on Windows, Mac, and Linux/Unix operating systems.

What kind of imaging data is needed to use TOPPCAT?
To use TOPPCAT, you will need MR images in this form:
  1. A dynamic T1-weighted contrasted enhanced perfusion imaging series. This usually consists of a 3D SPGR or FLASH MR sequence that is repeated for a given imaging volume during the intravenous injection of gadolinium contrast agent.
  2. Maps of T1 (in msecs) and S0 (equilibrium magnetization) for the image locations covered in the perfusion imaging sequence. TOPPCAT can calculate these maps if the user performs T1 mapping sequences using multiple flip angle SPGR images of the relevant locations. It is important to note that the repetition time (TR) for these sequences should be kept constant.
What kind of user input will be needed to use TOPPCAT?

The user input required is:

  1. The user must place a region of interest in a vascular structure to provide a surrogate for capillary plasma concentration.
  2. The user must designate the time point in the perfusion imaging series that represents the last time point before arrival of the contrast agent.
What methods does TOPPCAT use?
There are many methods which can be used to extract perfusion parameters from perfusion MR images. For the purposes of this initial demonstration, TOPPCAT uses Patlak analysis (Patlak CS, Blasberg RG, Fenstermacher JD. Graphical evaluation of blood-to-brain transfer constants from multiple-time uptake data. J Cereb Blood Flow Metab. Mar 1983;3(1):1-7) to calculate Ktrans and fV maps from maps of contrast agent concentration over time.
In Patlak analysis, contrast agent transport is assumed to be unidirectional (from plasma space into extracellular extravascular space). Although this model has the advantage of simplicity, it is important to note that the model will give inaccurate results when this assumption is incorrect. As a general rule, the Patlak model is most appropriate for use when the duration of the experiment is short (?first pass? studies), when the volume fraction of the extracellular space is large, and when Ktrans is small. For conventional gadolinium-based contrast agents (which have a relatively low molecular weight), the assumption of unidirectional transport is frequently not valid, particularly for experiments of long duration.
The methods are further outlined in the TOPPCAT Methods document.
How can I be sure that TOPPCAT was correctly installed?

To test that TOPPCAT was correctly installed:

  1. Click the “Download the test data” link found on the right side of this page (this link will appear when you are given access to the TOPPCAT download). Download the zipped package of test data and unzip the contents.
  2. Open the test T1 Mapping MR image data (Map Stack) in ImageJ.
  3. Open the test Dynamic MR image data (Dyn Stack) in ImageJ.
  4. Open the test superior sagittal sinus region of interest (SSS.roi) so that it appears on the Dyn Stack stack.
  5. Open ImageTimeTable.txt in ImageJ.
  6. Open the test macro (TestMacro.txt) in ImageJ.
  7. Run the macro (click on Dyn Stack which makes it active, then click on the TestMacro.txt macro and press control-R) The resultant images should match (i.e. K = K.tif, FV = FV.tif, etc).
How do I upgrade to the new TOPPCAT version?

First delete all the class files for the old TOPPCAT version from your ImageJ plugins folder. Then download and unzip the new TOPPCAT software into the subdirectory TOPPCAT under your ImageJ plugins folder. The latest version of TOPPCAT depends on other utility classes that can be obtained by clicking the link for “Download the Utilities” on the right side of the TOPPCAT homepage. Unzip the file called DBLAB.zip and save it in the main ImageJ plugins folder i.e. Image_Homeplugins (where ImageJ_Home is the home of your ImageJ installation). This will save DBLAB.jar into your ImageJ plugins folder. Then, restart ImageJ. Note that TOPPCAT version 1.5 works on ImageJ version 1.36 and higher.

Where can I get support, discuss issues related to TOPPCAT, or discuss issues related to DCE MR imaging in general?

Only limited support is available for this free software.

Please submit questions to us through email. Your comments, questions, and complaints are welcome. Email is also a location where issues related to DCE MR imaging could be discussed.

What is the easiest way to stay informed about new software releases?

By email: Click on the “Contact Us” link on the left side of the lab homepage. In the Comments field type in keyword “Mailing List,” and we will send you periodic email about software upgrades available from the lab, as well as other news. Let us know if you would like to be taken off of the mailing list.

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