T1-weighted perfusion imaging parameter calculation toolkit
Questions and answers:
- What is TOPPCAT?
- How do I download TOPPCAT?
- How do I install TOPPCAT?
- 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?
- What kind of hardware / software is required to use TOPPCAT?
- What kind of imaging data is needed to use TOPPCAT?
- What kind of user input will be needed to use TOPPCAT?
- What methods does TOPPCAT use?
- How can I be sure that TOPPCAT was correctly installed?
- How do I upgrade to the new TOPPCAT version?
- Where can I get support, discuss issues related to TOPPCAT, or discuss issues related to DCE MR imaging in general?
- What is the easiest way to stay informed about new software releases?
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.
TOPPCAT is available for download for individuals affiliated with industrial or academic institutions.
To get and use TOPPCAT:
- Fill out the Leave a Reply form on this page with your name and email address.
- In the Comment section, enter your institution name and mention that you would like to download TOPPCAT.
- Click the Post Comment button. Your comment will be submitted to us but will not be published on the website.
- You will receive an email with the link to where you can download the TOPPCAT software and related files.
- Read and abide by the software disclaimer:
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 firstname.lastname@example.org 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
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.
- A User’s Guide to TOPPCAT is available here.
- TOPPCAT Release Notes are available here.
- A summary of methods used in TOPPCAT is available here.
- TOPPCAT test data instructions are available here.
- The TOPPCAT dashboard is available here.
- 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 ?
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.
- 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.
- 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.
The user input required is:
- The user must place a region of interest in a vascular structure to provide a surrogate for capillary plasma concentration.
- The user must designate the time point in the perfusion imaging series that represents the last time point before arrival of the contrast agent.
To test that TOPPCAT was correctly installed:
- 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.
- Open the test T1 Mapping MR image data (Map Stack) in ImageJ.
- Open the test Dynamic MR image data (Dyn Stack) in ImageJ.
- Open the test superior sagittal sinus region of interest (SSS.roi) so that it appears on the Dyn Stack stack.
- Open ImageTimeTable.txt in ImageJ.
- Open the test macro (TestMacro.txt) in ImageJ.
- 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).
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.
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.