ROI Propagation - Introduction

The ROI Propagation tool is used to propagate ROIs that change slowly over time or space. A set of ROIs is defined at one or more time points in (typically) a cine image, outlining certain features of the image that are of interest. The tool can then fill in any gaps between time points where the ROIs have not been defined, or extrapolate them over the whole time course.

You can constrain the propagation so that the ROIs propagate smoothly, and you can also enforce periodicity so that there is a smooth transition from the end of the time course back to the beginning, as should be the case when propagating through a cardiac cycle.

When the propagation is complete, there are tools to perform further analysis using the ROIs; these tools are typically what is needed for cardiac-related analysis, but you can also easily write your own tool using the Java programming language, and load it as a plugin into the ROI Propagation tool.

Start the ROI Propagation tool from the Process menu: Launching the ROI Propagation tool
This will bring up:

The ROI propagation tool

Image to be Analysed

The image to be analysed is typically a cine MR image, with multiple time points and possibly multiple slices per time point. Load the image into Jim's main display.

Initial ROI Definition

You need to tell the ROI Propagation tool which structures you are interested in, by outlining them at one more time points. At each time point where you outline the structures, you must outline the same structures (i.e., there must be the same number of ROIs defined at each time point where there are ROIs). You do not need to outline the structures at every time point, but if the shape or position of the structures changes a lot during the time course, you should choose to do the outlining at some of the time points where the structures are noticeably different.

When drawing the outlines, you can use:

If you draw any other type of ROI, an error message will be shown. Whichever type of ROIs you use, the result will be a set of closed Spline ROIs, which are like the one you draw, but propagated across all time points, following the features you have outlined.

Note: at the time points where you have defined the ROIs, the propagated ROIs will not be exactly the same as the ones you have defined, because the tool will attempt to make the ROIs follow the outlines of shapes as precisely as possible.

When you have defined the ROIs at your chosen time points, save the ROIs to a disk file.

Options that influence the ROI propagation are described in the processing options section.

Jim Home