Propagation Options

The propagation options for the ROI propagation tool

You can set the following options to tailor the way that the ROI Propagation tool propagates the ROIs:

  • Set the number of shape coefficients manually. Jim will automatically determine the 'complexity' of the shapes you define, and will create output Spline ROIs with an appropriate number of spline knot points for this complexity. However, you may wish to constrain the shape, or allow greater complexity by manually setting the number of shape coefficients. Setting the number of coefficients to 1 will constrain all propagated outlines to be circular. Setting it to 2 will allow the outlines to be elliptical. Increasing further allows greater complexity of the outline shapes. In general:
  • Leave Jim to decide the best number of shape coefficients, unless it is not doing a good job.

  • If the propagation does not follow the outline accurately, but deviates wildly, set the number of shape coefficients manually and use the smallest number of shape coefficients that is needed to accurately describe the outline shape. Good results can often be obtained with only 2 or 3 shape coefficients for vessel outlining.

  • Specifies that the shape changes are periodic. This tells the ROI Propagation tool that the changes in shape are periodic, with a period equal to the total number of time points in the sequence. Thus, this enforces a smooth transition from the last frame in the sequence back to the first, with no disjointedness. If the sequence is not periodic, the ROIs at the last point are propagated without regard to first time point.

  • Set the number of time coefficients manually. By default, Jim will not enforce any continuity between time points - it simply uses the image data to drive the changes in shape between time points. However, when the image quality is poor in some image frames, this can result in the shape and position of propagated ROIs changing in an unsatisfactory way for some time points. You can constrain the propagation to enforce smooth transitions in ROI shape and position by setting the number of time coefficients manually.

Reducing the number of time coefficients forces smoother transitions from one frame to the next, while increasing it allows greater freedom for the ROIs to follow complex, rapid motion. Using the minimum number number of time coefficients that still allows proper description of the motion will decrease the risk that the ROI Propagation tool will not track the images features reliably.

When you have set to the options, press the Button to start the propagation of ROIs button to begin the propagation. Depending on the number of shape and time coefficients used, processing can take a few moments. The propagated ROIs will be loaded into Jim's main display, for you to review. If you are not satisfied with the result, you can make changes to the propagation options and try again, or you can manually edit the propagated ROIs to your satisfaction.