Quick and Dirty Tracing using Thresholded Region Growing
MultiTracer version 2
Before you contour, you should define the structure.
Before opting to use this approach rather than manual tracing, consider the following limitations:
- The contours generated by region growing are defined in the original images, not the magnified display images.
Consequently, the contours will not have subvoxel resolution.
- The starting and ending points of the contours are defined by the region growing algorithm and
have no intrinsic anatomic meaning. Seeding the algorithm at a different point may generate the same
contours, but with different start and end points.
- Only closed contours can be generated.
You can use a threshold based, two-dimensional region growing algorithm to trace structures as follows:
- Go to a plane where the structure is visible (use the "-" or "+" buttons on the control
panel at the bottom of the main window or type a plane number into the box between these buttons).
- Using the popup menu at the top of the control panel at the bottom of the main window,
select the name of the structure you want to trace.
- If MultiTracer is not currently in wand mode (indicated by red text on the "Wand" button on
the control panel), click on the "Wand" button to activate tracing mode. You may need to click
on this button a second time to bring up the "Wand Control" panel.
- Hold down the shift key and click seed points on the image that you want to be included in the
thresholded structure until the Wand Control panel becomes active (while inactive, the panel
will appear lighter in color and the sliders will not respond). Note that this sets the
"Min" and "Max" thresholds in the "Wand Control" panel to the minimum and maximum values of
the voxels you clicked.
- In the "Wand Control" panel, adjust the "Min" slider downward and the "Max" slider upward to grow the selected
contour to the desired size (the contour may not appear until both have been adjusted). Moving
the sliders in the opposite direction will shrink the region.
The contour is redrawn each time that you release the slider control.
- Once you are happy with the thresholds, you can click elsewhere on the current slice or on a
new slice. Click at the location where you want to seed the region, and the contour will
be generated automatically. You can refine the thresholds interactively in the "Wand Control"
panel to grow or shrink the region.
- To reset the "Wand Control" for a new structure, simply hold down the shift key while
clicking on a region and then repeat the above steps.
- If you want to improve the contour manually, you can modify it.
- If multiple images are displayed, the thresholds apply to the image used to seed the wand
Since anatomic protocols often forbid multiple traces for the same structure on a given
plane, MultiTracer will warn you if you complete additional traces using the same structure
name. To prevent this warning from being displayed, click the checkbox labelled "Don't show
this message again". The message will be suppressed until the next time you launch MultiTracer.
If you choose to allow more than one trace for a given structure on the same plane, you should
be careful to assure that the different traces do not overlap--areas and volumes will be computed
as if the structures were not overlapping, so overlaps will result in overestimates of areas and
©2001-2012 Roger P. Woods, M.D.
Modified: August 26, 2012