Display segment names on images

(Justin Cramer) #1

Is there a way to display segment names on every slice in a way similar to annotations on e-anatomy? (see attached image) The verbiage gets confusing because “label” and “annotation” already have different meanings in Slicer, but I essentially want to annotate my segmentation for the purposes of creating an anatomy reference.


(Andras Lasso) #2

You can use Markups module to mark points and assign a label to each point. The layout is not flexible: label is always displayed near the marked point.

You could write a short Python script to create markups automatically for a selected slice. For example, it could place a markup in the center of gravity of each segment. You could then move the markups manually as needed.



Also, dependent on the look-up table that you use, you could associate anatomical names with particular labels. On mouse over those names are displayed in the - data probe area of slicer
I used the brain atlas as example. It comes with its own custom look-up table.



Download the brain atlas: http://www.spl.harvard.edu/publications/item/view/2037

Standalone viewer: http://openanatomy.org/

(Justin Cramer) #4

Thanks for the suggestions. Sounds like that specific functionality isn’t available at this point. As a feature request, just a checkbox in the Segment Editor saying “Display visible segment names” would be awesome for creating educational content.

(Andras Lasso) #5

This would be certainly nice to have and would be happy to help anyone who would have some time to work on this.

In the meantime, we are starting a project on improving Slicer’s segmentation/atlas export to Open Anatomy. This may make the information almost as easily accessible as static images, but offer much more flexibility.