Segmentation

On the Segmentation tab, the user can find multiple tools for delineating structures in CT images. The current delineation tools include Hounsfield Unit-based thresholding, as well as a HU-based brush and eraser tool. The Segmentation module also included functions to export key statistics such as volume, and centre-of-mass, and export the structures as a mask in .nifti format. On this page, the user can find an extensive explanation of the possible functionalities.

Creating empty structures

In order to use one of the segmentation tools, the user first has to create an empty structure. This can be seen as an empty canvas on which the segmentation will be 'drawn'. The user has the option to create a structure for the select volume only, or for all the loaded image volumes. 

Create single empty structure

To create a single empty structure, first click on the image volume for which you want to create an empty structure. Next, input the name of structure to be created and press on "Create structure". The structure will then be added to the list on the left, after which the user can select the created structure.

Create empty structure for multiple volume

If the user wants to delineate a certain structure in multiple image volumes, the user can use the "All series" option, to quickly create an empty structure for all the loaded image volumes. First, select on of the image volumes, and input the name of the structure to be created. Next, make sure the "All series" option is selected and press "Create structure". A structure will now be created for all the loaded volumes, and displayed in the list on the left. 

Manual delineation tools

For manual delineation, the user can use the brush, erase and undo functionalities. First, select structure to delineate and select the brush tool under the Manual edits tab. The user can specify the HU range to clip the brush and erase tool, using the sliders and the HU distribution graph on the top. The undo button can be used to undo the latest brush or erase stroke. Additionally, the user can specify brush size, which is useful when delineating small or large structures.

Exporting

Once the user has delineated the structures of interest, they can go to the Analysis tab. First, the user can press "Calculate statistics"  to calculate some statistics of the structure such as the volume and the center-of-mass. Next, the user can select the structures to export using the checkboxes. The user can then export the statistics of the selected structures as an .csv file by clicking on the "Export statistics" button. Lastly, the user can export the 3D masks corresponding to the structures in nifti-format by clicking on "Export structures".