Editing Structures

Editing a Structure Set

1. With a patient selected, choose the Structures tab.
2. In the toolbar above the interactive viewer, press the Edit Structure Set button.

See below for further instructions on how to add, edit, and delete structures.

Running Auto-Segmentation on an Existing Structure Set

1. With a patient selected, choose the Structures tab.
2. In the toolbar above the interactive viewer, press the Run Auto Segmentation button.
3. Select the Algorithm from the list of algorithms configured for the workspace.
4. Optional: Select a structure set Template. When processing the auto-segmentation result, the system will apply a structure set template by comparing the structures in the result to the list of structures defined in the template. The system will initialize an empty structure for each structure defined in the template that does not exist in the auto-segmentation result, using the type and color specified in the template.
5. Place a check mark next to the algorithm-defined structures that should be included in the result structure set.
6. Remove a check mark next to the algorithm-defined structures that should not be included in the result structure set.
7. Enter the Desired Structure Name for each structure. Use the undo button to revert the name back to the name defined by the algorithm.
8. Choose the Color for each structure. Use the undo button to revert the color back to the color defined by the algorithm.
9. Press Run to invoke the auto-segmentation algorithm.
10. When the task is complete, the list of structures on the left will refresh with the auto-segmented structures.

Downloading Structure Templates

While editing a structure set, press the Export Structure Template button (denoted by a download icon) located in the toolbar at the top of the left sidebar. This will produce a CSV file, containing columns for the structure name, the structure type, and the RGB components of the structure color. Exported structure templates can then be imported (with modification if desired) using the procedure below to facilitate the standardization of structure names, types, and colors.

Importing Structure Templates

1. With the Structures tab activated, press the Edit Structure Set button located on the right side of the contouring toolbar.
2. Press the Import Structures button at the top of the left sidebar.
3. Choose Import Structures from Structure Set Template, Import Structures from Existing Structure Set, or Import Structures from File.
4. If you select Import Structures from Existing Structure Sets (this will be the default option):
   1. Choose the Structure Set you wish to import.
   2. Select how duplicate structures should be handled by choosing one of the following options described below.
      • Keep both structures. Conflicting structures will be resolved by checking for the presence of structure data (contours, lines, and points). If one structure does not contain structure data, it will be ignored in favor of the other structure. Otherwise, both structures will be kept, and duplicates will be resolved by adding the name of the structure set or a numeric identifier in parenthesis as a suffix.
      • Keep current structures (ignore imported). Conflicting structures will be resolved by retaining the structure from the current structure set and ignoring the structure from the structure set selected for import.
      • Keep imported structures (overwrite current). Conflicting structures will be resolved by overwriting the structure from the current structure set with the structure from the structure set selected for import.
5. If you select Import Structures from Structure Set Template:
   1. Choose a Template you wish to import.
   2. Select how existing structures with the same case-sensitive name should be handled. Choose either Leave existing structure color and type unchanged or Update structure color and type to match template.
6. If you select Import Structures from File:
   1. Press the Select File button to browse for the CSV file that contains structure template information from your computer.
   2. Select how existing structures with the same case-sensitive name should be handled. Choose either Leave existing structure color and type unchanged or Update structure color and type to match template.
7. Press the Import button.

Adding a Structure

1. While editing a structure set, press the create structure button (denoted by the plus symbol) located in the left sidebar.
2. Choose a Name, Type, Description, and Color for the structure. Structure names must be 80 characters or less. Descriptions must be less than 1024 characters.
3. Choose a creation Method as described below. Note that there are also Clone Structure and Create New Structure as Uniform Margin shortcut icons that are available in the toolbar below a selected structure. See the notes in the Clone Existing Structure and Apply a Uniform Margin to an Existing Structure methods below.
4. Press the Create button to create the structure.

Manually Contoured

This method creates an empty structure with no contours. After the empty structure is created, use the contouring tools to add contours.

Clone Existing Structure

Select the Structure to Clone to create a copy of that structure.

Note: By selecting the structure you wish to clone and clicking on the Clone Structure icon in the toolbar beneath the selected structure, the Create Structure dialog will open with Type, Method, and Structure to Clone automatically populated,

Add Two Structures Together

Select the First Structure and the Second Structure (to Add) to create a structure that is the union of the two selected structures.

Subtract One Structure from Another Structure

Select the First Structure and the Second Structure (to Subtract) to create a structure that is the difference of the two structures.

Create an Intersection of Two Structures

Select the First Structure and the Second Structure to create a structure that is the intersection of the two structures.

Apply a Uniform Margin to an Existing Structure

Select the Structure to Clone and Add Margin and enter the Margin (mm) to create a structure with a uniform margin around another structure. Negative margins can be applied.

Note: By selecting the structure around which you wish to apply a uniform margin and clicking on the Create New Structure as Uniform Margin icon in the toolbar beneath the selected structure, the Create Structure dialog will open with Type, Method, and Structure to Clone and Add Margin automatically populated.

Create a Ring Structure from an Existing Structure

Select the Structure to Offset and enter the Inner Margin (mm) and Outer Margin (mm) to create a ring structure from the existing structure.

Create a Structure from an Isodose

Enter the Isodose (Gy) of the iso-surface from which to create a structure.

Editing a Structure

1. While editing a structure set, choose the structure you wish to edit by clicking on it.
2. In the row of tools that appears below the selected structure, select the edit button denoted by the pencil icon.
3. Set the Name, Type, Description, and Color for the structure.
4. Press the Save button to save your changes.

Deleting a Structure

1. While editing a structure set, choose the structure that you wish to delete by clicking on it.
2. Confirm that you wish to delete the structure by pressing the Remove button.

Updating Contours Using the Contouring Tools

While editing a structure set, click on a structure to select it. Then use the tools described below to edit the contours for the selected structure.

Draw

Click on the draw tool to activate it. With the draw tool activated, you can contour a structure in a point-and-click fashion or by clicking and dragging to draw a continuous line. To add to an existing contour, start from inside the contour and draw outwards. To remove from an existing contour, start from outside the contour and draw inwards. Toggle the default add/edit mode by holding down the Shift or Alt key. You must close each draw operation at the same point you began.

Paint

Click on the paint tool to activate it. With the paint tool activated, you can contour a structure by clicking and dragging the paintbrush across the image. Toggle the default add/edit mode by holding down the Shift or Alt key.

Interpolation

To interpolate between slices, click on the Interpolate button. Once clicked, ProKnow DS will attempt to generate contours for the current structure on all empty slices between slices containing contours. There are several situations in which warnings will be reported after the interpolation has completed. Please note that when these warnings are displayed, only the indicated range will have not been interpolated. Any other empty slices able to be interpolated will be completed. The most common warnings include:

• Unable to interpolate between the slice at X.XX mm and the slice at Y.YY mm as the slices each contain multiple contours and the contour orientations are not consistent (most commonly caused by complex bifurcation scenarios). This is an uncommon case that can occur when attempting to interpolate between slices that have the same number of contours, but the orientations of the contours are not consistent from one slice to the other. For example, in the following images, you can see two slices, Slice A, which contains two contours: a circle and a hole; and Slice B, which also contains two contours: two circles. Please note that in both of these images, the "interior" portion of the contours have been slightly filled to aid in the visual distinction.
  
  
  In this case, the contour orientations between the two slices (1 CCW and 1 CW in Slice A and 2 CCW in Slice B) do not match, and indeed, there is no obvious solution for how to interpolate between these two slices.
• Unable to interpolate between the slice at X.XX mm and the slice at Y.YY mm as no valid combination of overlapping contours could be found. This situation can occur when interpolating between slices that contain different numbers of contours. When there is a different number of contours from one slice to another, for example, between Slice A and Slice B below, ProKnow DS attempts to determine the most suitable pairwise combination of contours by looking at the overlapping area between all contours from one slice to another. ProKnow DS interpolates, in order of greatest overlapping area, from each contour on the first slice to the corresponding contour on the second slice. For example, when interpolating between Slice A and Slice B, ProKnow DS will interpolate the larger circle from Slice A to the single circle on Slice B since, if superimposed onto the same slice, their areas would overlap.
  
  
  However, when interpolating from Slice B to Slice C, the circles share no area in common and thus, ProKnow DS will report a warning when attempting to interpolate between these two slices.
  
  In general, it is always best to interpolate between highly similar slices, especially in cases where there are multiple contours present on each slice.

In addition to the warnings listed above, there are also several situations which can cause critical failures during interpolation. If you receive a message indicating that the "Interpolation Failed," then ProKnow DS encountered an error that prevented interpolation from completing. There are two cases where you may encounter errors during interpolation:

• Slice at position X.XX mm contains contour data but does not exist in the slice position list. This can occur in rare cases where the source structure set was contoured on image slices that have not been uploaded to ProKnow DS. In other words, contour information exists outside of the visible range of the image set slices. In this case, double check that all image slices have been uploaded to ProKnow DS and try again.
• Interpolation failed because ProKnow detected a mismatch in contour orientations between two slices. This is a rare case that can occur if there is an issue with the source contour data. Generally, it indicates that the source contour data is malformed or otherwise corrupt. Please contact ProKnow support and they can help investigate the issue.

Copying Contours

To copy from the inferior slice, press the Copy from Inferior Slice button. To copy from the superior slice, press the Copy from Superior Slice button.

Clearing Contours

To clear the current slice, press the Clear Current Slice button. To clear several slices at once, press the Clear Slices... button and choose from one of the available options ("Clear all," "Clear every other slice," and "Clear specific slices").

Managing Drafts

When you press the Edit Structure Set button, a structure set draft is created for you if one does not exist already. While editing a draft, the structure set remains locked from other edits, meaning that other users cannot edit the same structure set. Your contours are saved in the background as you edit.

When you are finished contouring, you have three options. If you would like to delete the draft completely, press the Delete Draft button. This operation is permanent and will discard all changes to the structure set. To save the draft without making it the current version of the structure set, press the Save as Draft & Close button. To save changes and make the draft the current version of the structure set, press the Commit. When you commit a structure set, you'll be prompted to give it an optional label and commit message.