The basic workflow is as follows:

1. Initialization

   • Load the target image and the template label/color.

   • Select the node of the template label/color.

   • Decide the grid size for FFD.

2. Rough Alignment

   • Determine the placement, size, and orientation of the template.

3. Manipulating Control Points (Non-Rigid Deformation)

   • Specify the direction and position of the section to be operated on.

   • Deform to fit the anatomical structure of the target image.

4. Output Results

   • Apply deformation to the template.

   • If needed, use the deformed label as a new template for finer alignment (Back to Step 1).

To begin the segmentation process in the [Initialize] panel, first select the label template and color table you will use. 

Next, set the interval between control points. (Note that the grid size can be set separately for in-plane and out-of-plane orientations.) 

After these settings are adjusted, press the [Start Segmentation] button to complete initialization.

(Tips: If you intend to segment the side opposite to the template label, checking [Flip Label] beforehand allows you to start with a mirror-inverted label template.)

Upon completion of initialization, the label names specified in the color table will be displayed in the Visibility panel. 

You can toggle the visibility of individual labels using the checkboxes located in front of each label name. 

Furthermore, buttons are available to collectively show or hide all labels at once.

In the Position panel, you can set the rough placement of the template. 

When the [Interaction ROI] button is pressed, the template’s bounding box will be displayed in the slice view. 

By manipulating this bounding box, you can adjust the template’s approximate position and size (drag the center point to change the position, and drag the outer points to change the size). 

Furthermore, adjustments for angle changes due to different limb positions can be made by altering the values in the [Rotation] tab.

Note: The accuracy of alignment at this stage affects the difficulty of subsequent operations, so it should be done carefully.

Display control points and perform non-rigid deformation.

• Plane Combo Box

  • Set the direction of the section in which you will manipulate control points.

• Current Slice Box

  • Set which slice position in the above-specified plane direction you will operate on.

• Reset Button

  • Reset the control points in the currently operated slice to their initial state.

Output the results of the deformation.

• Deform Labelmap Button

  • Select the destination label map node. You can register a new label map in the Scene.

• Resample Button

  • Outputs the deformation results in the same image size as the target image. Used to obtain the final segmentation.