Segment Editor

Module Segment Editor

This is the advanced version of the editor module, in this the tools have been improved and the workflow varies as there are more possibilities in the interaction with the data. (Figure 1)

Figure 1: Module Segment Editor

Interface

The module now allows you to work with different sets of segmentations, depending on the volume you are interacting with, as you can see in the first two drop-down menus of the interface.

The segmentations are generated individually, by means of the button bar that appears next to these menus (Figure 2):

Figure 2: Segments bar

The functions of these buttons are quite intuitive:

• Add: creates a new segmentation
• Remove: removes the selected segmentation
• 3D show: shows active 3D segmentations
• Segmentations: leads to the module of that name

Effects

Figure 3: Effects

The first two rows of icons correspond to the Segment Editor module itself, but the third is the SegmentEditorExtraEffects' extension, which is recommended to be installed, as it complements this module.

first fow

Figure 4: Effects row1

• None: returns the pointer to its default behavior
• Paint: Paint (select) areas of the image
• Draw: draw contours for drawing
• Erase: erases the zones marked with the two previous tools
• Level tracing: traces areas of similar intensity
• Grow from seeds: create segmentations from areas marked with the paint tool
• Fill between slices: segmentation between different sections of the volume
• Threshold: threshold. Selects areas of related intensity throughout the image.

second row

Figure 5: Effects row2

• Margin: Enlarges or contracts the selection in a fixed increment
  • Smoothing: smoothes the surface of the selection, eliminating bumps and holes. It has several application parameters:
  • Medium: eliminates small details while preserving as much contour as possible.
  • Opening: eliminates packages smaller than the specified size.
  • Closing: fills holes smaller than the specified size.
  • Gaussian: softens all the contours, at the cost of contracting the segment.
  • Joint smoothing: applied to multiple segments simultaneously, to smooth them out and eliminate gaps between them.
• Scissors: cuts (removes) parts of the selection
• Islands: manipulates the independent surfaces within the segmentation. Its settings are listed below, and their effect will vary depending on the mask used: everywhere (everywhere), inside all segments (affects only the segmentations), inside all visible segments (affects only the visible segmentations), outside all segments (affects only what is not part of the segmentation) and outside all visible segments (affects only what is not part of the visible segmentation).
  • Keep largest island: retains the largest island
  • Remove small islands: removes all islands smaller than the specified size
  • Split islands into segments: separates the islands into segments
  • Keep selected island: keeps the selected island
  • Remove selected island: removes the selected island
  • Add selected island: adds the selected island to the segmentation you are working on
• Logical operators: operations with logical operators between segmentations
  • Copy: replaces the selected segment with the modifier
  • Add: adds the modifier segment to the selected one
  • Substract: substracts the selected segment by the modifier
  • Intersect: intersects the selected segment with the modifier
  • Invert: inverts the selected segment
  • Clear: Deletes the selected segment
  • Fill in the selected segment
• Fast marching: Expands the selected segment to regions with similar intensity.
• Flood filling: filling of area byflooding through the voxels with similar intensity

third row: extra effects

Figure 6: Effects row3: extra effects

• Mask volume: Utilice el segmento seleccionado como máscara. La máscara se aplica al volumen maestro por defecto.

La operación de llenado interior y exterior crea un volumen de mapa de etiquetas binario como salida, con los valores de llenado interior y exterior modificables. (de la descripción de la herramienta)

• Surface cut: Use marcas de referencia para rellenar un segmento. La superficie se genera a partir de los puntos colocados. (de la descripción de la herramienta)
• Watershed: Crece segmentos para crear una segmentación completa. Se tienen en cuenta la ubicación, el tamaño y la forma de los segmentos iniciales y el contenido del volumen maestro. Los límites finales del segmento se colocarán donde el brillo del volumen maestro cambia bruscamente. (de la descripción de la herramienta)

Documentación en Slicer.org

[Segment Editor]

Flujo de trabajo

Before the segmentation

• Con el módulo Crop Volume comprobar que la resolución en las tres dimensiones es la misma
• En ese mismo módulo, ajustar el ROI al área en la que se vaya a trabajar, para así reducir la carga de procesado

Procedimiento

• Crear una nueva segmentación para cada estructura anatómica
• Delimitarla de forma aproximada con la herramienta Paint
• Repetir los dos pasos anteriores con cada una de las segmentaciones a crear
• Aplicar el efecto Grow from seeds para generar automáticamente las segmentaciones

Refinado

• Mediante los efectos de la segunda fila de herramientas, ajustar las segmentaciones generadas automáticamente para que se ajusten a la realidad anatómica deseada