Editor

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Editor Module

This module is complemented by the Segment Editor. Both serve to segment volumes, but the Segment Editor can be considered as an advanced version of the Editor. What changes between them are the funcionality of the available tools. In fact in the module screen recommends the use of the Segment Editor module. (Figure 1)

Figure 1: Module Editor

Sections

When the module Editor opens a floating window prompts which table of colours goes to use in the data processing.

A color table associates scalar values of the medical image with the color to be used in its representation in Slicer. Certain medical modalities, such as CT, provide absolute values that allow to establish the correlation between tissue types and scalar values of the image. However, in other modalities like MRI, this does not happen because the values are relative; it is necessary to perform this correlation semi-automatically.

There is more information about the different color tables available by default in Slicer within the module documentation [Colors], in the ' Categories section.

Create and Select Label Maps

• Master Volume: Contains the original images of the scanner. You can select from any of the different volumes loaded in the scene.
• Merge Volume: Contains the representations of the scene, to which the corresponding color map has been applied.

See Figure 1.

Edit Selected Label Map

First row

Figure 2: Module Editor - Toolbar row 1

• Default Tool: allows selection of elements
• Erase Label: Erase changes made to the image
• Paint Effect: Color the area you click and drag on the mouse. When selecting this tool, the following options appear under the two toolbars: the label of the label, the radius of the brush tip and the way the applied color will behave. It works by clicking with the left button of the mouse and dragging, to make a freehand drawing.
• Draw Effect: similar to the previous one but based on straight lines that are defined based on clicks.
• Wand Effect: Select all pixels of similar color, according to the tolerance set, when clicked.
• Level Tracing Effect: delimits with a line all the pixels with a value similar to the one selected and left-click exports the contour line to the label map.
• Rectangle Effect: make a selection with rectangular shape by clicking with the left button and dragging, releasing closes the rectangle.
• Identify Islands Effect: applies a unique label to the entire interconnected area within the label map. In case there are other areas with the same values, but not connected to the selected one, they will not be altered or selected.
• Change Island Effect: applies a different color to the closed contour that is selected.
• Remove Islands Effect: removes all unlabeled pixels / voxels within an area that is tagged and replaces them with ones of identical value to those in the tagged area. It is used to eliminate holes / noise within the selections.
• Save Island Effect: behaves just like the previous tool and also allows saving the selection for later uses.

second row

Figure 3: Module Editor - Toolbar row 2

• Erode Effect: collapses the number of pixels set in the tool options.
• Dilate Effect: Expands the selection the number of pixels set in the tool options.
• Grow Cut Effect: consists of an algorithm that segments based on multiple color labels to automatically separate the areas belonging to the selected anatomical structures.
• Watershed from Marker Effect: Algorithm similar to the previous one, is used when objects with well-defined edges are available.
• Threshold Effect: Defines the ranges for the values ​​thresholds that will be used when painting, for example. An upper and lower threshold is defined.
• Change Label Effect: to change each pixel / voxel in the input label map to the value of the output label map (from master volume to merge volume).
• Make Model Effect: Automatically creates models for all those values ​​other than zero in the label map.
• Fast Marching Effect: allows you to select by a segmentation algorithm, areas of values ​​similar to those defined as seed value automatically.

Documentation in Slicer.org

[Editor]

Workflow

The general procedure to be followed is as follows:

1. Open the scene/files with the data and enter the module editor
2. Select one of the label maps in the slicer to assign labels to the colors/intenses to work with.
3. With the Paint Effect tool, assign a label (from the previously selected label map) and paint the corresponding area in the image.
4. Repeat the previous step for each type of fabric to be segmented.
5. Apply the Grow Cut effect to Slicer to automatically select all areas similar to the selected ones.

At this moment, the segmentation will be done and the corresponding volumes will be generated:

1. Apply, within the Per-structure Volumes tab, the Split Merge Volume effect. This creates a separate volume for each segmented structure.
2. Adjust each volume with the Threshold Effect tool, checking that the anatomically correct is selected in this case
3. Debugging the selection, removing islands or adding parts as necessary
4. Once the volumes have been adjusted, create the final 3D volumes with the command Merge and Build

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