Inobitec DICOM Viewer

6.4. Structure editing

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Functionality is available in the Pro edition
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When working with segmented structures pay attention to which structure or volume is selected. All editing operations are performed with a selected visible structure or volume. If the Visible flag is currently unchecked for this structure or volume then editing is not possible.

If the volume model is open (see Section 5.15) then the created structure appears simultaneously on the model. This causes an additional load on the processor. If you want to reduce the load, click the arrow on the right side of the Growing Region PIC button and uncheck the Interactive 3D Update item. After this the structure on the volume model will be updated after the completion of the next stage of creation of a structure.

To edit the structure use specialized tools (described below) and volume editing tools:

  • Polygon Cut (see Section 3.4.1);
  • Inverse Polygon Cut (see Section 3.4.2);
  • Delete Area (see Section 3.4.3);
  • Delete All Areas except Selected Area (see Section 3.4.4);
  • Brush Cut (see Section 3.4.6);
  • Brush Restore (see Section 3.4.6). The use of the tool is possible only if the part ot the structure is already created;
  • Grow (dilation) (see Section 3.4.7);
  • Srink (erosion) (see Section 3.4.7);
  • Remove noise (opening) (see Section 3.4.7);
  • Remove holes (closing) (see Section 3.4.7);
  • Fill (see Section 3.4.7).
  • Cut Invisible Volume (see Section 6.6);
  • Vessels Tree Segmentation (see Section 6.4.4).
  • Union (see Section 6.6);
  • Subtract (see Section 6.6);
  • Intersect (see Section 6.6);

6.4.1 Tools for automatic structure filling

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Functionality is available in the Pro edition
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The Segmentation from point by mask tool allows you to create a structure for a bound area. It is necessary that the mask for this area does not touch the masks of the neighboring areas. To create a structure:

  1. Activate the Segmentation from point by mask PIC tool.
  2. Click on the bound area.
  3. If the segment was created for a larger area than required, undo the action by clicking the Undo PIC button. Change the window width and level so that the mask for this area is not in contact with the masks of the neighboring areas and create the structure again.

The "Vessel tree segmentation" PIC tool works in the same way, however, the vessel tree is used as a mask instead of a bound area. Study must be done with contrast.

If it is impossible to get a bound area completely separated from other tissues, then if you use the tool Segmentation from point by mask, there will be leaks (segmentation beyond the required area). To quickly and with minimal leaks create a segment, use the tool Region growing PIC :

  1. Activate the Region growing tool. The tool modes are described in Section 6.4.3.
  2. Select the point on the mask about the center of the region you want to segment.
  3. Move the cursor in any direction holding the left mouse button. The segmented structure will grow. Growth occurs faster in those directions in which the curvature of the surface is less (in thin sections growth is slower to avoid leaks). The direction of the cursor movement does not matter, the distance from the starting point of the movement is important. When the cursor moves in the opposite direction, the structure does not decrease.
  4. If the structure is completely created or the faster growth will lead to leaks stop growing by releasing the left mouse button.
  5. If necessary repeat growth for tissue not yet segmented.
  6. To undo action click the Undo PIC button, to redo the canceled action click the Redo PIC . However, keep in mind that the tool will operate at regular intervals, so with a single click on the Undo button you can only delete that part of the structure that was added during the next actuation, and not in the whole path of the cursor movement.

6.4.2 Brush restore tool

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Functionality is available in the Pro edition
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To fill out the structure using the Brush restore tool:

  1. Activate the tool Brush restore PIC .
  2. Set up the tool diameter. To do this, move the mouse cursor up and down holding the Alt key on the keyboard.
  3. Move the mouse cursor to the area for which you want to create a structure.
  4. Click the left mouse button. Tissues that are under the mask and inside the sphere will be added to the structure. Color tissue changes to the one set for the structure.
  5. To undo the action, click the Undo PIC button, to repeate the canceled action, click on the Redo PIC button.
  6. To add a large area to the structure, move the tool Brush restore PIC holding the left mouse button. However, keep in mind that the tool will operate at regular intervals, so with a single click on the Undo button you can only delete that part of the structure that was added during the next actuation, and not in the whole path of the sphere movement.
  7. To remove a part of the tissue from the structure, activate the Brush cut PIC tool. The tool works in the same way as to the Brush restore tool, but unlike Brush restore tool removes the tissue from the structure.
  8. To disable or enable the mask, click the Segmented structure creation PIC button.

6.4.3 Region growing tool

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Functionality is available in the Pro edition
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When using the Brush restore tool, there may be leaks (segmentation beyond the required area). The PIC Region growing tool takes into account the shape and density of the segmented areas and allows to minimize leaks. The tool has two modes: EDT Method and Level Set Method. To switch the mode, click the arrow on the right of the PIC button and select the desired mode. The current mode is marked by the flag.

The EDT Method mode allows you to create a structure in the masked space. To create structure:

  1. Activate the Region growing PIC and select the EDT Method mode if necessary.
  2. Select the point on the mask about the center of the region you want to segment.
  3. Move the cursor in any direction holding the left mouse button. The segmented structure will grow. Growth occurs faster in those directions in which the curvature of the surface is less (in thin sections growth is slower to avoid leaks). The direction of the cursor movement does not matter, the distance from the starting point of the movement is important. When the cursor moves in the opposite direction, the structure does not decrease.
  4. If the structure is completely created or the faster growth will lead to leaks stop growing by releasing the left mouse button.
  5. If necessary repeat growth for tissue not yet segmented.
  6. To undo action click the Undo PIC button, to redo the canceled action click the Redo PIC . However, keep in mind that the tool will operate at regular intervals, so with a single click on the Undo button you can only delete that part of the structure that was added during the next actuation, and not in the whole path of the cursor movement.

If the Level Set Method is selected the tool use its own mask created according to a special algorithm, so created structure can go beyond the standard mask and when you change mask boundaries will be visible. To create a structure:

  1. Activate the Region growing PIC and select the Level Set Method mode if necessary.
  2. Select the point on the mask about the center or the region you want to segment.
  3. Press and hold the left mouse button. The own tool blue mask appears in the window in which you work. If the mask is poorly visible against the background of the standard mask, reduce the opacity of the standard mask. To do this, click the arrow on the right side of the PIC Add a new segmented structure button and reduce the Opacity value in the dialog that opens.
  4. Evaluate the coverage of the tissues with a blue mask. Density of tissues that are under the blue mask depends on the density under the cursor. If the blue mask is not built correctly, then release the left button, cancel the structure creation by clicking the Undo PIC button or deleting the structure; move the cursor to the tissue section with the desired density, and repeat this step.
  5. The red circle around the cursor shows the curvature of the areas that will be segmented (the smaller the diameter of the circle allows to segment the tissue with the greater curvature, that is, the thinner tissues are segmented). To change the diameter of the circle, move the cursor up or down pressing the Alt key on the keyboard.
  6. Move the cursor in any direction holding the left mouse button. The segmented structure will grow under the blue mask. If the blue mask goes beyond the standard mask, the structure can be build beyond the standard mask, but it will be visible only within the standard mask.
  7. If the structure is completely created or the faster growth will lead to leaks stop growing by releasing the left mouse button.
  8. If necessary repeat growth for tissue not yet segmented.
  9. To undo action click the Undo PIC button, to redo the canceled action click the Redo PIC . However, keep in mind that the tool will operate at regular intervals, so with a single click on the Undo button you can only delete that part of the structure that was added during the next actuation, and not in the whole path of the cursor movement.

If the volume model is open (see Section 5.15) then the created structure appears simultaneously on the model. This causes an additional load on the processor. If you want to reduce the load, click the arrow on the right side of the Growing Region PIC button and uncheck the Interactive 3D Update item. After this the structure on the volume model will be updated after the completion of the next stage of creation of a structure.

6.4.4 Vessel tree segmentation tool

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Functionality is available in the Pro edition
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This tool is used for segmentation of vessel trees for studies performed with contrast. To create segment in Multiplanar Reconstruction window:

  1. Set the mask so that only the vessels are under the mask.
  2. Activate the Vessel tree segmentation PIC tool. Initialization of the tool takes some time and depends on the performance of the computer, the selected study and the mask.
  3. Click the left mouse button in the arbitrary point of the vessel that you want to segment. The tree of vessels is segmented. The completeness of the segmentation depends on the correct selection of the mask and the configuration of the vessel.
  4. If the vessel is not completely segmented, click the left mouse button on those areas that need to be segmented.
  5. If necessary change the mask. After that you need to re-activate the tool and wait for it to initialize.
  6. It is recommended to open the volume reconstruction window in the multiplanar reconstruction window (see Section 5.15) and turn off the visibility of the main volume.
  7. The tool can also be used in the preview window of the volume reconstruction. The main volume should be is visible.

To specify the maximum branch angle of a vessel that can be segmented, click the arrow on the right side of the Vessel tree segmentation PIC button, select the Options... and in the dialog that opens set the value in degrees.

In the volume reconstruction window the tool works in the same way.

All editing operations are performed with a selected visible structure or volume. If the Visible flag is currently unchecked for this structure or volume then editing is not possible.

6.4.5 Watershed segmentation tool

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Functionality is available in the Pro edition
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The tool is used for segmentation using the watershed method and allows you to split the volume into several non-overlapping parts.

The tool has two modes (directions for basins filling):

  1. low dencity for soft tissues separation surrounded by more dense tissues: organs containing air, the brain. In this case, the filling of the basins occurs from a lower density of tissues to a greater one. The minimum density of tissues (Min dencity) is the point from which the filling of the basins begins, and the Max dencity value limits the density of the tissues to be segmented from above.
  2. high dencity for dense tissues surrounded by less dense tissues: bones, contrasted organs. In this case, the filling of the basins begins with the maximum density (Max dencity) and occurs in the direction of its reduction. The minimum density of the tissues to be segmented is limited from below by the Min dencity value.

To speed up the segmentation process and avoid creating unnecessary segments exclude unnecessary tissues from the segmented volume using the cutting tools.

To perform Watershed segmentation:

  1. Select the volume to be segmented.
  2. If necessary, cut tissues that do not need to be segmented.
  3. Click the Watershed segmentation PIC button.
  4. In the dialog that opens set the following parameters:
    • Min dencity;
    • Max dencity;
    • Min depth: minimum depth of basins which can be combined;
    • Max basins: maximum number of created structures (no more than 31);
    • Select a mode (Low dencity High dencity);
    • To hide the source volume after segmentation check the "Hide source structure" box.
  5. Click OK to perform segmentation or Cancel to cancel action. The process takes some time.

6.4.6 Multi-segment growing tool

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Functionality is available in the Pro edition
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This tool is used when it is necessary to increase several segmented structures so that they do not intersect. It is similar to Grow (dilation) (see Section 3.4.7), but can be applied simultaneously to an arbitrary number of structures and to the base volume. To use the tool:

  1. Build the required number of segmented structures that you want to grow without intersection.
  2. Activate the Multi-segment growing PIC tool (see Section 3.4.7). The dialog shown in Fig. 6.7 will be displayed.
  3. The currently selected structure (base volume) is marked with a flag in the dialog. Check all the structures (base volume) with flags that you need to simultaneously increase. If only one structure (volume) is checked then the tool works similarly to the Grow (dilation) tool.
  4. Set the maximum growing radius in the Growing radius (mm) field.
  5. Click OK to apply the tool or Cancel to cancel action. The process takes some time. If the building structures is incomplete repeat steps 2-4.
  6. To undo or redo the action use the Undo PIC and Redo PIC buttons for each structure you have built up.