Difference between revisions of "Segmenting Images Using Contours and Masks: Generating Masks"

Latest revision as of 18:11, 21 February 2012

A mask is a filter that selectively includes or excludes certain values. You can create a mask that includes the VOI areas and excludes all other areas. Masks are particularly helpful if you use other applications to further analyze images because those programs may require that you supply a mask. An example of a mask appears in Figure 1.

You can create masks using a variety of methods:

• Use paint tools to manually create a mask
• Use Paint Grow Segmentation tool
• Use binary or short mask utilities
• Use the Advanced Paint tool
• Use the Power Paint tool

MIPAV also provides algorithms that you can use to generate masks. These algorithms are addressed in volume 2 of the User's Guide.

Manually creating a mask using paint

You can manually create a mask using the tools on the Paint toolbar, which is located in the MIPAV window. To create the mask, you first select the intensity level of the paint, along with the paint color and opacity value. Next, you paint on the image using the paint brush. You can adjust the size of the paint brush tip. When complete, you then commit the paint by choosing one of the following icons:
- Masks Inside the Painted Area
- Masks Outside the Painted Area

When you click one of these icons, it applies the intensity permanently to the image. You can then choose to save the image.

If the Paint toolbar does not appear in the MIPAV window, select Toolbars. The Toolbar menu lists four commands: VOI Toolbar, Paint Toolbar, Scripting Toolbar, and Image Toolbar. If a toolbar command has a check mark next to it, the toolbar is displayed; otherwise, it is hidden. To display the Paint toolbar, select Paint Toolbar. See also "MIPAV toolbars" in Chapter 3.

Manually generating a mask includes the following four steps:

• Step 1, Selecting the paint intensity level
  
• Step 2, Selecting a paint color
  
• Step 3, Adjusting the opacity level of the paint
  
• Step 4, Applying the paint
  

Step 1, Selecting the paint intensity level

The first step in manually creating a mask is to select the intensity level of the masked area.You can select the intensity level by using the eyedropper tool to select an intensity value that is already present in an image or by typing a specific intensity value in the Desired Paint Intensity dialog box.
To select the intensity level using the Eyedropper tool
- Eyedropper
The eyedropper allows you to copy an intensity level that is already present in the image. To use this tool, complete the following steps:
1 Click the Eyedropper icon, on the paint toolbar in the MIPAV window.
2 Click the area of the image that has the intensity level you want to copy. The intensity shown at the bottom of the MIPAV window changes to the intensity level in the part of the image you've selected.
Example: Initially, the intensity level button shows a zero on the button. However, when you click an area of the image, it displays the number that is associated with that part of the image, such as 250.
You can enter a specific intensity level value in the Desired Paint Intensity window. To do this, complete the following steps:
1 Click the Intensity button.
Note: If you changed the intensity level using the eyedropper or this button previously in your current MIPAV session, the number on the Intensity button would have changed from 0 to the number representing that earlier intensity level.
The Desired Paint Intensity dialog box opens.
2 Notice that the minimum and maximum intensity values appear in parentheses. These values depend on the image type, or data type, of the image.
Tip: You can look at the exact intensity levels in the image using , the Magnify region icon.

3 Type the desired level of intensity.
4 Click Apply to apply the intensity level to the paint. Note that the number on the Intensity button changes to the number you entered.
5 Click or Cancel to close the dialog box.

Step 2, Selecting a paint color

- Change Paint Color
After you select the intensity level, the next step is selecting the paint color. The program applies this color to the image so that you can easily see where you applied the new intensity. When you commit the changes to the image, the grayscale intensity level that you indicated in step 1 is permanently applied to the image.

To select a color, use the Change Paint Color icon, to display the Pick Paint Color dialog box (Figure 4). This dialog box includes three tabbed pages: Swatches page, which is always displayed first; the HSB page; and the RGB page. You can select a color on any of the pages.

To select a color from one of the 310 color swatches
1 Click the Change Paint Color icon. The Pick Paint Color dialog box (Figure 3) opens.
2 Stay on the Swatches page, or, if you moved to HSB or RGB pages, click Swatches to return to the Swatches page.
3 Click the desired color in the larger grid. The color appears in the Recent color grid on the right.
4 Click Close when done. The Pick Paint Color dialog box closes. The color you selected becomes the current paint color.

To select a color using the HSB model
1 Click the Change Paint Color icon. The Pick Paint Color dialog box opens.
2 Click HSB. The HSB page appears (Figure 4B).
3 Specify a color by entering specific numbers for the hue, saturation, and brightness values, or select the color from the color graphic.
Enter specific values into the H, S, and B boxes:
Type the hue value in H. The hue can be any number from 0 to 359. The numbers correspond to the degree numbers on the color square (Figure 5). For example, to specify a shade of blue, enter a number from 255 to 270. The slider automatically moves the correct hue on the color strip.
Type the saturation value in S. The level of saturation can be anywhere from 0 (gray) to 100 (full-strength hue). When you type a value into this box, a circle appears in the color square around the color with the specified saturation level. Colors to the left of the color graphic are circled if the saturation level is high. Lower saturated colors are found to the left of the color graphic.
Type the brightness value in B. The level of brightness can be anywhere from 0 (dark) to 100 (light). In the color graphic, a circle appears around the color with the specified brightness level. Colors near the top of the color graphic are circled if the saturation level is high. Darker colors are found near the bottom of the color graphic.
Select the hue, saturation, and brightness on the color square or color strip:
Drag the slider to select the desired hue from the color strip.
Select the shade you wish to use in the color square.
4 Click Close when done. The Pick Paint Color dialog box closes. The color you selected becomes the current paint color.

Pick Paint Color dialog box options

To select a color using the RGB model
1 Click the Change Paint Color icon. The Pick Paint Color dialog box opens.
2 Click RGB. The RGB page (Figure 4C) appears.
3 Specify the numbers for the three components (red, green, and blue), or use the sliders to select a color.
4 Click Close when done. The Pick Paint Color dialog box closes. The color you selected becomes the current paint color.

Step 3, Adjust the opacity level of the paint

You can further refine the appearance of the paint selecting its opacity level. Opacity levels can range from 0.0 (transparent) to 1.0 (opaque).
< To change the opacity level
- Change Opacity of Paint
1 Click the Change Opacity of Paint icon on the Paint toolbar. The Paint Opacity window appears (Figure 7).
2 Drag the slider to the desired level of opacity. The current level appears in the bold print underneath the slider.
3 Click Close to apply the opacity level. The opacity level on the image changes according to your specifications.

Step 4, Apply paint

Having selected the intensity level, paint color, and opacity level, you are now ready to paint on the image with the paintbrush.

- Draw Using a Brush

To paint on the image

1 Click the Draw Using a Brush icon, on the Paint toolbar in the MIPAV window.
2 Specify the size of the paintbrush tip.
3 Click and drag the mouse button to paint on the drawing. You can select one pixel at a time, or drag the mouse button to draw paint strokes on the image.
Tip: You may need to use the magnification buttons to adjust the magnification level of the image.
If you make a mistake, you can erase or undo the painted area.
To erase paint from a specific area
- Erases Paint
1 Click the Erase icon.
2 Select the size of the eraser tip.
3 Use the mouse to begin erasing. You can select one pixel at a time, or you can drag the mouse.
Tip: When erasing the paint, it may be easier to magnify the size of the image using the magnification icons.
To resume painting, click the Draw Using a Brush icon.
To erase all paint
- Erase All Paint
- Undo
1 Do one of the following as appropriate:
Click the Erase all paint icon, which removes all paint from the image.
Click the Undo last region paint icon, which allows you to undo the last paint stroke.
2 Click the Default Mode icon, when you have finished painting the image.

Step 5, Commit

When you visualize a dataset in MIPAV, a composite of several layers appears in the default image window. The image layer contains the original image. The next two layers contain the results of applied utilities, algorithms, and paint. The fourth layer contains VOI contour information. When you click the commit icons. e.g. the Masks Inside Painted Area icon or Masks Outside Painted Area icon, the paint and utility/algorithm layers are merged with the image layer and saved as a new file.

To commit changes, select one of the following commit icons: - the Masks Inside Painted Area icon. This tool shows the image without the area you painted (Figure 8-C).
- the Masks Outside Painted Area icon. This tool removes the painted area from the image and shows only the removed area (Figure 8-B).
The software redraws the dataset with the intensity levels indicated on the image. You may need to adjust the lookup table (LUT) to see the image more clearly, as it has been dome for the image shown in Figure 8-C. Instructions for adjusting the LUT appear in Chapter 5, "Visualizing Images."

Section Con't in Creating a mask using the Paint Grow Segmentation method