Visualizing Images: Displaying images using the triplanar-dual view

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The triplanar-dual view displays two image datasets (referred to as Image A and Image B) and a blended version of both Image A and Image B from three orthogonal planes.

To view image datasets using this view
1 Open two 3D or 4D images, which become known as Image A and Image B.
2 Load Image B into Image A.
3 Select Image > Views > Triplanar-Dual. The triplanar-dual view appears in an image window.

Figure 1. Image A, Image B, and Image B loaded into Image A

ExampleImageABLoaded.jpg


The image window for the triplanar-dual view is quite similar to the image window for the triplanar view. The File and Options menus contain the same commands except for one command-the Options menu for the triplanar view contains the command Link to Another TriImage. Since the triplanar-dual view shows two datasets in the image window and allows you to manipulate them together, linking to another image is not necessary. Most of the icons and buttons on the toolbars for both views are the same with one primary difference: The triplanar-dual view allows you to create VOIs on the images; the triplanar view does not.

Like the triplanar view, you can use the icons and buttons on the toolbar to change magnification, draw, change colors, change opacity, and apply a new intensity to selected voxels in the images.

Showing and hiding axes, cross hairs, and Talairach grid

By default, the triplanar-dual view automatically shows the axes and cross hairs on Image A, Image B, and the blended dataset.

To show or hide axes on images
To hide the axes, select Options > Show Axes (Figure 2). The check mark disappears from the check box in front of the command on the menu, and the axes disappear from all of the images.

Figure 2. Show Axes command on the Options menu in the Triplanar-Dual window

MenuOptionsShowAxes.jpg

To display the axes on the images again, simply select Options > Show Axes. The check mark reappears in the check box in front of the command.

To show or hide cross hairs
Showing or hiding cross hairs works just as showing or hiding axes. To hide the cross hairs, select Options > Show Cross Hairs. To show them, select Options > Show Cross Hairs again.
To show or hide the Talairach grid
By default, the Talairach grid does not automatically display on the images unless you specifically select it to do so. To show the grid, select Options > Show Talairach Grid. The grid appears on all of the images shown in the triplanar-dual view. When you want to hide the grid, select Options > Show Talairach Grid again.

Creating VOIs on images

You can create point or line VOIs on the images.
To create point VOIs
1 Click IconPoint.jpg .
2 Click in the image where you want to create a point.
3 Repeat steps 1 and 2 for all other desired points.

To draw line VOIs
1 Click IconDrawLineVOI.jpg .
2 Click in the image where the line should begin and drag the line to where it should end.
The numbers beneath the line indicate the length of the line in millimeters.
To change the line VOI, simply click on the VOI and then drag it to another position in the image.

File:MIPAV VisualizationTools169.gif

You can only create one line VOI per orthogonal plane, although you can create a line VOI in each one of the three orthogonal planes.

To delete line VOIs
You cannot delete a line VOI. However, you can remove the display of the line VOI on the image. To do so, click IconTraverseImage.jpg . The line VOI disappears.

Figure 3. Triplanar-Dual window

WindowTriplanarDual.jpg

File
Close Frame-Closes this window.
Options
Show Axes-Displays the XY (top left), ZY (top right), and ZX (bottom left) axes on the images.
Show Cross Hairs-Displays the cross-hair lines on the images. When you move these lines on one image, it also moves to the corresponding points all of the other images.
Show Talairach Grid-Displays a Talairach (stereo tactic) grid on the images.
ButtonTraverseImage.jpg Traverse image
Aligns two images.
IconMagnify.jpg Magnify image 2.0x
Enlarges the images to twice their current size. It might be necessary to manually resize the window and use scroll bars to view all of the images.
IconMagnifyImage0.5x.jpg Magnify image 0.5x
Reduces the images to half of their current size.
IconOriginalMagnification.jpg Magnify image 1.0x
Restores the images to their original size.
IconDrawLineVOI.jpg Draw line VOI
Draw a line VOI.
IconCenterVolume.jpg Identify center of volume
Reassigns a new center to each dataset. The location that you select appears in the center of each image.
IconAlignmentTool.jpg Alignment tool
Allows you to apply a transformation matrix to an image dataset.
IconApply.jpg Applies rotations and translations
Applies the rotations and translations made to the images.
IconPoint.jpg Add point
Draws a point on an image. This point is only on the image you select.
IconNewVOI.jpg Initiate new VOI
Indicates that the next VOI is a new VOI rather than a change to the currently existing VOI.
IconDelete.jpg Delete point VOI
Removes the point VOI from the image.
IconCropVolume.jpg Identify crop volume
Displays the bounding box, which is outlined in red, on each image.
IconCropbutton.jpg Crops image delineated by the bounding cube
Displays in a separate image window only the area enclosed by the bounding box. When you click this icon, the Crop Image dialog box opens.
DialogboxCropImage.jpg
IconDrawBrush.jpg Draw using a brush
Allows you to draw with a brush on the image.
IconEyedropper.jpg Picks up a color from the image
Changes the color of the paint used to the color selected on the image.
IconPaintGrow.jpg Fills an area with desired color
Allows you to fill an area with color. When you select this icon, the Paint Grow dialog box opens.
IconErase.jpg Erases a portion of the image
Removes the paint from the specific spot that you select.
IconEraseAll.jpg Erase all paint
Removes all paint from all of the images.
IconSmallPoint.jpg Draw using small size
Indicates the size of the paint brush tip. Click this icon to paint one voxel each time the mouse button is clicked.
IconMediumPoint.jpg Draw using medium size
Indicates the size of the paint brush tip. Click this icon to paint 16 voxels (4 x 4 square) each time the mouse button is clicked.
IconLargePoint.jpg Draw using large size
Indicates the size of the paint brush tip. Click this icon to pain 100 voxels (10 x 10 square) each time the mouse button is clicked.
IconChangeIntensityLevel.jpg Change intensity level of paint
Allows you to change the intensity value of the paint. When you click this icon, the Desired Paint Intensity dialog box opens.

DialogboxDesiredPaintIntensity.jpg


You can specify an intensity between -32,768 and 32,767. After you type an intensity level, the icon displays the level you entered.
IconChangePaintColor.jpg Change paint color
Changes the color of the paint used. This icon is often used in conjunction with the Draw icons. When you click this icon, the Pick Paint Color dialog box opens. After you change the color, this icon displays the color.
IconOpacity.jpg Opacity
Allows you to change the opacity of the paint. When you click this icon, the Paint Opacity dialog box opens.

DialogboxPaintOpacity.jpg

IconCommit.jpg Changes image where painted
Permanently applies the intensity level to the images.
IconUndo.jpg Undo last region paint
Removes paint from the last area to which it was applied.
IconCalculateVolume.jpg Calculate volume of paint
Determines the volume, or number of pixels, in the painted area of the image.
RadiobuttonImageA.jpg Image A
Performs the action only on Image A.
RadiobuttonImageB.jpg Image B
Performs the action only on Image B.
RadiobuttonBoth.jpg Both
Performs the action on both Image A and Image B.


To delete point VOIs
1 Click the first point on the image aligning the middle of the cursor with the center of the point.
2 Click IconDelete.jpg . The point disappears.
3 Repeat the first two steps for every point you want to delete.

Aligning the datasets

The Alignment Tool icon, IconAlignmentTool.jpg , allows you to create a new transformation matrix for the dataset.
< 1 Click IconAlignmentTool.jpg .
A closed angle appears on each of the images in the triplanar-dual view. On Image A, the angle is red; on Image B, it's yellow; on the blended image, the angle is green.
2 Move the cursor to the arrow on the thin line to the right, and align the cursor with the end of the arrow. At this time, the cursor should be a red cross.

Figure 4. Closed angle that appears on each of the images

ExampleAngle2.jpg

3 Change the size of the angle by dragging the arrow on the thin line up or down depending on the type of angle you want to create. The exact number of degrees appear on the left below the angle.
4 Release the mouse button when you reach the desired number of degrees.

Figure 5. Changing the angle by dragging the arrow on the thin line

ExampleAngleDegrees.jpg

5 Click on the image or on any other area of the triplanar-dual view. The arrows disappear from the angle.
6 Click on the angle again to be able to change the angle again. The arrows reappear and you can repeat the previous steps.

Finding the center of image datasets

To find the center of the dataset, click IconCenterVolume.jpg . The center of each image dataset, shown as CrosshairBlackWhite.jpg , appears in each image in the triplanar-dual view.

Erasing part or all of drawings

If you used the paint brush to draw on the image, you may at times find a need to erase a part of the drawing or the entire drawing.
File:MIPAV VisualizationTools189.gif

Make sure that you want to erase a part of the drawing or the entire drawing. There is no undo.
To erase a part of the drawing
1 Select the image that contains the drawing you want to erase. In other words, select Image A, Image B, or Both.
2 Click IconErase.jpg .
3 Click on the part of the drawing that you want to erase.
4 Repeat step 3 for as long as needed.

To erase all of the drawing
1 Select the image that contains the drawing you want to erase. Specifically, select Image A, Image B, or Both.
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2 Click IconEraseAll.jpg . MIPAV removes all of the paint from the image.
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Cropping images

MIPAV allows you to extract the crop volume as a separate image, which is helpful if you need to work with or use only that portion of the image. The first step in cropping images is to identify what portion of the image is in the crop volume. Then you need to use the bounding cube for cropping the image.

To select the crop volume
1 Click IconCropVolume.jpg . A red box appears on each image in the triplanar-dual view.
2 Align the cursor with one of the corner points of the box, and enlarge or reduce the size of the box.
3 Repeat the previous step on each corner point as required to enclose the portion of the image you want to be included in the cropped image.
The numbers on the sides of the box indicate the length and width of the box in millimeters.

File:MIPAV VisualizationTools202.gif

Note: The size of the box changes proportionally on all of the images shown in the triplanar-dual view.
4 Release the mouse button when you are finished making changes to the box.

To crop images
1 Select one of the following:
Image A if you want only the cropped area in Image A
Image B if you want only the cropped area in Image B
Both if you want both the cropped area in Image A and the cropped area in Image B
2 Click IconCropbutton.jpg . The Crop Image dialog box appears.

Figure 6. Crop Image dialog box
Apply
Applies the transformation to the image dataset according to the specifications in this dialog box.

DialogboxCropImage.jpg

Cancel
Disregards any changes that you made in this dialog box and closes this dialog box.
Help
Displays online help for this dialog box.


3 Click Apply.
The cropped area in the image you selected appears in a separate image window. So, if you selected Image A only or Image B only, one image appears. If you selected Both, two image windows appear: one for Image A and one for Image B.

If you selected . . .
Then . . .
Image A
The cropped area appears in a separate window.
Image B
The cropped area appears in a separate window.
Both
Two small windows-one displaying the cropped area of Image A and the other displaying the cropped area of Image B-appear.


After you generate the cropped images, you can run algorithms on the images, apply a quick LUT on the images, or use any other image processing that's available in the MIPAV window on them.

Magnifying or minifying images

Like the image toolbar on the MIPAV window, the Triplanar-Dual window includes the following magnification icons:
IconMagnify.jpg
the Magnify image 2.0x icon -To magnify images to twice their current size
IconMagnifyImage0.5x.jpg
the Magnify image 0.5x icon< -To reduce images to half their current size
IconOriginalMagnification.jpg
the Magnify image 1.0x -To restore their original size
For information on how to use these icons, refer to "magnify or reduce a region of the image. You can magnify images to 32 times their original size, reduce them to one-fourth their original size, or restore them to their original size.".

Drawing on images

You draw on images in the triplanar-dual view in the same way as you do in the MIPAV window. However, any of the changes you make on the triplanar-dual view are also made on the original images.

For example, if you highlight a particular area in the image in the triplanar-dual view, the same change is made on all of the images in the triplanar-dual view, but also on the images in the default view.

To change the paint color
Click IconChangePaintColor.jpg , the Change Paint Color icon. The Pick Paint Color dialog box opens. For instructions on how to use this dialog box to change the paint color, refer to "To change background and border colors".

Figure 7. Painting an area on images in the triplanar-dual view

ExampleTriplanarDualPaintedArea.jpg

Painting an area on images in the triplanar-dual view affects images in the default image view

To change paint opacity
1 Click IconOpacity.jpg . The Paint Opacity dialog box opens.
2 Move the Opacity slider to the level of opaqueness you want. For example, to make the paint color more opaque, or solid, move the slider to the right. To make the paint color more transparent, move the slider to the left.
3 Click Close when you have finished. The Paint Opacity dialog box (Figure 8) closes.

Figure 8. Paint Opacity dialog box
Opacity
Indicates the opacity of the paint. The further right you move the slider, the more opaque the paint color. The further left you move the slider, the more transparent the paint color.

DialogboxPaintOpacity.jpg

Close
Closes this dialog box.

To calculate the volume of paint
The software can calculate the volume of a painted area in the number of pixels. To do so, do the following:
1 Paint the area of the image in which you are interested.
2 Click IconCalculateVolume.jpg to discover the volume of paint. The software lists the number of pixels in each image and the volume in millimeters on the Data page of the Output window.
3 Amend and save, as an option, the information on the Data page.

Figure 9. Output window after calculating the volume of paint
WindowOutput CalculateVolume.jpg

To fill an area with color
1 Click IconFills.jpg . The Paint Grow dialog box opens.
2 Complete the dialog box.
3 Click Close.

Figure 10. Paint Grow dialog box
Cursor position and voxel intensity
Indicates the location of the cursor and the intensity value at that point

DialogboxPaintGrow.jpg

Delta above selected voxel intensity
Indicates the range of paint beyond
Delta below selected voxel intensity
Indicates the range of paint
Unrestricted size
Limits the total volume in 3D or 4D images or area in 2D images
Maximum size (null)
In development.
Unrestricted distance
Limits the distance from the seed point
Maximum size (null)
In development.
Fuzzy connectedness
Applies the fuzzy algorithm
Initial variance from selected VOI
In development.
Display fuzzy image
In development.
Fuzzy threshold
In development.
Close
Applies the parameters you specified
Cancel
Disregards any changes that you made in this dialog box and closes the dialog box
Help
Displays online help for this dialog box

To erase an area of paint from images
1 Click IconErase.jpg .
2 Click the area of the paint that you want to remove.
3 Repeat the previous step for each area of paint to be removed.
4 Click IconTraverseImage.jpg when done to return the cursor to the default state.

To erase all painting from images
Click IconEraseAll.jpg . MIPAV removes all of the paint from all of the images.
Visualizing Images: Displaying images using the surface plotter view