Visualizing Images: Displaying images using the triplanar view

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The triplanar view allows you to see three orthogonal planes of 3D or 4D datasets. The three orthogonal views enhance the visualization of important aspects of the anatomy and, in some cases, aids some manual segmentation processes.

Displaying image datasets in triplanar view

To view an image dataset in triplanar view, open an image and then select Image > View > Triplanar in the MIPAV window. The triplanar view (Figure1 ) appears in an image window.

The image window for the triplanar view includes a File menu, an Options menu, a toolbar, and three views of the dataset. The bottom right corner of the window displays the currently selected coordinate. Two guidelines (cross hairs) also intersect at the selected point. Additionally, the axis appears in the upper left corner in each view of the dataset.

You can use icons and buttons on the toolbar to change the magnification level, draw a point or line, apply paint, and apply a new intensity values to selected voxels in the image.

Designating new center points for image datasets

You can designate a new center point for the dataset. To do this, complete the following steps:
1 Click IconVolumeCenter.jpg , the Volume Center icon, to display the center of a volume. The cross hairs intersect where the center of the volume has been calculated.
2 Drag the cross hairs to the point that you want to designate as the new center.
3 Release the mouse button.
4 Click Apply. The Apply Transformation Matrix dialog box (Figure 2) opens.
5 Complete the dialog box.

Figure 1. Image window showing the triplanar view

ZeroBAsedTriPlanatViewVolumeTab.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 cross-hair lines on the images. When you move these lines on one image, it also moves to the corresponding points on the other two images. Notice that the Absolute and Position values at the bottom right of the screen also change when you move the cross hairs.
Show Talairach Grid-Displays a Talairach (stereo tactic) grid on the images.
Show Talairach Position-Lists the Talairach position.
Link to Another TriImage-Links this image to another image in triplanar view.
IconTraverseImage.jpg Traverse image
Aligns two images.
IconMagnify.jpg Magnify
Magnifies the image. It might be necessary to manually resize the window and use scroll bars to view all of the image.
IconMinify.jpg Minify
Minifies the image (reduces the magnification level).
IconOriginalMagnification.jpg Original magnification
Displays image at the original magnification level.
IconVolumeCenter.jpg Volume center
Reassigns a new center to the dataset. The location that you select appears in the center of the image window.
IconAlignmentTool.jpg Alignment tool
Allows you to apply a transformation matrix to an image dataset.
IconApply.jpg Apply
Applies the rotations and translations made to the image.
IconPoint.jpg Point
Draws a point on an image.
IconNewContour.jpg New Contour
Assigns the subsequently drawn contour to a new group. If this icon is not selected, all subsequent contours are assigned to the existing group.
IconDelete.jpg Delete
Deletes a single contour or a group of contours.
Caution: When you select this icon, the contour is not copied to the clipboard. It is permanently deleted.
IconCropVolume.jpg Crop Volume
Indicates the volume that should be cropped.
IconCropbutton.jpg Crop
Crops the specified volume.
IconPaintBrush.jpg Paint Brush
Selects paint brush tool. You can use the paint brush to fill specific voxels with color.
IconEyedropper.jpg Eyedropper
Changes the default intensity to the one sampled by the eyedropper. Click this icon, then move the pointer to the image. The sampled intensity becomes the default intensity.
IconPaintGrow.jpg Paint Grow
Applies the paint grow segmentation method. This method uses voxel aggregation to group voxels into larger regions. The effect is much like a fill operation; when you click a voxel, this algorithm is used to determine whether adjacent voxels should be filled with the default color or intensity.
IconErase.jpg Erase
Deletes painted sections of the image. To delete, click the icon and move the pointer on painted areas of the image.
IconGlobalErase.jpg Global Erase
Deletes all paint from the image.
IconSmallPoint.jpg Small Tip
Used with the paint brush and erase icons. Click this icon to indicate the size of the eraser or the paint brush tip. Click this icon to paint or erase one voxel each time the mouse button is clicked.
IconMediumPoint.jpg Medium Tip
Used with the paint brush and erase icons. Click this icon to indicate the size of the eraser or the paint brush tip. Click this icon to paint or erase 16 voxels (4 x 4 square) each time the mouse button is clicked.
IconLargePoint.jpg Large Tip
Used with the paint brush and erase icons. Click this icon to indicate the size of the eraser or the paint brush tip. Click this icon to paint or erase 100 voxels (10 x 10 square) each time the mouse button is clicked.
IconPaintIntensity.jpg Paint Intensity
Indicates the intensity value.
IconChangePaintColor.jpg Change Paint Color
Changes the color of the paint used. This icon is often used in conjunction with the Paint Brush and Paint Grow icons. Click this icon and select the desired color from the window that appears.
IconOpacity.jpg Opacity
Indicates the opacity level of the paint. When this icon is clicked, a window appears that allows you to indicate the opacity of the paint: 0 is transparent, 1 is opaque. By default the paint is translucent (0.3), which allows you to see the original image under the paint.
IconCommit.jpg Commit
Permanently applies intensity level to the image.


6 Click Apply. A progress message appears as the image is transformed. In a few moments, the new image either appears in a new window or replaces the image in the current window depending on your choice.
7 Select IconVolumeCenter.jpg again. Notice that the image center was moved to the center you designated.

Figure 3. Apply Transformation dialog box showing choices in the Interpolation list
Interpolation
Determines the intensity of the additional voxels using one of the three following methods:
Bilinear-Weighs the average of the four nearest voxels (to the newly interpolated voxel). The interpolated voxel is assigned the resulting intensity.
Bspline 3rd order-Weighs the average of the 27 nearest voxels (to the newly interpolated voxel).
Bspline 4th order-Weighs the average of the 64 nearest voxels (to the newly interpolated voxel).

DialogboxApplyTransformationInterpolation.jpg

New image
Indicates where the results of the transformation appear. If you select this option, the transformed image appears in a new image window.
Replace image
Indicates where the results of the transformation appear. If you select this option, the transformed image replaces the current active image.
Apply
Applies the transformation to the image dataset according to the specifications in this dialog box.
Cancel
Disregards any changes that you made in this dialog box and closes this dialog box.
Help
Displays online help for this dialog box.


Aligning image datasets

You can use IconAlignmentTool.jpg , the Alignment Tool icon, to create a new transformation matrix for the dataset (refer to Figure 4).

The following instructions explain how to use the alignment tool:

1 Click IconAlignmentTool.jpg . A closed angle, which looks like a line that is slightly thicker on one end, appears on each of the three images displayed in triplanar view.
2 Click the angle. Arrows appear at the end of each ray. The measurement of the angle appears beneath the angle.

Figure 4. Using the alignment tool in triplanar view

ExampleTriplanarAlignmentTool.jpg


3 Open the angle. The angle degree indicates the direction and distance to rotate the image. You can open the angle with or without constraints. (If an angle is opened with constraints, it only opens in 90-degree increments.) Do the following:
Position the pointer over the shorter ray of the angle. The pointer changes to a cross-hair shape. (The cross-hair pointer looks much like a plus sign.) Drag the shorter ray to the desired location. The new angle measurement appears below the angle.
Position the pointer over the longer ray of the angle. The pointer changes to a cross-hair shape. The cross-hair pointer looks much like a plus sign. Drag the longer ray to the desired location. The new angle measurement appears below the angle.
4 Click Apply. The Apply Transformation Matrix dialog box (Figure 3) appears.
5 Complete the dialog box.
6 Click Apply.
A progress message appears as the image is transformed. In a few moments, depending on your choice in the dialog box, the new image either appears in a new window or replaces the image in the current window.
7 Click IconTraverseImage.jpg , the Traverse Image icon, to return the cursor to normal mode.

Creating, modifying, and deleting point VOIs

You can create, modify, and delete a point VOI. For more information on how to do this, see Chapter 7.

Cropping images

To crop an image, complete the following steps:
1 In an image window that is displaying the image dataset in triplanar view, click IconCropVolume.jpg , the Crop Volume tool.
2 Draw a rectangle around the area of the image that you want to remain. The area outside of the rectangle will be cropped.
3 Click IconCropbutton.jpg . A confirmation box appears.
4 Click Apply. The cropped area appears in a separate window.

Changing the intensity

For information on how to change the intensity of a portion of the image, refer to "To change the number of intensities displayed in the LUT" and "To invert intensities". In addition, refer to "Generating masks".

Visualizing Images: Displaying images using the triplanar-dual view