Contours around a region of interest are grouped together to form a volume. You must first create and name a volume. Go under the Volume pulldown and select New Volume. Then add contours to that volume. The volume is created considering the contours. The contours are first sorted into coplanar groups. Between contours in each group, the shape is interpolated about every millimeter. A volume is bit mapped for each group of contours, dividing the volume into voxels and assigning 0 to voxels outside the volume and 1 to voxels inside the volume. This is called a cuberille. The resulting volume is the union of the volumes formed from each group of coplanar contours. You can therefore outline a volume on successive transverse slices followed by outlining on successive coronal images, for example. This might be desirable so that a volume has a rounded end instead of a flat end. After the final cuberille is formed, a surface is generated for the volume forming a connected mesh of triangles.

Because shape interpolation, bit mapping, and surface generation may take some time, once you begin contouring an object the generation of the volume is blocked until you are finished. Turning contouring off will cause a popup to come up where you can unblock the forming of the volume. This window provides other options, such as forming holes, which will be described below.

There are six tools provided for outlining regions of interest. Four tools for creating contours, one edit tool, and one tool to delete contours. Under the Volume pulldown you can delete a volume and change the material properties of a volume.

All the contouring tools and most of the functions under Volume pertain to the volume that is currently selected on the Select Volume option menu. Note also that both the Select Volume option menu and the contouring tool option menu are tear off menus. You may form a separate window frame around each and keep them at a convenient place on the screen while you are working on contours. This will allow you to easily switch between volumes and contouring methods. To tear off a tear off menu, hold the left mouse button down on the dotted line that appears on the pulldown menu and then release the mouse button. A window frame will form around the menu. However, when done you should close the window using the window control on the upper left hand corner of the window frame.

Most importantly, the contours are added to the volume that is showing when you accept the contours, not when you started the contouring.

Mouse Contouring

Selecting mouse contouring brings up a popup rather than a tool bar. You simply select a frame and begin contouring with the mouse. The cursor will turn to a pencil shape and you can either click with the left mouse, or hold it down and drag. Use the middle mouse button to back up one point at a time. A button is provided on the popup to do the same. Likewise you close the contour with the right mouse or use the close button on the popup. Closing the contour will cause the contour to connect to the first point entered. Hitting the right mouse does not enter a new point. After you close the contour you can still back the contour up, which will reopen the contour.

The mouse contouring popup tool.

When you are satisfied with the contour, hit the Accept button on the popup. The contour will be added to the currently selected volume that is showing on the option menu for selecting volumes.

Project Parallel Plane Contour

As an aid, you can have projected onto the plane you are contouring contours from other planes that are coplanar. Each time you hit the Show Next button, the next closest parallel contour is projected onto the current frame. These projected contours can be used for information which you can trace over or near. Or you may hit the Use button to select the latest contour shown with Show Next to create a copy in the frame you are working in. You will be at the same state with this copy as if you had just closed a contour. Hit the Reset Next to erase all the projected contours and to allow the projection process to start over again.

Edit Contour

You may edit a contour once you have closed it by hitting the Edit Contour button. With the contour editor you can splice the contour or add and move points. When you hit the "Accept" button the contour will be added to the current volume selected as mentioned above, and the mouse contouring tool will return. Otherwise the edit contour tool works independent of the mouse contouring tool. See the Edit Contour tool below.

Tolerance

Once the contour is closed, you can adjust the number of points with the "Tolerance" scale. An algorithm is used where by points can be eliminated from the contour as long as the eliminated point is within the tolerance distance from the resultant remaining line. A back up copy of the contour is kept which allows you to adjust the scale either way. However, if you reopen a closed contour with the "Back up one point" button, the backed up copy is first copied from the current contour on display.

Accept

If you don’t accept the contour, the contour will not be added to the volume. Hitting the return button on the contouring tool bar or selecting another contouring method will cancel the current contour. Also simply starting to draw in another frame will cancel the current contour.

BE SURE WHEN YOU HIT THE ACCEPT BUTTON THAT THE CORRECT VOLUME IS SELECTED. YOU MUST HIT ACCEPT TO SAVE THE CONTOUR.

Ellipse/Circle Contouring

This tool will create a contour consisting of a circle or ellipse. You may then move individual points or add points to the contour. This tool can also be used to project the prior contour made with this tool onto the next image plane to be used as the starting point for the contour in the adjoining image plane.

Click the mouse in a frame showing an image of the selected image set if you do not currently see a circle afterselecting this tool. Since a circle is a special case of an ellipse, we may refer to the contour as an ellipse. Below we will simply refer to the contour.

You can more the contour by dragging with the left mouse button, or you may use the top wheel controls labeled Horizontal and Vertical. When moving points the wheel controls will still provide a means to move the entire contour.

Ellipse Contouring Popup Tool.

Below that you may change the size of the contour and rotate it. Below those two controls are Width and Height. Either of these two controls will change the aspect ratio of the contour. The width refers to the horizontal before the contour was rotated, and likewise for the height. These controls initially change a circle into an ellipse.

You may change the number of points with the Number of Points slider. To see the points push in the Move Points toggle button. However, changing the number of points will reset the shape back to an elipse as noted below.

When the points are showing and the Move Points toggle button is selected, you may drag a particular point. You may no longer drag the entire contour.

Note that moving the Number of Points slider will also do a Reset to Shape function. The contour will be regenerated as an ellipse with a different number of points. If you have a really contorted contour to make, use the Mouse Contouring tool instead. You can also accept the contour as is and use the edit contour control to change some part of the contour.

Use the Add Points toggle button to add additional points to the contour. When you click the mouse, a point will be added at the mouse location connecting to the nearest line segment that the point bisets. You should position the mouse close and next to the line segment that you want to add the point to. If you hold the mouse down you can drag the point that you just added. But to move other points you must select the Move Point mode.

Note that you may change frames with the contour appearing on the new frame.

The contour is added to the current region of interest volume only when you hit the Accept Contour button.

Auto Frame Contouring

Auto Frame Contouring Popup Tool.

Use this method for automatically contouring an area on an image that has a contrast difference. This tool works on a designated area whereas Auto Contour Screen below can find all such areas with the same threshold on all images on a screen.

Threshold value

Here you click the mouse on each side of the area with a contrast difference. The pixel value is shown at the top of the popup for each point. This is the pixel value after the image has been put through the contrast window, as the contouring is done after going through the contrast window. You may want to first adjust the contrast to get better separation of the area of interest.

The threshold value is initially the average of the pixel value of the two points you click on. But you can adjust the slider provided to weigh toward one point or the other. Just view the result until you get what you want.

Tolerance distance

Contour points are successively eliminated that fall within a tolerance distance. A line is drawn from a point to successive points, skipping points, until a skipped point would lie outside the tolerance distance. This procedure reduces the memory needed for contours and decreases processing time for shape interpolation later. You can change the tolerance distance with the slider provided.

Accept button

When you are satisfied with the contour, hit the Accept button. The contour is added to the volume currently selected.

Auto Contour Screen

Auto Contour Screen PopupTool.

Auto Contour Screen is a little more complicated than Auto Frame Contour above with additional features. Here a threshold value is similarly determined, but the entire image is search for contours with the threshold value. Further, the process may be repeated automatically on all images on the same screen.

Trace value

The trace value may be found by clicking the mouse on either side of a contrast boundary, and a slider is available to weight between the two points as in Auto Frame. In addition you may simply type in the trace value. Again, here the pixel values refer to the image after being put through the contrast window and does not refer to the original pixel value of the image.

Tolerance for point elimination

There is the same tool as in Auto Frame to control the tolerance for eliminating points found on the contours (see above).

Keep Contours control

Because contours are searched for over the entire image options are provided to select out contours. You may select to keep only those contours that are not inside another contour with Keep Outside Contour. That option would be useful for finding a skin boundary for example. Or you may select to only keep contours that are inside a contour. In both cases we are referring to contours found on the same image during this same operation with the same threshold value, not to any prior contours. Keep inside contours would be useful for contouring lung where you would want to reject the skin boundary.

Locate table top

You can also optionally locate a table top to keep contours from going below some level (the table top) on all the images. This can be done on transverse or sagittal images. The level found will apply to all the images contoured when applying to all the frames on the screen. No contour will be permitted to go below the horizontal line defined. We realize most CT and MRI couches are curved, but the option may be more useful when using a flat insert.

Minimum contour size

There is also a minimum size that can be used to reject small areas. The default is 1 cm. Type in different values. A contour that does not span this distance is not kept or shown.

Apply buttons

The program will not contour anything until you hit one of the two apply buttons. Make selections above the apply buttons and then hit an apply button to see the result. Generally you should apply to the current frame only to be sure you are getting what you want. Then hit the Apply to All Frames in Screen button to repeat the operation automatically on all the frames that are part of the current screen.

Accept and Cancel button

After applying you can either cancel or accept the contours. Hit accept to keep the contours. If you hit the return button on the contouring tool bar or select another contouring tool, the contours will also be canceled. If you do this accidentally, the operation is easy enough to repeat.

Unwanted contours

If you get some contours you don’t want, you can accept the contours and delete the unwanted contours later. For example, in contouring a skull that has a stereotactic frame parts of the frame may also be contoured. You can delete and edit out the frame contours with the Edit and Delete tools below.

Edit Contours

Edit Contour Popup Tool.

There are three methods available to you. You may splice a new piece into a contour, replacing a segment, you may move points, or you may add new points to the contour. You may switch between the methods as you work on a contour. The method is selected with the radio box at the top of the popup tool.

Selecting a Contour to Edit:

If you got to the editor from the mouse contouring tool, then a contour is all ready selected to edit. Upon acceptance, this contour is added to the currently selected volume, rather then replacing the contour that was selected as below. Otherwise first select a frame. The current frame will have a high lighted (usually red) border around it. Then click the mouse on the contour that you want to change. You can only edit contours that belong to the volume that is currently selected, and the mouse must be clicked within the pixel distance shown on the slider. You may move the slider to select a different tolerance distance. Only contours that lie in the plane of the image displayed may be edited in this manner. When a contour is selected, the cursor will turn to a pencil shape and the contour will be high lighted in a different color (the color used when drawing contours).

Splice a Contour

Begin drawing in the section of the contour you want to replace. Notice that the program will show where the contour will tie into the existing contour. From the first point you enter, the closest point on the contour is found and becomes the first point of the patch that your are drawing.

Continue drawing in your patch. You may drag the mouse with the left button down, on click the mouse successively. The middle mouse will back up one point at a time or you can use the Back Up push button on the pop up tool.

To end the patch hit right mouse or hit the End Segment button on the popup tool.

You must now click the mouse on the segment of the contour that you want to delete and your patch to replace. The resultant contour will now be drawn. You may now edit another portion of this same contour by repeating the above starting with entering another patch.

Move Points

The points will be drawn in larger splotches than the contour line. If points are on top of each other, you may have to reduce the number of points first with the tolerance slider. Then simply click on or near a point and drag it.

Add Points

Simply click the mouse on the contour where you want to add the point, and continuing to hold the mouse button down, you may drag the point to a new location.

Tolerance Distance

By adjusting the tolerance distance you can reduce the number of points on the contour. An algorithm is used whereby points are eliminated as long as the eliminated point is within the tolerance distance of the remaining resultant line. Once you splice, move, or add a point to a contour, that contour becomes the orginal contour that the tolerance scale uses to produce a new contour. Otherwise move the scale back toward zero will restore the original working contour.

Accept Contour

Finally, you must hit Accept to keep the changed contour or Cancel Edit to cancel the change to the contour. If you hit the return button on the contouring tool bar or select a different contouring tool, your change will also be canceled.

YOU MUST HIT THE ACCEPT BUTTON TO KEEP YOUR CHANGES.

Delete Contour

Delete Contour Popup Tool.

First select the volume that holds the contour you want to delete. You can only delete contours in the volume currently selected. Then click the mouse on the contour that you want to delete. The contour will be redrawn in the overlay color. Then either hit the delete button to delete this contour, or if you don't want to delete the high lighted contour you can either hit cancel or select a different contour by clicking the mouse on a different contour.

The scale controls how close to a contour in window pixels you must click in order to select a contour.

When you hit the Delete Contour button, a confirming message will appear. The confirm toggle button will allow you to delete a contour without the confirming message, so that you can delete contours simply by clicking on a contour. Only use this if you don't need to see the contour high lighted first. With confirm turned off you can more rapidly delete contours with single mouse clicks on the contours, but you have no protection from deleting the wrong contours (except the contour must belong to the currently selected volume).

Body Surface Contouring

This pop up is similar to the Auto Contour Screen tool. Here however, we work on images BEFORE they are contrasted, that is, put through the contrast window, and we specifically are looking for a body surface outline. If you need to find the body surface outline on contrasted images, then use the Auto Contour Screen tool instead. With that tool select Keep Outside Contours and you will have to define the trace value on a particular image.

The automatic body surface outline tool goes across the top of the image and periodically searches down until the trace value is encountered. Then that contour is traced throughout the image.

If you get some contours you don't want, or the contours need some editing, first accept the contours and then use the Edit tool, or any other outlining tool such as the Delete tool or Mouse Contouring tool.

The Pop Up Tool for Body Outlines

Body Outline Popup Tool.

Voxel Values

While the tool is up, you can click the mouse in any frame to get the voxel value, which is the pixel value of the image before image processing or contrasting. If the image plane is between images of the image set and the image was generated with interpolation on, than the value reported will be an interpolated value. For CT scans, a Hounsfield number of zero (water density) corresponds here to a voxel value of 1024, with 24 being -1000, and 2024 being +1000 Hounsfield units. This tool is provided to assist you in determining a good trace value.

Trace Value

The trace value is either typed in or set with the slider. A file in the program resources directory, "AutoBodySurface", sets the default value for the trace value. Contours are traced so that on one side of the contour are values less than the trace value, on the other side are values greater than the trace value.

Tolerance

This sets the amount of error tolerated when reducing the number of points for any found contour. Successive points are eliminated as long as the points that are being eliminated are within the tolerance distance to the new line connecting the two points that span the eliminated points. Decreasing tolerance will generate more points and slow down processing with the contours.

Minimum Size Contour

Since we are finding the body surface outline specifically, we can automatically eliminate any contours that might wrap around a small object outside the patient. If the contours is smaller in size than this value, the contour will be omitted. The default value is 1 cm.

Table Top

You can set a table top limit using a transverse or sagittal image. No contour will go below the line you choose. If you set this button you will be prompted to select a frame. Holding down the mouse in the current frame will allow you to drag a horizontal line. Upon release, the line will be fixed and define a coordinate for which no contour in any of the images may go below. If you want to find the table top a second time, simply unset the button and then reset it. This table top tool assumes a flat table top in that it establishes a horizontal barrier.

Apply Frame

Push this button to find contours for the current frame.

Apply to Screen

Push this button to find contours for all the frames on the current screen.

Accept Contour

Be sure the volume you want to add these contours to is the current selected volume showing at the top of your tool bar. The contours are simply added to the currently selected volume. If you have not made a volume yet, you can do so while this contouring tool is up. Select New Volume under Volume on the top tool bar. You should choose a name with body or skin surface in it.

Cancel Contour

You can only cancel this operation BEFORE you accept the contours. After you accept contours this tool resets for a new set of contours. Normally with only one image set you would only define one body surface volume.

Volume and Surface Generation

Unblock 3d Surface Generation.

3d surface generation is blocked while in any contouring mode. Selecting Contouring Off or hitting the Return on the contouring tool bar will exit from contouring mode. A Unblock 3d Surface Generation popup will appear. The same choices can also be accessed under the Volume pulldown to redo surface generation. After making any choices on the popup, hit the unblock or OK button to allow 3d drawing of this region of interest volume. The 3d surface will be created when drawing occurs into a 3d frame or when some other function needs the surface.

The controls on the surface generation popup

Surface Generation Controls Popup.

Shape Interpolation

A toggle button controls shape interpolation. Shape interpolation can take some time, up to two minutes, for large volumes such as the body contour. But this process occurs only once upon first drawing the 3d-view (and the bit map is also saved to a disk file for later program runs). Generally leave shape interpolation on unless you have some reason not to.

Voxel size slider

Processing time will also decrease if you increase the voxel size, but you will lose volume resolution if you do so. The minimum size of a voxel dimension is constrained here by the pixel size of the image set, and a default minimum value that is set in the program resource file ROIvolume. The resolution of the cuberille determines the resolution for computing a volume in cc (1 cc = 1 milliliter) and for volume histograms. You may increase the voxel size here with the slider.

Maximum Dimension for Surface Generation

After the cuberille is made, the solid surface is generated. The maximum dimension determines what size cuberille the surface generating routine starts with. If the cuberille from above has a dimension larger than this value, then the volume will be averaged in that dimension to a lower resolution. A number here larger than the default will greatly increase the amount of time to generate the surface. Only a large volume would be likely to exceed the default value in any case.

After the surface is found, the number of triangles in the surface will reduced to form a lower resolution version of that surface. The system will then pick a resolution to display according to the size of the triangle that projects onto the screen. As an object occupies a smaller area on the screen, a lower resolution of the surface is displayed, which decreases the drawing time. The number of pixels that a triangle or rectangular element covers on the screen is found by projecting the size from the center of the object.

This means that as lower resolutions are displayed on the screen, details will disappear. You can control the resolution that is displayed by going into the contour tool bar and selecting Frame Control under Volumes. You can set with the Number of Pixels the resolution that will be drawn, with higher resolutions being chosen as the number of pixels for a surface element is decreased. This control is on a frame by frame basis, and controls for the current frame selected only.

You might want to have a screen with only 2d views before unblocking more than one volume to give yourself some walk away time, as the actual generation will occur when a surface is needed in a 3d frame.

Holes in Volumes

Normally, with Allow Holes off, the toggle button out, the inside of any contour is inside the region of interest. If one contour is inside a second, the inside contour will have no effect. Another way of saying this for on a given plane, pixels are marked inside that are in the union of the inside of all contours on that plane. In this mode you cannot create a hole inside a volume using only contouring.

With Allow Holes on, contours are treated differently. If one contour is inside another on the same plane, the inside contour becomes a hole in the volume. The rule that applies is this, on a given plane any pixel that is inside an odd number of contours on that plane is inside the volume. Any pixel that is inside an even number of contours is outside of the volume.

By making a second contour inside a larger contour, the second contour will create a hole on that plane. Shape interpolation will proceed unaffected.

If you intend a hole inside a volume, and you also contour on another set of coplanar planes, then you must also contour the hole on the second set of planes. The reason is that each set of coplanar planes is bit mapped and shaped interpolated separately. Then the resulting volume is the union of all such sets. If the second set of contours included the same region and did not have a hole, then the hole would be filled in while taking the union.

Another way to create a hole is to contour the hole as a separate volume. Then create a new volume as the first minus the second.

When allowing holes be careful of the planes you choose for contouring. If two planes are closer than 1 mm, or closer than the minimum voxel dimension you pick above, than two contours from those two separate planes may be projected onto the same plane. Thus two contours there were intended to be outside contours would be projected onto the same plane. The consequences will be that their overlapping area will become a hole.

New Volume from Other Volumes

New Volume from Old Popup Tool

Under the Volume pulldown select New Volume from Old. This is a powerful tool for combining volume, subtracting volumes, and adding and subtracting margins to a volume.

In the text field at the top of the popup supply a name for the new volume. Choose a color with the push button to the right of the name text field. Then on the left selection box select the volumes that the new volume is to be a union of. On the right selection box, select volumes that are to be subtracted. For example, if one volume were inside another, this method could be used to create a volume that is the area inside the larger volume less the inside volume.

The slider may then be used to specify a margin to add or subtract. A positive number enlarges the volume, a negative number makes the volume smaller. The new volume is computed by convoluting a ball of radius equal to the absolute value of the margin. As the center of the ball sweeps over the entire surface of the volume, the ball either sweeps out an area to be added to the volume when the margin is positive, or the area to be subtracted from the volume when the margin is negative. In this manner the margin is added or subtract in all three dimensions. Note that the slider includes a thumbwheel for fine increments and a text field for typing in a value.

At the bottom of the popup is an option to produce contours around the volume. Above we contoured an object and then created a volume out of it. Here we start with the volume and produce contours around it. A reason for generating contours would be to see the contours on 2d images. Otherwise the volume will only show up on 3d views. These contours, once generated, can be edited like any other contoured volume, with the volume then regenerated from the contours.

Volume Properties

Volume properties can be changed under the Volume pulldown.

Name and Description

You can change the name of a volume, but the name has to remain unique within the stacked image set that the volume belongs to. You can also bring up a text field to type in a description for the volume.

Material Properties Popup Tool

Color and material properties

There are two ways to change the color of a volume. The first is to access Color under volume properties. The color chosen will be for both the front and back surfaces of the volume. By default the front and back surfaces have the same color. You may access the material properties popup which will allow you to change the front surface color or back surface color separately. You will not be able to see the back surface unless you turn on two sided lighting in a 3d view frame (hit the Rotate button and select Light Model). By default, two sided lighting is off (but the default is controlled by the LightModel file in the resources directory). To see a back surface you also will probably have to cut the surface with a cutting plane.

The material properties besides color that may be specified for the front and back surfaces are ambient, diffuse, and specular reflectance. These are set the same for all three colors (red, green, and blue). Emission and shininess may also be set. The material properties are discussed in the Open GL reference books.

You must hit the Apply button to see the effect of changes in the material properties popup.

Line width

Lastly, under volume properties, you can change the line width by which the contours are drawn on 2d images. The contours will use the front face color of the volume.

Frame Control

Frame Control for Outlined Volumes

For a particular frame, the appearance of the volume can be changed. First select a frame to make current (by clicking the mouse in the frame), then select Frame Control. The control will be only for the selected frame. A popup will come up.

At the top of the popup is a toggle button for turning contours on or off. On 2d frames the contours will be on by default. The default is off for 3d frames (you can display the contours on a 3d view in wire frame). You can change the state with the toggle button. These are the contours from which the volume was generated.

Controls that pertain to 3d views only

Transparency control

The transparency of the surface can be changed with the slider. Not all systems will support a different transparency for the front and back surfaces. The transparency/opacity slider controls how transparent the surface appears. The top slider sets the transparency for both the front and back faces of triangles. The next two sliders will allow you to set the front face and back face differently. When setting those two sliders the value on the top slider has no effect, although the average value is shown. All the way to the left makes a surface completely transparent, and all the way to the right makes it opaque. Transparent back faces might not appear transparent on some, or any, systems.

There are limitations on drawing transparent surfaces. If two transparent surfaces intersect, the one that is drawn first can be seen inside the surface drawn second. But the one that is drawn second cannot be seen inside the surface that is drawn first. The same applies for one transparent surface inside another. Any object drawn inside a transparent surface or further from the eye location than an intervening transparent surface after the transparent surface was drawn will not be visible. For this reasons this program draws solid objects first, then transparent objects. However no attempt is make to order the drawing of transparent objects according to which is closest to the viewer, except that the skin surface is drawn last if transparent. Volumes found with the body outlining tool are so marked to be drawn last. To avoid confusion, select only one surface to be transparent.

Off, Wire, Solid

This choice should be obvious, controlling whether a solid surface is drawn or just the edges of the corresponding triangles or rectangles are drawn, or not to draw the surface at all.

Resolution Scale

When the solid surface is drawn, a resolution is picked so that a triangle that would be situated at the center of the volume will project to the display window and have a dimension of at least the number of pixels chosen. Lower resolutions are found with a triangle simplification algorithm that is applied to the triangle mesh that covers the surface.

As you move the slider to the right, lower resolution versions of the triangulation will be drawn. The purpose of drawing lower resolution is so that as an object gets smaller on the screen, a smaller number of surface elements will be drawn, increasing the drawing speed. The default value for this parameter can be set in the Frame3dDrawable file in the program resources directory.

When dragging a viewing control, triangles are skipped so that only a small number of triangles are drawn.

Set Active or Inactive

This control will allow you to turn a volume off in all frames. There is a separate toggle button for 2d and 3d views. The choice is also saved, so that when the program is restarted and the same image set is selected, the drawing of the volume will be governed by the choice previously made here. The setting here not to draw will override any choice made in Frame Control above.

Volume of a volume

The volume in cubic centimeters (one cubic centimeter equals one milliliter) can be computed and displayed. Be aware that this volume depends upon the pixel size from the original image files read in from the imaging system. If the imaging system passed on an incorrect pixel size then the volume calculation will be incorrect as well, and so will be the scale shown on 2d images. The volume is calculated by simply counting up all the voxels in the cuberille forming the volume and multiplying the total count by the volume of a voxel.

Copy Volume

Copy Volume Popup Tool

With this tool you can copy an outlined region of interest to make a new volume. You can copy the volume into a different stacked image set ONLY if the two image sets were fused. This tool is selected under the Volumes pulldown menu.

Same Image Set

You will have to give the new volume a different name, since it can't have the existing name because each volume must have a unique name. Your only reason for copying a volume in the same image set would be to make some change to it. Note also the New Volume from Old tool that will allow you to make a copy and add or subtract a margin. Here the volume is copied in all respects except its name.

Into a Fused Image Set

You don't have to rename the new volume if the stacked image set that you are copying the volume into does not all ready have a volume with that name.

Select the image set that you are going to copy the volume to. Then select the image set you are going to copy from. A list of the volumes that are in the "from" image set is than listed. You must pick one of these volumes by clicking the mouse on that choice. Then hit Copy.

If the two image sets are not fused, you will get an error message.

If the volume name all ready exist in the "to" image set, you will also get an error message. You will then have to type in a new name that the volume is to have in the "to" image set, and hit the Copy button again.

The new volume will come up active to draw in all 2d and 3d frames, regardless of the status of the volume copied from.

Hit Dismiss if you decide not to copy a volume.

Output Contours

Output Contours Popup Tool

This is an option under the Stacked Image Sets pull down menu, on the Stacked Image Set Options toolbar. The option will allow for writing out the contours of the image set in two different forms, 2D contours coupled with images, and 3D contours.

Select Volumes

The user must select the outlined volumes whose contours are to be written out. More than one volume may be chosen.

Write Out 2D Contours

The first option will write back out the Dicom image files with the contours that lie within each image spliced into that file. Note that only contours that are coplanar with and lie on the image plane will be written out with the image. Other contours that do not lie in any image in the image set will not be written out, such as contours outlined on reformatted planes. The contours will be written in the pixel system of the image with two coordinates per point. Each contour will be labeled with the name of the outlined volume that the contour came from. There is a limit of 128 contours per image file under the 50xx group tag, but you are unlikely to have outlined more than 128 contours on a single image in the image set.

Write Out 3D Contours

The second option is to write all contours out into a Dicom file that will not contain an image. The file will hold all three coordinates for each point on each contour in the coordinate system assigned to the image by the imaging system. The coordinates will be in centimeters. As Dicom has a limit of 128 contours per file using the 50xx group tag, more than one file will be written out if there are more than 128 contours in total. Each contour will be labeled with the name of the outlined volume that the contour came from.

Output File

The byte order of the file will be that of the image files for the image set that were read. A file header as specified by PS 3.10 will not be appended to the front of the files.

In either case the user must select or create a directory to write these files to, and provide a root file name. The file names will have a comma and number appended to the root name for each file.

Moving an ROI Volume

Simply pick any two dimensional display of the image set. Click the left mouse on the frame to make that frame current. Then click the left mouse any where on that image. The nearest contour that is also parallel to that plane will be drawn. As you drag the mouse, the contour will move. In a plane where the contour intersects the plane (such as contour from a transverse plane in a coronal or sagittal view) the intersection of contours will be drawn with that plane. If there are a lot of contours, some will be skipped for the drawing to improve the draw time. You can change which frame you want to move in.

Moving Couch Model Example

An example of dragging a TomoTherapy Couch ROI volume after selecting it from a template is shown below. On a Windows machine the contour is drawn in XOR logic as it is dragged. On linux you will see a red outline (in the overlay planes).

You will drag the contour to align it with the CT image. Be sure to check a sagittal view and a 3D view.

In the sagittal view you will see the intersection of the contours with the plane:

In the case of a couch model, if the template couch model is not long enough, then simple go to each end CT scan. Select Mouse Contouring, hit Show Next, then Use, then Accept, to add the contour in the plane you are in. Do the same at the other end CT scan.

The contours will not be redrawn until you hit the "Done" button.

Beaware that contours from a prior stacked image set might not correspond to a plane in the new set, and so will not be drawn anywhere. Review the ROI volume in a 3D view. Use frame control to display contours as well as the surface rendering.

A volume that has no contours cannot be moved. Nor can the movement be dragged in a 3D view.

Save Volume as Template

This function will copy the currently selected file to a sub-directory VolumeTemplates.d of the data directory which is defined by the location file DataDir.loc in the progam resource directory (in turn defined by the file rlresources.dir.loc in the current directory where the software is loaded).

Each ROI volume is a directory, and the directory name defines the name of the volume. Therefore you can rename the template by renaming the directory for that template.

Select Template for Volume

This function will allow you to select a stored template and read it in and add it as an ROI volume to the currently selected stacked image set. After you have done so, use the Move Volume on the Volume pulldown menu to move the volume to a correct location. See the Help button on the move control popup. Be aware, that a contours from a different image set might not correspond to any CT scan coordinate in the set you are moving to, and so might not show up (except when using the move function). Review the volume in a 3D view.

See comments above in Move Volume if you are copying in a couch model.