Side View

 

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This tool enable will open a new window on the left of the current axial view. This window will display a side view of your volume.

 

 

You can also used this tool, in association with either the "2D Label" tool to assign labels to all the axial frames in your volumes.

 

In the "Slice" and "Volume" modes, selected slices are in white and un-selected slices will have a blue tint.

 

Note:

 

•The Side View will only display an image if you have a 3D volume.

•The "Ray" button is only enabled if you have a CUDA compatible graphic card.

 

 

From the Graphic Interface

 

 

 

Without a CUDA compatible graphic card, the Side View interface will have 2 display modes "Slice" and "Volume"

With a CUDA compatible card, you also have the "Ray" display mode.

 

Rotation

You can rotate the view in the "Side View" window using this slider.  The view csn rotate 360 degres. You can go from sagital (completely to the left) to coronal (90deg) and more.

 

Display mode

Depending on the selected button, the Side View window will either show a cut plane going through the volume (Slice), a 3D volume visualisation using point cloud (Volume), or a ray traced view of the volume (Ray).  In these 3 modes, you can rotate the view aroun the "z" axis using the "Rotation" slider.

 

Slice

Volume

Ray

 

Note:

The first time you select either "Volume" or "Ray", the program has to pre-compute a number of components to create the side view.  It will take some time.  After that the refresh should be much faster. 

In order to help interactions, when the image is refreshed, the view will be of a lower resolution.  As soon as you stop interacting with the volume, the image will be recomputed at full resolution.

 

Light Intensity

For the Volume and Ray options, you can change the intensity of the light sources.

 

Note:

The light sources are defined and can also be controled by the "3D Light" tool.

 

GLI Threshold /

TAG transparency

 

If the TAG "None" is selected, this slider is used to select the threshold used to display any voxels that are not tagged. 

 

The threshold values of the slider cover the range of values of the voxels (range = highest value - lowest value).  The density of the voxels will go from 0 at (threshold - 1/4 range) to 1 at (threshold + 1/4 range).  The resulting volume is quickly affected by any changes to the threshold slider, we suggest you use the mouse wheel when the cursor is over the slider to change its value.

 

If any of the other TAG buttons are selected, the slider is used to compute the opacity of the tissues under the selected TAG. 

 

When the slider is in the left half of its range, the opacity is function of the gradient of the voxels (this help display the tissues boundaries), in the right half, the opacity is applied to the complete volume of the tissue.

 

When this slider is pushed completely to the left, the corresponding tissues will be turn off and no longuer be visible and the yellow indicator on the matching TAG button will turn grey.

 

TAG selection

In the "Volume" and "Ray" modes, all tagged tissues used in the volume will have their matching TAG buttons enabled.  You can change the opacity of each of these tissues by selecting their TAG value and changing the "TAG transparency" slider.

 

In the "Slice" mode, all the TAG buttons will be disabled.

 

Slice selection

You can use the selection box in the side view window to select specific slices from the volume.  The "Slice" and "Volume" display modes will show unseleted slices in a blue tint.

Select in Box will mark all the slices inside the red selection box in the side view window as the selected slices.  Any operation that affect multiple slices will only opearate on the selected slices.

Select All will mark all the slices loaded in sliceOmatic as selected.

 

 

 

From the Display Area

 

 

In the Side View window:

 

In the side view window, you can use the mouse to create and drag a "selection" box.  This box can be used to select the slice inside the box ("Select in Box" button) or to label the slices inside the box with the "2D Label" tool.

 

The position of the current frame will also be displayed as a yellow horizontal line crossing the side view window.  You can change the current frame by pressing the "." (period) key on the keyboard while the cursor is over the side view window or simply by doing a double click on the desired location..

 

 

In the axial window:

 

In the axial view, the current frame will display the rotation center and rotation plane.  You can change the rotation center by dragging it with the mouse.  The angle of the rotation plane can only be changed with the "Rotation" slider.

 

Note:

You can only drag the rotation center if you are in a mode where the mouse is not used for something else.  For example, you can not drag it in the "edit" mode, since the mouse is used to paint.  but you can drag it in the "Display (TAG/2D)" mode or any othermode that does not have a display area interaction

 

 

 

Working with the "2D Vetebral  Label" tool:

 

 

If you open the "2D Vertebral Label" tool, then a vertical "vertebral color" line and the associated vertebral labels will be displayed on the right hand side of the "side View" window.

 

The interaction between the "Side View" window and the "2D Vertebral Label" tool will enable to assign vertebral labels to all the slices in your volume.

 

When you create a selection box in the "Side View" window, you will also see a red line at the right of the "vertebral color" line.  This red line cover all the slices that have been touched in the selection box.  All the slices marked by this red line will be affected if you select a lable in the "2D Label" tool.

 

Once you assign a vertebral label to a group of slices, the "color" line for these slices will take the color of that specif label.  And, if there is enough room, the label will be displayed inside a circle. 

Labels that have been assigned manually will also have a white border.  Labels that have been interpolated by the computer will not have this border.

 

 

Here's how you can assign labels to all the slices in a 3D dataset using "Side View" and the "2D Label" tool:

 

 

When you start, all the slices are marked as "Undefined"

 

You click and drag a box around the first vertebra of the volume.

 

You then assign a label to all the slices in this box

 

You create a new box around the last vertebra.

 

And assign a label to the slices of that box.

 

Once you have labelled the 2 extremities, the program will interpolate the labels for all the slices in between.

 

If the interpolation is wrong, you can refine it by manually labelling a few more vertebra using the selection box and the Vertebral Label tool.

 

Note:

 

•The "Volume" option has a couple of limits: If you have a Nvidia or and AMD graphic card, it will limit the number of voxels you can display depending on the available GPU memory. And even with a lot of memory, It will not let you see a volume with more than 250 millions voxels (that's a little over 1000 slices at 512x512 each).  If you have more than  160 million voxels, the program will need to do some computations each time you rotate past a 90° mark (90°, 180°, 270°) so the rotations will not be as smooth.  

•The "Ray" option is also limited by the amount of GPU memory available.

 

 

From the Keyboard

 

 

 

Key map

Action

 

 

.

"." has been mapped to the command: "Side: Select".

 

Pressing the "." key while over a side view will change the current frame of a group to the frame at the corresponding position on the side view. 

 

Alternatively, a double click on the desired location in the side view window will have teh same effect.

 

 

From the Command Line

 

System Variables defined in this tool:

 

 

$SIDE_VIEW_SELECT_NB

(U32)

Number of frames inside the selection box.

 

$SIDE_VIEW_SELECT_PT

(P)

Pointer to a list of frame pointers for the frames inside the selection box.

 

$SIDE_VIEW_POINT_SIZE

(F)

Size of the points used in the "Volume" representation. (Default = 1.0)

 

 

Text commands defined in this tool:

 

Slice: Select

Activating this command while the cursor is over a side view will change the current frame of a group to the frame at the corresponding position on the scout.

 

Note:

 

The "Side: Select" command use the current mouse position.  So the command is only valid while the cursor is over the side view window.