Segmentation Workspace
Overview
This workspace is an imagery one, please read the Visualization workspace documentation to know the basis of using it.
Running a process
- Choose your toolbox in the right panel within the * Choose a toolbox * combobox.
- The "?" button in the right of the toolbox header can give you information about the toolbox.
- Use the central view to drop as many data as you need.
- Choose your parameters if needed, and click on "Run", or interact directly with the view.
The Segmentation workspace groups several segmentation toolboxes:
Toolboxes
Paint Segmentation
To draw a brush mask on your volume in the view. You can change the value of the drawn mask using the label parameter.
- Paint / Erase: a left click on the volume in the view draws a mask area under the mouse cursor, a right click removes it. The mouse cursor area can be adjusted using the "Brush Radius (mm)" slider, or Ctrl+mouse wheel.
- Magic Wand: this component computes region growing segmentation. A left click on the view gives you in the toolbox the seed value that you need, to define your minimum and maximum value for the region growing.
- The "3D mode" parameter applies a 3D region growing.
- The "RealTime Computation" parameter updates the computation each time you change a parameter of the Lower and Upper Threshold, and not just when you click on the volume.
Polygon Roi
Enter a data in the view and click on 'Activate Toolbox'.
- Create contours
To segment a volume using polygons, Shift+click on the volume to draw your nodes. Close the contour (ROI) by clicking on the first node.
Switch to a new slice and you can draw a new contour.
- Correct a contour with Repulsor
You can adjust your segmentation with the Repulsor tool. Click on the Repulsor button, then click on your data somewhere close to the contour you want to correct. A circle cursor appears allowing to "push" your contour.
- Labels
Any ROI drawn takes the color of the label defined and selected here:
Click on the "+" or "-" buttons to add or remove a label and begin to draw. You can double-click on the name (or right-click on a node) to rename it:
On the homepage, you can select: Settings / Start Up / Segmentation speciality and choose for now "Default" or "Urology". Save and restart the application to change the speciality. The "Urology" specialty then displays its own specific labels required for segmenting:
You can change the current label of a contour: hover a node with your cursor, right-click and choose the 'Change label' menu.
- Remove node/contour/label
To remove a component of the segmentation, put the cursor over it and use Backspace, or right-click and choose 'Remove' in the menu.
- Interpolation
Use 'Interpolate between contours' to automatically generate interpolated contours across multiple slices of your volume. While you already have a polygonROI segmentation covering the desired body part to be segmented, relying solely on 'approximation' isn't sufficient. You can manually refine an interpolated contour, elevating it to the status of a 'master contour', much like manually drawn contours. Subsequent contours are then automatically reinterpolated.
- Copy-Paste
To copy a segmentation in the current slice, use Ctrl/Cmd + C or put the cursor on a node then right-click and choose menu 'Copy'.
Paste it on an other slice using Ctrl/Cmd + V.
- Save
Click on 'Mask(s)' or 'Contour(s)' to save your segmentation. You can also right-click on a node and choose the 'Save' menu.
VOI Cutter
Drop a volume in the view and switch to 3D mode. You can rotate your volume in order to display an area to remove, then click on "Cut Volume" to manually draw a polygon by clicking on the view. If you press Backspace, the projected area will be removed from the mask, if you press Enter this area will only be kept. Click on "Save Image" to save your new volume.
Variational Segmentation
The idea here is to define the contour of your mask by placing landmarks. Drop a volume, click on "Start Segmentation", then place some landmarks representing the contour and at least one inside or outside the area you want to segment. When you are done, click on "Apply segmentation" to see the result, and you can generate your binary volume.