GenericSegmentationPlugin

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For users

Manual Correction of meshes

Description: Deform a surface mesh using the mouse pointer over the 2D slices.

Author: Luigi Carotenuto

Usage

  • Shift + left mouse click: Deform the mesh
Manual Correction of meshes

Otsu Segmentation

Description: Apply OTSU segmentation to an input image using itk::OtsuThresholdImageFilter and Marching Cubes

Author: Maarten Nieber

Otsu Segmentation

Region Grow Segmentation

Description: Apply region growing segmentation to an input image using a set of input points and lower and upper thresholds. Generates an output mask image and surface mesh. It uses the filter itk::NeighborhoodConnectedImageFilter.

Author: Maarten Nieber

Region Grow Segmentation

Surface mesh to ROI image

Description: Convert a surface mesh to a mask image

Author: Xavi Planes

Surface mesh to ROI image

Threshold Segmentation

Description: Apply threshold segmentation to an input image using lower and upper thresholds. It also computes the isosurface mesh

Author: Maarten Nieber

Threshold Segmentation

Transformation Box

Description: Apply a rigid transformation to surface meshes, volumetric meshes and images. The transformation can be specified manually by filling up an appropriate table or automatically calculated by interacting with a vtkBoxWidget object that can be shown around the data and graphically modified by the user.

Author: Luigi Carotenuto

Furthermore the tool can be used both for time-resolved and single timestep data. In the first case, the user can chose whether to apply the transformation to one only timestep (the currently active one) or to all timesteps.

Transformation Box Widget

To specify a transformation manually, the user can directly edit the text box in the transformation table:

TransformationBoxWidgetTable.png

The first line specifies the translation in the x, y, z directions respectively. The second line permits to apply a scale factor along the same directions, while the last line specifies the rotation angle around each of the three axes. (Note: according to VTK implementation, the rotation will be applied in the following order: RotZ, RotX, RotY)

An alternative way of specifying the transformation matrix is by manually interacting with the rendering data. To do this, simply click on the “Show Box” toggle button. A box will appear around the data and the button caption will change in “Hide Box”.

The box interaction works in this way:

  1. Drag one of the six points on the box’s faces: the corresponding face will be moved according to the mouse direction.
  2. Click and drag on a face will permit to rotate the corresponding face
  3. Ctrl+Mouse move: the box is scaled according to mouse movement.
  4. Shift+Mouse move or drag the center of the box: the box is translated according to mouse direction.

Each time the box is moved, the corresponding transformation will be shown in the transformation table. When satisfied, apply the transformation by clicking on the “Apply”.

If the selected data is time-resolved, then the “Apply to all time steps” checkbox can be used to decide whether to apply the transformation to the current timestep only or to all timesteps at the same time.