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Manual Segmentation Drawing with 3D Volume tools

Segmentation Dialog

  • In the menu: Volumes > 3D Volume tools
  • Or click on the button on the left of the screen

Before you start

  • Open a VMR
  • Save the VMR with a different name, because there is no “undo” button for drawing.

Range: select all voxels in the value range (here 100-120) and make them blue. Selection can be limited in 3-D space by the bounding box.

"Grow Region" selects voxels in the value range, starting at the cursor position. Voxel selection can be limited in 3-D space by the bounding box.

Expand the existing selection. Click multiple times to expand further. Expansion can be controlled by increasing/decreasing the value range. Expansion can be limited in 3-D space by the bounding box.

Fill the box defined by the bounding box

Reload all: revert to the last saved stage of the VMR. Warning: if you save a VMR with blue voxels on it, they will be saved in the VMR and can’t be reverted to the original VMR data!

Draw 2D/3D. Click the enable box, set the pencil size and use Ctrl + left mouse button to draw. Shift + Left mouse button removes voxels (set value to 0).

Pen colors

 

Example use of the bounding box

  • Segmentation of temporal lobe
  • Look up proper x, y, z dimensions (cursor coordinates are displayed in status bar on the lower left of the screen)
  • Set the bounding box
  • Place cursor in temporal lobe and click grow region

Result