PDF – Exporting an MHD and Raw File from 3D Slicer and Creating a Color Transform XML with MHD Color Transform

Steps to export a 3D data object from Slicer as an .mhd file, then use the file to create a color transform .xml that can be used in Unity:

Software authored by: Kumar Punithakumar

Scripts required: https://github.com/Know-Thyself-as-a-Virtual-Reality/MHD-ColorTransfrom

VIMEO link: https://vimeo.com/726185031 (Color transform instructions start at 00:02:43)

Step by step (exporting from Slicer):

Start with a scene in Slicer, it should contain the object you want to work with.
Select the volume rendering module from the dropdown menu (fig. 1).
Select the model you want to export. Ensure it is the only model selected (the eye icon can be clicked to toggle model visibility).
Select file in the top dropdown menu, then click save (fig. 2).
When the save scene window opens, ensure only the model you want to export is selected (fig. 3). Change the file format to .mhd in its corresponding menu.
Click the box for show options (fig. 4) at the top right of the window and deselect compress for the file (compressed files won’t import to Unity correctly).
Select a location to export the file to and click save.

Step by step (creating color transform .xml – starts at 00:02:43 in video):

Close or minimize Slicer and move into Color Transform.
Click load meta image at the bottom of the screen (fig. 5). A window should open to allow you to locate and open the .mhd file you just created in Slicer.
Under the lighting tab, shading can be turned off (fig. 6) so the model’s colors can be seen more easily.
Select the opacity and color tab, then click transfer function editor to open a window where the model’s colors can be edited.
Click the circular nodes to select, then click the color button to change the color (fig. 7). More nodes can be added by double clicking on the line.
Click and drag the nodes to adjust value and opacity as desired. The window can be closed when the colors look as desired.
Also in the opacity and color tab, the adjust transfer function window can be opened and used to edit the color curve.
Navigate back to the lighting tab and test how the model looks with shading on.
When you’re ready, click save settings (fig. 8), ensure .xml is the file format selected, then click save.
You can now use the load settings menu to toggle between the available color transforms (fig. 9).

Fig. 1
Select the volume rendering module

Fig. 2
File then save, or Ctrl+S (PC) to access save scene menu

Fig. 3
Select only the model you want to export, check that no others are selected

Fig. 4
Don’t forget to deselect compression. Select show options to do so

Fig. 5
The load meta image button is under the general controls tab