Combine labelmap from different models into one and save the data


I have several surface models (in .stl format) and would like to create one single labelmap which contains all individual models. Here’s is a screenshot for the model.

Currently I can only export the labelmap individually as .nrrd file. However, it lost the relative coordination information between the models. I also tried to merge the models but:

  1. only two models can be merged at a time;
  2. once merged, colour (label) assigned to corresponding model get lost.
    Before Merging:

    After Merging:

May I ask how I can combine all the label maps into one and export it into some format that can be loaded into Matlab?

Many Thanks!