Combine labelmap from different models into one and save the data

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Hi,

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.

Combine lablemap from diffeernt stl models into One
Combine lablemap from diffeernt stl models into One1920×1040 121 KB

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:
    Before merging
    Before merging2560×1440 496 KB

    After Merging:
    After merging
    After merging2560×1392 449 KB

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!