You can go Model -> Segmentation -> Labelmap, all from within the Data module. In your screenshot two above, you see “Convert model to segmentation node”. It’s equivalent to creating a new segmentation and doing the import in the Segmentations module.
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Thank you so much for your kind assistance, Csaba. I will use the steps that you mentioned, but first I need to overcome what seems to be my last obstacle.
Could you please download the 2 files below, to replicate my work?
3D Cranium Model in OBJ Format
-Ramon
JFK Numbers
I don’t see the problem. As you highlighted in the screenshot you need to select the master volume in order to do any editing. What I did:
- Drag&drop obj into Slicer
- In Data module right-click the model, choose ‘Convert model to segmentation node’
- Right-click segmentation node, choose ‘Export visible segments to binary labelmap’
- Go to Segment Editor
- Select labelmap as master volume
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Great! I too overcame my last obstacle. Your 5-step method is very easy to follow and repeat.
In conclusion: that model that you used, from CG Studio, works fine. The scissors icon is enabled. The lack of accuracy implied by carving an injury based on 24 frames from a video remains a big issue for my particular purpose. I am considering contacting the author, Dr. Peter Cummings, to see whether he will share the 3D model shown in the PBS documentary.
I am currently downloading the real, high quality cranium model that I want for my project from the Behr Bros. website:
Very High Definition 3D Cranium Model
That one is consistently crashing (a memory-related exception is being thrown). As soon as I have it in my server, I will ask for your help again. Please don’t go too far. 
-Ramon
JFK Numbers
Hi Csaba:
I downloaded the latest versions of the Behr Bros. cranium. The OBJ files are here:
High Resolution OBJ Models of a Cranium
in 3 qualities. Can you please check to see whether your PC has the same problem (a memory allocation exception is triggered) that my computer is having?
TIA,
-Ramon
JFK Numbers
It seems that you’re running out of physical memory. You can increase the virtual memory, or you can adjust the resolution of the labelmap so that it fits. The formed is described many times in this forum and you can find it with a search. However, it may not be feasible due to the very long processing time in the case of such a large model (the high resolution model is specified to be physically larger so the default 1mm isotropic spacing is probably cannot be used).
The latter can be done in the Segmentations module.
- Create new segmentation node
- Make Closed surface the master representation in the Representations section
- Import skull model in Export/import section
- In the Representations section long-click the Create button, then in the pop-up menu select Advanced create…
- Click on the only offered conversion path, then in the bottom section click Specify geometry
- In the pop-up window choose the skull model as source geometry, and secify a spacing that is large enough so that the labelmap fits into memory
This happens because the model’s scale is off by a factor of 10x. Probably because the designer person used 0.1mm as unit, while Slicer (and most of the medical imaging world) uses 1mm as unit. If you apply a transform of 0.1x scaling to the model in Transforms module then memory usage should be OK. Use this transformation matrix:
0.1 0 0 0
0 0.1 0 0
0 0 0.1 0
0 0 0 1.0
Please see table below, as a reference.
The OBJ files are here:
High Quality 3D Cranium Models in OBJ Format
-Ramon
JFK Numbers
Still, when you load them into Slicer, this is not what we see. In this screenshot the small red object is the low res skull and the gray one is the medium res skull. If you just open the two obj files in a text editor you see why, the magnitude of the point cooridnate values is quite different. For some reason also orientation is different, and I’m not sure why is this difference when they are supposed to describe the same object.
This is why I suggested scaling up the labelmap resolution, and @lassoan suggested scaling down the skull.
Hi Csaba:
I just sent an e-mail to Joerg Behr, one of the Behr Brothers:
Behr Brothers - Anatomy Section
In it I reported all these issues, since this should be solved at the source.
-Ramon
JFK Numbers
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Behr Brother models look nice aesthetically from the outside, but they miss most of the internals of the skull. If you cut it then you can see that the internal bone surface is completely missing (as if the whole cranium would be solid bone):
You can make this model somewhat usable by scaling it by 0.1x to anatomical size and applying shell operation (to create internal bone surface in the cranium).
To save you some time, I’ve done this and saved resulting files here.
I’ve also tried playing with this in virtual reality:
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