Loaded models are sometimes in different coordinate system, and sometimes not. What exactly is going on?

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1

Operating system: Windows
Slicer version: 4.11.20210226
Expected behavior: A model should be loaded into a consistent coordinate system
Actual behavior: When I load some models, it appears to interpret the vertices as being in the RAS coordinate system. And for other models, it appears to use the world coordinates.

For example,

I have .vtu file. I load it up into 3d slicer. The x and y coordinates of all the vertices are flipped. I assume this is because the application is interpretting the vertex values to be in the RAS coordinates. No problem, I just apply a transformation [[-1,0,0,0, 0,-1,0,0, 0,0,1,0, 0,0,0,1]] and all is fine!

However, i have a .ply model too. When I load this model the application uses the actual coordinates of the vertices and it does not appear to be loaded in the RAS coordinate system, so I dont have to apply the transformation above to this model.

Why is there an inconsistency here?

How can I control which coordinate system a model’s vertices are interpreted to be in?

Thanks!

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2

If you know the model’s coordinate system, when loading expand the dialog box and specify whether it is LPS or RAS and your model should be imported correctly.

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image1477Ă—348 21.5 KB

Inconsistency comes from the lack of standardization in those formats.

3

Thank you for the reply. I noticed this dialogue box, and I tested it by importing the same model twice but with the different options (LPS and RAS) chosen. There was no difference (and my model is definitely not symmetric about the x and y axes!)

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4

For VTU files, it actually works. I see a difference depending on the LPS / RAS option chosen in that dialogue box.

For my .ply file it does not work. There is no difference between RAS and LPS option

5

Ok, update:

It must be something weird with this specific .ply file. I just tried another .ply file and it worked…

6

Confirmed. The file must have been corrupted somehow. I loaded it up in paraview, and exported it to a new .ply file, and then tried it in slicer, and it works!

My last question on this topic, is how do I do this programtically in python when i load a model?

i’m using slicer.util.loadModel(…) function

7

You will need to use the slicer.util.loadNodeFromFile() function and specify this somehow in the properties.

slicer package — 3D Slicer documentation

slicer.util.loadModel() is a simplified wrapper for loadNodeFromFile() but lacks the ability to pass in properties. I couldn’t quickly find an example, but perhaps you can follow the code a bit deeper to find out what the property you want is and how to specify it: https://github.com/Slicer/Slicer/blob/10fc1df859fa094691e2358d6c0b420bce477700/Base/Python/slicer/util.py#L619

8

I cannot seem to locate it by following the python code.
I’m wondering if it is even possible.

I noticed this noted in one of the files:


  /// Coordinate system options
  /// LPS coordinate system is used the most commonly in medical image computing.
  ///   Slicer is moving towards using this coordinate system in all files by default
  ///   (while keep using RAS coordinate system internally).
  /// RAS coordinate system is used in Slicer internally. For many years, Slicer used
  ///   this coordinate system in files that it created, too.
  enum
  {
    CoordinateSystemRAS = 0,
    RAS = 0, ///< for backward compatibility
    CoordinateSystemLPS = 1,
    LPS = 1, ///< for backward compatibility
    CoordinateSystemType_Last
  };

from:

9

Found it! Check out here: https://github.com/Slicer/Slicer/blob/49320e0294eee6b0a471d97664f32aaaf31e5a17/Modules/Loadable/Models/qSlicerModelsReader.cxx#L118

The property is called “coordinateSystem” and the correct value is the integer 0 (for RAS) or 1 (for LPS). For these you could also use a more descriptively named enum.

An example of using properties for a different kind of node can be found here: Script repository — 3D Slicer documentation

So, properties are given as python dictionaries, where the key is the property name and the value is the property value.

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