A bit of confusion about the slicer coordinate system

The itk coordinate system is lps, and the slider is ras. However, why does the cursor on the slider display coordinates that are not actually ras? For example, the dicom coordinates are (1, 1, 1), while the actual coordinates in the slider are (-1, -1, 1), and the slider cursor displays coordinates that are (1, -1, 1)

such as this

Why is R the opposite

Here is a good explanation about the usage of the RAS and LPS coordinate system by Slicer:


in summary RAS to LPS transition (or vice versa) involves negating the signs of the first two coordinates (not just R. In your case both R and A had inverse signs).

I’m referring to the slider. The slider yellow is -0.5, Green is 212, RED is -99, and it doesn’t correspond to either RAS or LPS.

I am speculating, but that’s probably related to some other radiological convention being used. Reported measurements are still consistent, but as you said it is neither RAS, nor LPS, but LAS (look at the wording on the title bars Green is A, Red is S, and yellow is L).

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In Edit->Application Settings you can change whether patient right is screen left or not.


That work came out of the following PR if you are curious about the conversation that led to it.

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Just a small observation here: when I called the first versions of Subject hierarchy “Patient hierarchy” it was deemed not appropriate because Slicer is not strictly for use in humans. Just as demonstrated here in this topic - the images are pre-clinical. In the same spirit I don’t think we should call these options “patient right is screen left” etc, but use the word “subject”. @pieper @lassoan

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I’m okay with changing to consistently use “subject”. We do use Patient in the DICOM module, since that’s what’s used in the standard, but I don’t think it shows up much anywhere else in the program.

I agree when it’s not DICOM then “subject” would be better than “patient”. It is my fault, I just haven’t considered this when I introduced the name of the new setting.

For pre-clinical images that use DICOM as the file format, is it standard to use “Patient” instead of “Subject” or “Animal”? I’m not familiar with the usage of pre-clinical image metadata in DICOM format.

Yes, I remember David Clunie telling me they always use patient, even if it’s just a normal control subject or even a phantom. Legacy I guess, but it’s the standard.

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