# A bit of confusion about the slicer coordinate system

**URL:** <https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883>\
**Category:** Support\
**Tags:** dicom\
**Created:** [June 7, 2023, 2:28am UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883 "2023-06-07T02:28:07Z")\
**Posts on this page:** 14\
**Page:** 1

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**Author:** ![ma1282029525](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ma1282029525/32/66047_2.png) [@ma1282029525](https://discourse.slicer.org/u/ma1282029525)\
**Post date:** [June 7, 2023, 2:28am UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883/1 "2023-06-07T02:28:07Z")

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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)

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/7/f79f254a5662cf3415d96394fa85a859c06525df.png)  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/f/0ffaa64221e959f2447cb6bb1201ea933bb93211.jpeg)  
such as this

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**Author:** ![ma1282029525](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ma1282029525/32/66047_2.png) [@ma1282029525](https://discourse.slicer.org/u/ma1282029525)\
**Post date:** [June 7, 2023, 2:29am UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883/2 "2023-06-07T02:29:52Z")

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![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/c/7/c7fbaa1580a8d18f08c6f69b4fc9e2d9863215a1.png)

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**Author:** ![ma1282029525](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ma1282029525/32/66047_2.png) [@ma1282029525](https://discourse.slicer.org/u/ma1282029525)\
**Post date:** [June 7, 2023, 2:30am UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883/3 "2023-06-07T02:30:54Z")

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Why is R the opposite

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**Author:** ![jamesobutler](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jamesobutler/32/7511_2.png) [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Post date:** [June 7, 2023, 10:34am UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883/4 "2023-06-07T10:34:52Z")

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

[https://slicer.readthedocs.io/en/latest/user\_guide/data\_loading\_and\_saving.html#on-use-of-lps-ras-coordinate-systems](https://slicer.readthedocs.io/en/latest/user_guide/data_loading_and_saving.html#on-use-of-lps-ras-coordinate-systems)

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [June 7, 2023, 4:57pm UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883/5 "2023-06-07T16:57:03Z")

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> [@ma1282029525](#):
>
> Why is R the opposite

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).

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**Author:** ![ma1282029525](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ma1282029525/32/66047_2.png) [@ma1282029525](https://discourse.slicer.org/u/ma1282029525)\
**Post date:** [June 12, 2023, 1:50am UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883/6 "2023-06-12T01:50:59Z")

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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.

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [June 12, 2023, 5:58pm UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883/7 "2023-06-12T17:58:20Z")

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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).

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/f/dff17eb3f74b6252af62b64a4d04aea86f4b1635.jpeg)

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**Author:** ![jamesobutler](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jamesobutler/32/7511_2.png) [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Post date:** [June 12, 2023, 7:36pm UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883/8 "2023-06-12T19:36:07Z")

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

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/8/58170b7a1a10ddacde79884c1a0f1d5fb401d008.png)

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

> <https://github.com/Slicer/Slicer/pull/5536>
>
> User can choose between radiology and neurology view directions (patient left/ri…ght on screen right).

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**Author:** ![cpinter](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cpinter/32/7995_2.png) [@cpinter](https://discourse.slicer.org/u/cpinter)\
**Post date:** [June 19, 2023, 12:55pm UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883/9 "2023-06-19T12:55:59Z")

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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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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [June 19, 2023, 6:26pm UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883/10 "2023-06-19T18:26:16Z")

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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.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 19, 2023, 8:01pm UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883/11 "2023-06-19T20:01:17Z")

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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.

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**Author:** ![jamesobutler](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jamesobutler/32/7511_2.png) [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Post date:** [June 19, 2023, 9:23pm UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883/12 "2023-06-19T21:23:48Z")

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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.

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [June 19, 2023, 10:08pm UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883/13 "2023-06-19T22:08:37Z")

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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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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [January 24, 2025, 8:54pm UTC](https://discourse.slicer.org/t/a-bit-of-confusion-about-the-slicer-coordinate-system/29883/14 "2025-01-24T20:54:55Z")

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I would rather have the standard terms radiology vs neurology convention used.

[https://nipy.org/nibabel/neuro\_radio\_conventions.html](https://nipy.org/nibabel/neuro_radio_conventions.html)

And I second replace patient with subject.