# My segment is flipped when exported when opening in MRIcron

**URL:** <https://discourse.slicer.org/t/my-segment-is-flipped-when-exported-when-opening-in-mricron/18226>\
**Category:** Support\
**Created:** [June 19, 2021, 3:57pm UTC](https://discourse.slicer.org/t/my-segment-is-flipped-when-exported-when-opening-in-mricron/18226 "2021-06-19T15:57:18Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![pardisz](https://avatars.discourse-cdn.com/v4/letter/p/71c47a/32.png) [@pardisz](https://discourse.slicer.org/u/pardisz)\
**Post date:** [June 19, 2021, 3:57pm UTC](https://discourse.slicer.org/t/my-segment-is-flipped-when-exported-when-opening-in-mricron/18226/1 "2021-06-19T15:57:18Z")

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Hi  
I painted a segment using a template MRI scan and exported the segment using the same MRI scan as a reference. When I open the same scan in MRIcron and overlay it with the segment I have drawn I can see that it is flipped during the export process (i.e. it looks right in slicer but is flipped upon export). I can see there is a FAQ on flipped images but this is regarding flipped images in slicer, not the export. I wonder if anyone else has run into this problem (and solved it)?

Thanks

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**Author:** ![Juicy](https://avatars.discourse-cdn.com/v4/letter/j/74df32/32.png) [@Juicy](https://discourse.slicer.org/u/Juicy)\
**Post date:** [June 21, 2021, 7:49am UTC](https://discourse.slicer.org/t/my-segment-is-flipped-when-exported-when-opening-in-mricron/18226/2 "2021-06-21T07:49:00Z")

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I don’t know exactly what you mean, or anything about the other software (MRIcron) but maybe it has something to do with an RAS to LPS coordinate system change. Last I remember slicer uses RAS meaning the positive x direction is toward the right, positive y is toward the anterior and positive z is toward superior. Many other softwares use LPS which is obviously opposite in the x and y directions.

If all else fails you could possibly flip the coordinate system in the x and y directions in slicer before you export the segment by applying the following linear transform. I know that this does not seem like an elegant solution unfortunately:

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/b/9bdf816cc362634547377671b4a7e6eb76c162c9.png)

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**Author:** ![Juicy](https://avatars.discourse-cdn.com/v4/letter/j/74df32/32.png) [@Juicy](https://discourse.slicer.org/u/Juicy)\
**Post date:** [June 21, 2021, 8:05am UTC](https://discourse.slicer.org/t/my-segment-is-flipped-when-exported-when-opening-in-mricron/18226/3 "2021-06-21T08:05:21Z")

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This may help?

> [@Model files are now saved in LPS coordinate system](https://discourse.slicer.org/t/model-files-are-now-saved-in-lps-coordinate-system/10446):
>
> While Slicer uses RAS coordinate system internally, images, transforms, and markups files are stored in LPS coordinate system, because DICOM and all medical image computing software (maybe except a few very old ones) uses LPS coordinate system in files. However, Slicer has been still using its internal RAS coordinate system in mesh files (STL, VTK, VTP, OBJ, PLY), which [caused issues when interfacing with third-party software](https://issues.slicer.org/view.php?id=4445). Starting from tomorrow (Slicer-4.11.0-2020-02-26, revision 28794), …