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)?
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: