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 up…

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 t…

This may help? [image] Model files are now saved in LPS coordinate system Development 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 (may…

My segment is flipped when exported when opening in MRIcron

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Juicy June 21, 2021, 8:05am 3

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My segment is flipped when exported when opening in MRIcron

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