The problem is the following: I segment nasal turbinates in rodents and use Biomedisa. When I take my CT scans, I need to orient them in 3D Slicer, so I create a Transform and adjust the orientation. After that, I generate the slices that will be used by Biomedisa. After this step, I upload them to…

Have you tried using the Biomedisa extension? This would keep everything in Slicer. I’m guessing that perhaps your issue is related to rearranging image axes in the export-import process. [Tutorial: How to use Biomedisa’s Smart Interpolation in 3D Slicer]

Hi, take a look at this information: [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 me…

This is a classic RAS/LPS coordinate mismatch. Looking at your screenshots, the segmentation labels are spatially correct relative to each other but displaced and rotated relative to the scan volume. That is the exact signature of an axis flip happening during export or import, not a segmentation e…

Segmentation and Volume Misaligned After Using Biomedisa

Support

MrMarkus March 5, 2026, 8:09am 3

Hi,

take a look at this information:

Maybe that´s also the case in your situation?

Best,
Markus

Topic		Replies	Views
Importing segmentation into 3d slicer Support segmentation	10	4040	June 12, 2019
Model coordinates while exporting after segmentation Support	2	262	March 4, 2022
Wrong positionning of segments exported to files Support segmentation	3	43	March 16, 2026
Segmentation Transform Support	2	503	July 6, 2020
Saved surface model is not aligned with volume when viewed in external software Support	2	1940	April 18, 2021

Segmentation and Volume Misaligned After Using Biomedisa

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