I am trying to load nrrd as AXIAL, CORONAL, SAGITAL view and VTK file outside of the Slicer but the orientation is not matching as in slicer 3d Conventional view if we enable all three AXIAL, Sagital, and CORONAL views. There is some mismatch is there. Let me know how to solve this.

Probably the external code needs to take into account the coordinate systems: https://www.slicer.org/wiki/Coordinate_systems

A similar question came up in another context - does anyone know if there is a surface mesh format (other than DICOM!) that can specify the coordinate system?

STL, PLY, VTK, VTP could all store the coordinate system (anatomical orientation), but there is no standard or commonly followed practice. MetaIO (supported by ITK, VTK, etc.) can store surface mesh (MetaSurface object) and anatomical orientation in a standard way, but this file format is rarely us…

Thanks, I will forward this info to Christian Bauer who asked this question to me.

Hi Pieper, Andrey Fedorov, Andras Lasso, I have gone through this link : https://www.slicer.org/wiki/ Coordinate_systems but I am unable to find out how to make vtk model to load exactly on the bone structure on Slices(Axial,Sagital,Coronal) from backend without any adjustments from UI. Only in …

Most common issue is LPS/RAS coordinate system mismatch. So, may try to convert your data from LPS to RAS coordinate system by transforming it using Transforms module by a matrix that has [-1,-1,1,1] in the diagonal: [image]

Hi - The patient coordinate system (RAS in Slicer’s case) provides a frame of reference for the data. When you have the data in Slicer you can explore this with the Data Probe. Exported VTK models will be in this space with the vertices expressed in mm. The nrrd header also tells how the volume …

DICOM and VTK file orientation Issue

Development

Topic		Replies	Views
AXIAL, CORONAL, SAGITAL, Slice Views - VTK model alignment Issue Support transforms , views	6	2409	August 17, 2017
Specifying coordinate system in surface mesh file Development	7	1635	August 4, 2017
Saved surface model is not aligned with volume when viewed in external software Support	1	1947	August 4, 2017
Orientation issue loading vtk mesh Support	1	736	March 11, 2020
Wrong positionning of segments exported to files Support segmentation	3	56	March 16, 2026

DICOM and VTK file orientation Issue

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