Exported NRRD file (segmentation) misaligned with the original DICOM file (MRI).

Hello all,

Using the following header I saved my segmentation volume stored in the variable ‘out’ in a NRRD file:

Loading both original MRI, and the segmented nrrd volume. We may check that the volume information of both structures are pretty close:

But some information is missing probably in the header file I saved since I couldn’t found a perfect position match between the NRRD and the original DICOM.

Here is how I see the 3D visualization of both volumes.


Would you have any idea what I can try next?

thanks a lot

Slicer uses RAS coordinate system internally (for backward compatibility) but uses LPS in all files (for compatibility with DICOM and other software). You can convert between two coordinate systems by inverting the sign of the first two coordinate values.