Able to view DCM created with SITK in ITK Snap but not Slicer


I have written a 3D DCM with SITK and am able to view it in ITK Snap. However, this DCM has color overlays which ITK Snap only displays greyscale, so I would like to view it in Slicer. For this project, the image must be saved as DCM.

The DCM, as written, is not viewable in Slicer. If I use the DICOM Patcher plugin in 3D Slicer, it produces DCM slices stored in individual folders that load properly into Slicer. Modifications to the DCM header produced by Slicer include: Image Position & Instance Number.

However, this change appears off. For example, in the patched image, slice 0 has Image Position -z of -2.5 whereas slice 3 has z position 37.1 in spite of the fact that slice thickness is 3.6 mm. The original DCM I wrote has correct z positions of slice 0: -2.5 and slice 3: 8.3

Directions here were used as a basis to write the DCM:

When I attempt to load a single DCM into Slicer, I get the message:

Error: Loading [DCM_slice.dcm] - load failed.

Is there minimal header info that must be included to load a DCM into slicer that is not included in the above example?

Are there changes being made other than to the DCM header by the Patcher?

Is there a way to see what exactly is causing the load to fail in Slicer?

Please let me know if you have any suggestions how to approach this. Thank you!

Image overlays are very obsolete method for limited annotation of images that was never intended to be used for storing image segmentation. I would strongly recommend not to use it.

Instead, DICOM Segmentation Object should be used for storing image segmentation.

Slicer can read/write segmentation as DICOM Segmentation Object after you install Quantitative Reporting extension. Outside Slicer, you can use DCMQI tool to read/write DICOM Segmentation Objects.