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

Support
1

Hello!

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:
https://simpleitk.readthedocs.io/en/v1.1.0/Examples/DicomSeriesReadModifyWrite/Documentation.html

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!

2

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.