[BUG] Codes used to describe segments in DICOM SEG writer should be improved

[fedorov]

Describe the bug
Codes used to describe segments in DICOM SEG writer should be improved.

Steps/Code to reproduce bug
See

monai-deploy-app-sdk/monai/deploy/operators/dicom_seg_writer_operator.py

Lines 440 to 463 in 294fb6e

	def create_label_segment(label, name):
	"""Creates segment labels"""
	segment = Dataset()
	segment.add_new(0x00620004, "US", int(label)) # SegmentNumber
	segment.add_new(0x00620005, "LO", name) # SegmentLabel
	segment.add_new(0x00620009, "LO", "AI Organ Segmentation") # SegmentAlgorithmName
	segment.SegmentAlgorithmType = "AUTOMATIC" # SegmentAlgorithmType
	segment.add_new(0x0062000D, "US", [128, 174, 128]) # RecommendedDisplayCIELabValue
	# Create SegmentedPropertyCategoryCodeSequence
	segmentedPropertyCategoryCodeSequence = Sequence()
	segmentedPropertyCategoryCodeSequenceDS = Dataset()
	segmentedPropertyCategoryCodeSequenceDS.add_new(0x00080100, "SH", "T-D0050") # CodeValue
	segmentedPropertyCategoryCodeSequenceDS.add_new(0x00080102, "SH", "SRT") # CodingSchemeDesignator
	segmentedPropertyCategoryCodeSequenceDS.add_new(0x00080104, "LO", "Anatomical Structure") # CodeMeaning
	segmentedPropertyCategoryCodeSequence.append(segmentedPropertyCategoryCodeSequenceDS)
	segment.SegmentedPropertyCategoryCodeSequence = segmentedPropertyCategoryCodeSequence
	# Create SegmentedPropertyTypeCodeSequence
	segmentedPropertyTypeCodeSequence = Sequence()
	segmentedPropertyTypeCodeSequenceDS = Dataset()
	segmentedPropertyTypeCodeSequenceDS.add_new(0x00080100, "SH", "T-D0050") # CodeValue
	segmentedPropertyTypeCodeSequenceDS.add_new(0x00080102, "SH", "SRT") # CodingSchemeDesignator
	segmentedPropertyTypeCodeSequenceDS.add_new(0x00080104, "LO", "Organ") # CodeMeaning
	segmentedPropertyTypeCodeSequence.append(segmentedPropertyTypeCodeSequenceDS)
	segment.SegmentedPropertyTypeCodeSequence = segmentedPropertyTypeCodeSequence

.

Expected behavior

1. SegmentationCategoryType should refer to the code corresponding to the specific organ. Currently, there is a general code for "Organ", with the specifics about which organ is segmented listed in the SegmentLabel. This is not the intended use of this object.
2. Codes should be using SNOMED-CT SCT codes, currently used SRT codes have been deprecated in DICOM.

Environment details (please complete the following information)

• SDK Version: current as of submitting

Additional context

• Relevant commit in dcmqi: QIICR/dcmqi@0cf2829
• why don't you just use highdicom to write DICOM SEG? https://github.com/herrmannlab/highdicom

[fedorov]

I am sure @dclunie will at least be interested to be aware of this discussion.

[dclunie]

I assume you mean SegmentedPropertyTypeCodeSequence, not SegmentationCategoryType.

See also https://dicom.nema.org/medical/dicom/current/output/chtml/part16/sect_CID_7151.html

[dbericat]

Thanks for the feedback! @MMelQin, @vikashg and/or @gigony will address the first part.

Regarding highdicom, we all want to do that. It's just that @CPBridge has been busy lately, right Chris? ;)

Check this out: #195

It is currently planned for 0.4.0. https://github.com/Project-MONAI/monai-deploy-app-sdk/projects/6

[hackermd]

@dbericat thanks for your feedback and sorry for the delay on our end. @CPBridge and I will finalize the PR as soon as possible.

[fedorov]

If the plan is to switch to highdicom, this issue will not be applicable - feel free to close.

[MMelQin]

Thanks for feedbacks. Agree the existing DICOM Seg Writer code needs to be enhanced, for its intended purpose, and also there is a defect I filed and need to fix.