Update SNOMED-CT mapping

fedorov commented 4 months ago

The updated mapping should now include all of the structures listed in totalsegmentator/map_to_binary.py.

To create this map, the content of the original SNOMED mapping CSV was merged with the exhaustive list of the labels from map_to_binary.py, and the mapping for the missing structures was populated.

Here's a google sheet in case anyone wants to review and comment in an easier manner than PR comments: https://docs.google.com/spreadsheets/d/1oEzXCmraoLgbbb5lNxWiHuYDza86aXxKqSUmUetwI7M/edit?usp=sharing.

Script I used to merge various things together, for the sake of historical perspective: https://colab.research.google.com/drive/16sKS1W6Z9LbwHhZMM_I0xwkv0ZBCj8Lg?usp=sharing

cc: @lassoan

fedorov commented 4 months ago

@lassoan I think it is ready for you.

lassoan commented 4 months ago

@fedorov the column names are still the long ones (it should be Category.CodingSchemeDesignator instead of SegmentedPropertyCategoryCodeSequence.CodingSchemeDesignator etc.) and I don't see the color columns.

fedorov commented 4 months ago

I am sorry, I lost track of the many files and sheets ... let me fix it.

fedorov commented 4 months ago

@lassoan it should be ready now.

fedorov commented 3 months ago

@lassoan this one is still waiting for you!

lassoan commented 3 months ago

Thank you for the reminder! I'll finalize this.

I don't remember if we added the total_mr segments as well?

fedorov commented 3 months ago

Yes! You can confirm this from the notebook I used for processing: https://colab.research.google.com/drive/16sKS1W6Z9LbwHhZMM_I0xwkv0ZBCj8Lg?usp=sharing

fedorov commented 3 months ago

Let me resolve the conflicts...

Done

wasserth / TotalSegmentator

Update SNOMED-CT mapping #324