Consolidate colors with the terminology csv file

[fedorov]

Right now colors are separated from label->code mapping, and this is confusing.

Related to https://github.com/ImagingDataCommons/Cloud-Resources-Workflows/pull/37.

Let's pick the mapping file from https://github.com/wasserth/TotalSegmentator/blob/master/resources/totalsegmentator_snomed_mapping.csv and augment it with the colors used in https://github.com/lassoan/SlicerTotalSegmentator/blob/main/TotalSegmentator/Resources/SegmentationCategoryTypeModifier-TotalSegmentator.term.json, then replace colors for vertebrae/ribs based on what is done in Related to https://github.com/ImagingDataCommons/Cloud-Resources-Workflows/pull/37.

When this is ready, I will discuss with Jacob and Andras re consolidating this to simplify maintenance. We can hopefully just put the resulting CSV file in the TS repo in place of https://github.com/wasserth/TotalSegmentator/blob/master/resources/totalsegmentator_snomed_mapping.csv.

[vkt1414]

Unfortunately, SlicerTotalSegmentator contains colors for only 80 body parts. Search for 3dslicerlabel on

https://github.com/lassoan/SlicerTotalSegmentator/blob/main/TotalSegmentator/Resources/SegmentationCategoryTypeModifier-TotalSegmentator.term.json

Looking at code in suggests he choose random colors when colors are not present in the json file.

https://github.com/lassoan/SlicerTotalSegmentator/blob/main/TotalSegmentator/TotalSegmentator.py

Please advise how we should proceed.

[fedorov]

We have the colors for all structures. Let's just add the colors we have to the terminology csv?

[vkt1414]

Unfortunately we do not have colors for the new body parts introducted in TotalSegmentator V2

[fedorov]

Let's add all the colors we have for v1, and leave the rest blank for now. If SlicerTotalSegmentator reuses this, the same logic already implemented can be maintained - when colors are missing, random colors can be assigned.

[vkt1414]

the PR #37 is now updated to address issues #39 and #10

The csv file now contains the colors for all body parts in totalseg v1.

Here's how the colors were curated:

• Mhubai colors as the base
• Replace them with deepa's colors wherever applicable
• the color for face was not present in mhubai, so I chose a random color.

The file that you requested is located at https://github.com/ImagingDataCommons/Cloud-Resources-Workflows/blob/config_fix2/configs/TotalSegmentator/totalsegmentator_snomed_mapping_with_partial_colors.csv