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lassoan / SlicerMONAIAuto3DSeg

Extension for 3D Slicer for running MONAI Auto3DSeg models
MIT License
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Missing data in model's labels.csv for DICOM-SEG conversion #80

Open ivantyj opened 1 month ago

ivantyj commented 1 month ago

Thank you for your great work! I’m working on converting the output to DICOM-SEG format by creating metadata.json for itkimage2segimage using labels.csv.

I noticed some missing data in labels.csv:

I’ve only checked these models and body-v2.0.0, so other models haven’t been reviewed yet.

lassoan commented 1 month ago

Thanks a lot for the review, these are very useful. Would you mind sending the files with the proposed changes (upload somewhere and post the link)?

Instead of converting to metadata.json, you might consider updating itkimage2segimage ro accept labels.csv directly. Json is great for developers, but I find many people are unable to create metadata files in json, while they are comfortable with putting together a csv file in Excel. We plan to further simplify the labels.csv format by shortening the column names (in the next couple of weeks).

ivantyj commented 1 month ago

Thanks a lot for the review, these are very useful. Would you mind sending the files with the proposed changes (upload somewhere and post the link)?

Sorry for the late reply. The updated .csv file is here: whole-body-v2.0.1_labels.csv abdominal-organs-v2.0.0_labels.csv

Instead of converting to metadata.json, you might consider updating itkimage2segimage ro accept labels.csv directly. Json is great for developers, but I find many people are unable to create metadata files in json, while they are comfortable with putting together a csv file in Excel. We plan to further simplify the labels.csv format by shortening the column names (in the next couple of weeks).

It's a good idea to have itkimage2segimage accept labels.csv. However, I'm not sure if the information in labels.csv is sufficient to create a DICOM-SEG file. I've hardcoded several properties (e.g., ContentCreatorName, ContentDescription, ClinicalTrialSeriesID, etc.) in metadata.json, and I'm unsure what effect that might have.

I've only tested some converted DICOM-SEG files in 3D Slicer. The segments load correctly, but the recommendedDisplayRGBValue is not displaying as expected.