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QIICR / QuantitativeReporting

Segmentation-based measurements with DICOM import and export of the results.
https://qiicr.gitbooks.io/quantitativereporting-guide
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How to add many characteritics labels (SegmentedPropertyTypeModifiers?) to a SEG? #277

Closed gacou54 closed 2 months ago

gacou54 commented 2 months ago

Hi,

We evaluate whether it would be possible to associate several characteristics with a pulmonary nodule segmented with the Quantitative Reporting extension/workflow, in particular some characteristics identified in Table 1 of https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3056962/ (It uses the RADLEX terminologies).

I am wondering if it is possible to input the nodule characteristics in the SEG DICOM (likely somewhere in the SegmentSequence) with Quantitative Reporting, and if yes how to do it?

I identified SegmentedPropertyTypeModifierCodeSequence https://github.com/QIICR/QuantitativeReporting/blob/166d695ea2965c1a40676107931a57aa2cb6cfad/DICOMPlugins/DICOMSegmentationPlugin.py#L714

that may be OK to use for this, but unfortunately I think the Terminologies Module from Slicer only allows one TypeModifier (it's a select widget).

TLDR: Is there a way to add more than one characteristic label (from a predetermined terminologies list) to a Segmenation within Quantitative Reporting workflow?

Thanks in advance :)

fedorov commented 2 months ago

@gacou54 if you want to describe the characteristics of a lung nodule, you would not use DICOM SEG, but DICOM SR for this.

Given your reference, you might want to take a look at this manuscript that applies the above in practice:

Fedorov, A., Hancock, M., Clunie, D., Brochhausen, M., Bona, J., Kirby, J., Freymann, J., Pieper, S., J W L Aerts, H., Kikinis, R. & Prior, F. DICOM re-encoding of volumetrically annotated Lung Imaging Database Consortium (LIDC) nodules. Med. Phys. (2020). http://dx.doi.org/10.1002/mp.14445

You can access the data referenced in that paper from Imaging Data Commons: https://portal.imaging.datacommons.cancer.gov/explore/filters/?collection_id=lidc_idri.

I am traveling the coming week, but let me know if you have questions and I will try to help when I am back. ​

gacou54 commented 2 months ago

Thanks for the response and the (very interesting) link. Indeed the SRs seem more appropriate for the characteristics. We will most likely take this route.

Thanks :) (You can close the issue)

fedorov commented 2 months ago

Excellent! Take a look at dcmqi and the accompanying code for lidc conversion!