Tools to go from a DICOM dataset into a collection of tables for the purposes of data repurposing and exploration using relational databases.
This is not a general purpose tool. Initial goal is to support exploration of the TCIA QIN-HEADNECK dataset.
Software:
- python
- pandas
- pydicom (must be installed from source! distribution available via pip is too old and does not have some of the DICOM dictionary entries we parse)
- dcmqi is required to generate certain object-specific tables for such objects as DICOM Segmentations and measurements structured reports; it is best if you make sure dcmqi converters are in your path prior to running the script
Data:
python tabulate.py -s schema.qdbd -d <location of a directory with DICOM data> -o <output location to store csv tables>
The script will create tables stored in CSV in the directory where it was executed.
- Andrey Fedorov https://fedorov.github.io