Overview

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.

Prerequisites

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:

• https://wiki.cancerimagingarchive.net/display/Public/QIN-HEADNECK

Usage

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.

Contact

• Andrey Fedorov https://fedorov.github.io