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.gitignore
DICOMParser.py
QDBDParser.py
README.md
SRCDParser.py
clientDataSchema.py
schema.qdbd
tabulate.py

README.md

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:

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