Code for working with the free-text reports

Useful code for working with the text of the radiology reports is provided in this folder.

This code was used to generate two files:

• mimic-cxr-2.0.0-chexpert.csv.gz
• mimic-cxr-2.0.0-negbio.csv.gz

Extracting findings/impressions from the reports

The findings/impressions section of the reports can be considered as the "conclusion" of the radiologist. The create_section_files.py script extracts these conclusions for each report text and outputs them to a folder of CSVs, with about 10,000 reports per CSV.

The script can be run (from this folder) as follows:

python create_section_files.py --reports_path /db/mimic-cxr/files --output_path /db/mimic-cxr/mimic-cxr-sections

... where you should replace /db/mimic-cxr/mimic-cxr-reports/files with the location of your MIMIC-CXR files folder.

CheXpert

Instructions for generating CheXpert annotations from the reports are available in the chexpert subfolder.

NegBio

Instructions for generating CheXpert annotations from the reports are available in the negbio subfolder.