Imaging BIDS is a package designed to convert imaging data into BIDS-compliant datasets. As the push for standardized datasets grows, harmonizing how we collect and store data has become increasingly important.
Note. This is not meant to replace larger tools like EZ Bids. It is designed to be a script solution for use when a web-based platform, or sharing data onto an external server, is not viable.
Imaging BIDS uses a datalake of known protocols at HUP to try and assign the correct BIDS keywords to your data. It also informs the users of its choices, and allows for a human in the loop to correct any mistakenly assigned keywords. New keywords can be saved for later use.
To do this, the imaging data requires a .json file associated with the data file, and the ProtocolName field cannot be missing.
python utils/acquisition/BIDS/IMAGING_BIDS.py --dataset ~/Documents/GitHub/CNT-codehub/user_data/RAW_IMAGING_DATA --bidsroot ~/Documents/GitHub/CNT-codehub/user_data/IMG_BIDS --subject 001 --datalake utils/acquisition/IMGBIDS/datalakes/HUP_BIDS_DATALAKE.pickle