Physio2bids

This python script was created to cconvert data from the Siemens 7T Magnetom to BIDS format. It requires a directory of physio files (*.puls and *.resp) and a BIDS directory.

Usage

python write_physio_to_bids.py -p physio_dir -b bids_dir

or

python write_physio_to_bids.py --physio_dir physio_dir --bids_dir bids_dir

Assumptions

This code is based on the information from: https://cfn.upenn.edu/aguirre/wiki/public:pulse-oximetry_during_fmri_scanning and makes the following assumptions:

• *.puls and *.resp files will be kept together in the same directory
• MDHLogStartTime and MDHLogStopTime are what should be linked to the acquisition times in the DICOMs
• A physio recording which starts before a functional run and ends after the function run is intended for that run
• The reported values for the physio data are not linked to a log of the times they were recorded and are instead assumed to be sampled at a rate specified in the json file.