physio2bids

Austin Marcus

Tarrlab @ CMU, October 2018

Converts Siemens physiological recording files (puls, resp, ext) to BIDS format, given matching Siemens DICOM files.

Installation:

• Clone repository
• Assumes default python interpreter is /usr/bin/python - change hashbang line of install.py if not the case on your system
• Run python install.py

Use:

• physio2bids.py -d <DICOM-dir> -p <Physio dir> -o <output-directory> -l <logfile-name>
• DICOM directory selected must contain DICOMs for the same scans as the Physio folder, since matching is done by checking timestamps
• Writes all converted files (tsv and json per physio file) to specified output directory
• Writes detailed log to specified file in append mode to permit log concatenation in looped use