xnat_dcm2bids

install

python -m venv ./venv
source venv/bin/activate
pip install https://github.com/nencki-lobi/xnat_dcm2bids/archive/refs/heads/master.zip

use

xnat-dcm2bids [OPTIONS] SESSION_ID SUBJECT_ID SESSION_NUMBER

Arguments:

• SESSION_ID – XNAT session ID
• SUBJECT_ID – BIDS subject ID (e.g., 01)
• SESSION_NUMBER – BIDS session number (e.g., 01)

Options:

Option	Description	Default
--bids-dir TEXT	Ścieżka do katalogu BIDS	./bids-dir
--auto_extract_entities BOOLEAN	dcm2bids option; skips run label if not necessary	True
--config TEXT	Path to config.json	{bids_dir}/code/config.json
--sourcedata TEXT	Path to DICOMs	{bids_dir}/sourcedata/{subject_id}

Example: run single subject

dcm2bids_scaffold -o ./bids-dir
xnat-dcm2bids --bids-dir bids-dir --config ./config.json 55b4c571-cc33-4d pilot2 01

Example: run multiple subjects

prepare csv as follows:

23fa0001-b839-40,2025-06-04,MW25a,pilot3,01
55b4c571-cc33-4d,2025-06-04,MW25a,pilot2,01
fd4197f4-72a3-48,2025-06-04,MW25a,pilot1,01

and run

MacOS/Linux:
while IFS=',' read -r id _ sub ses _; do xnat-dcm2bids --config ./config.json "$id" "$sub" "$ses"; done < subjects.csv
Windows:
for /f "usebackq skip=1 tokens=1,3,4 delims=," %A in ("subjects.csv") do xnat-dcm2bids --config config.json %A %B %C

more

• dcm2niix customization

• troubleshooting