physio_dcm

Convert Siemens PhysioLog DICOMs into BIDS _physio.tsv.gz files.

Handles files with conversion_type=’physio_dcm’. These are Siemens PMU physiological recordings embedded in DICOM private tag (7FE1,1010).

Each PhysioLog DICOM contains 5 concatenated log sections: ECG (SampleTime=1ms, 4 channels: ECG1-ECG4) PULS (SampleTime=2ms, 1 channel: pulse oximetry) RESP (SampleTime=8ms, 1 channel: respiratory belt) EXT (SampleTime=8ms, external trigger) ACQUISITION_INFO (volume/slice timing)

Output per BIDS spec for physio data:

• _recording-cardiac_physio.tsv.gz + .json (ECG channel 1)
• _recording-pulse_physio.tsv.gz + .json (PULS)
• _recording-respiratory_physio.tsv.gz + .json (RESP)

Requires: pydicom, numpy

Usage: python physio_dcm.py [] [--dry-run]

Source: src/python/raw2bids_converters/physio_dcm.py

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Functions

parse_pmu_text

Parse the full PMU text into per-section data.

parse_pmu_text(text)

Returns

sections : dict {section_name: {“sample_time”: int, “timestamps”: ndarray, “values”: ndarray}} acq_info : dict {“num_volumes”: int, “num_slices”: int, “vol_start_tics”: dict}

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convert_file

Convert a PhysioLog DICOM directory to BIDS physio files.

convert_file(dicom_dir, output_base, dry_run = False)

Parameters

• dicom_dir (str) — Path to the PhysioLog DICOM directory (contains one .dcm file).
• output_base (str) — Base path for output files. The recording entity and suffix will be
• appended (e.g. if output_base is) — sub-03/ses-04/func/sub-03_ses-04_task-CRencoding_run-01 then output files will be: …_recording-cardiac_physio.tsv.gz …_recording-pulse_physio.tsv.gz …_recording-respiratory_physio.tsv.gz
• dry_run (bool) — If True, print what would be done without writing.

Returns

bool True if conversion succeeded.

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