Physiologging: Code samples for DICOM extraction


Physiologging enables the reproducible recording of time-stamped physio data via a dedicated protocol parameter (for EPI BOLD & PACE).

These physio data can then be used to correct effects from physiological motion in the measured fMRI images. During data acquisition, all signals recorded by internal physiological sensors (such as respiratory sensor or belt, ECG, pulse sensor, Beat Sensor) are stored in an easily accessible and interpretable text data format (simple tables with time stamps and signal values) for further offline processing. A compressed xml structure containing the physio curves and time-stamps is also embedded in an additional non-image DICOM file. This DICOM can be archived together with the fMRI data if necessary.

The tools available on this page can be used to extract the embedded xml structure from the DICOM file and restore the original text files containing the physio data. Provided are demonstration source codes in 
a) C# (physioExtractor.cs) and 
b) python (

In addition, a batch file using the executable generated either from the C# or the python code is provided (physioExtractor.bat) for generating different types of text files, along with xsl style sheets defining the processing of the xml file.

More information on this feature can also be found in the IceUsersGuide in IDEA.