Collecting physiological data
It is possible to collect and record peripheral pulse, respiration, and electrocardiography data during any scan. In addition, two external trigger pulses may be recorded. The external trigger may be used to record the optical trigger out. This signal is currently available for BOLD echo-planar sequences and phosphorous spectroscopy, and may be added to other sequences if needed.
To record physiological signals, follow the instructions in the scanner operator manual. For peripheral pulse, simply place the pulse monitor on the subject’s fingertip, with the light facing the pad of the finger. Three sizes of transducer are available. The unit will begin measuring automatically and the results will be displayed in the monitor on the scanner.
To record the optical trigger, run a cable from the optical-to-digital converter box through the patch panel and into the external trigger in on the scanner. Alternatively, a second external trigger in is located in the equipment room.
Recording of physiological data files is initiated from the console and can be incorporated into any protocol. The files produced are text files, and begin with some header information and (for physiological signals) an average waveform. All signals have been resampled to 400 Hz, or a 2.5 ms sampling interval. Any detected triggers are marked with a value of 5000; these need to be removed from the file for accurate timing.
A command-line tool is available for converting these files to a more straightforward format is available to LCNI users. Currently it’s been compiled for Windows but can be recompiled for other platforms as needed.
This tool is run with the following options:
pmu_logfile_decoder filename [-t] [-r]
“filename” is the name of the logfiles, without extensions. The software will look for all matching logfiles in that location. The output files will have the additional extension “.out” and will consist of pairs of numbers: time in milliseconds and signal value, separated by a tab, with line breaks between pairs. Electrocardiogram signal files will be in groups of five: time, average, and individual channels.
The option -t indicates that all signals should be aligned with the external trigger in (currently this only works for the bay trigger, not ext2 located in the equipment room). All data before the first trigger signal and after the last trigger signal (plus the interval between triggers) is discarded for all signals. The option -r indicates that the “5000” trigger marks should be discarded. Both, either, or neither option may be chosen.