Physiological logging on Siemens MR scanners

This page describes two approaches to enable saving log files of the physiological recordings performed by Siemens MR scanners, i.e., respiration, PPU, ECG, and external trigger. Both methods result in log files being saved into C:\Medcom\log on the MR scanner console in the same file format, which may then be copied from the console using a USB memory stick. The difference between the methods relates to the way the logging is started and stopped, which in turn has repercussions with respect to temporal synchronisation between the MR acquisition and the data in the log files.

1. Enable physiological logging using pulse programming

Through a research agreement with Siemens Medical and attendance of their IDEA pulse programming course, pulse sequence source code related to specific projects may be requested. A simple modification enables physiological logging to be started at the beginning of the scan and stopped at the end. Details are provided on the Siemens IDEA web site; search for physiological. This technique may be applied to most pulse sequences and software versions with only minor modifications.

I have implemented this for the Siemens gradient echo EPI sequence. The sequence file is called ep2d_fid_physio. Once copied to a new folder, parameters can be set as for any other fMRI acquisition. The log files will be named physiolog followed by the day, month, and time that that logging commenced.

Advantages

• Starts and stops the logging in synchronicity with the MR acquisition (the end of both the scan and the log file may be the best point to sync).
• Logging occurs automatically to a unique filename; no user intervention required.

Disadvantages

• Requires modification in pulse programming of each sequence family.
• As such, all modified sequences need to be installed on every MR scanner used, and re-compiled and re-installed after every major scanner software upgrade.
• Despite the logging being started and stopped in the sequence code, there still appears to be some variability in the actual start or end times of the data in the log files, as well as variability between the start and end times between the different physiological measures, in the range of 0.5 s. As such, it may still be wise to use a strategy to improve the synchronisation between the log files and the images, such as provided by my syncphysio software.

2. Enable physiological logging using the fMenu command

Logging of the physiological signals may be started and stopped manually on the scanner console at any time, regardless of whether an acquisition is running, as follows.

• Enable Advanced User mode (Ctrl-Esc, Start / All Programs / Advanced User).
• Run a MSDOS command (Ctrl-Esc, Start / Run)
• Type telnet mpcu and click OK.
• At the -> prompt in the new command line window, type fMenu taking care to type the upper and lower case letters of this command as indicated.
• At the main menu, select option 3. At the next menu, also select option 3.
• At this stage, it is probably wise to select option 10 - stop all signals in case physiological logging is still ongoing from a previous scan whose users forgot to stop the logging.
• To start logging, select option 9 - start all signals (or alternatively, start just the signal you require by selecting the appropriate option).
• Enter the base filename (without any spaces) for the physiological log files. A unique name including the scan date and subject ID is recommended, e.g., 20100214_psm for subject psm scanned on 14^th February 2010. Logging is now enabled; there is no need to exit this submenu or close the window.
• Run the MR acquisition. As the acquisition is not synchronised with the physiological logging, depending on your post-processing technique, there may not be any need to stop and then restart logging between subsequent fMRI acquisitions on the same subject; one log file spanning the entire scanning period of a subject may be sufficient (see below for post-processing).
• At the end of the scan session, stop the physiological logging by selecting option 10 in the same fMenu as above. Type exit until the window closes.

Advantages

• Available on all modern Siemens scanners and should continue immediately across future scanner software upgrades.
• Works for all MR acquisitions without any pulse programming required. A research agreement with Siemens is not required.

Disadvantages

• Log files are not synchronised with subsequent MR acquisitions without further post-processing. One strategy for post-processing is provided by my syncphysio software.
• As log files are not saved automatically when the sequence is started, there is room for human error, in forgetting to enable logging manually prior to running the MR acquisition.

Whichever of the above methods is used, the physiological text files are saved in the same format, on the scanner console in C:\Medcom\log. The files may then be copied from the console computer using a USB memory stick. These files are the only recording of the physiological signals, they are not archived via PACS or DICOM export. Each physiological measure is stored in a separate text file, with the physiological measure type identified by the filename extension. The file format is fairly straightforward; full details are available from Siemens Medical.

Synchronised log files may be used to reduce artefacts from physiological sources in fMRI datasets using Chris Rorden's Physiological Artifact Removal Tool or PhysioNoise. The original waveforms may also be viewed using my stereo software by selecting the graph button followed by import Siemens physio log and then plot data.

References

More details are available on a recent website

• Pulse-oximetry during fMRI scanning, GK Aguirre Lab