Recording Physiology

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Our scanner is capable of recording physiological responses from subjects using built-in peripheral recording equipment that is part of the Philips scanning system. Pulse oximetry, respiration, and electrocardiogram recording equipment are available, in the form of fiber optic cabling that interfaces directly with the scanner. Data from this equipment are saved on the scanning console in text format and contain time-stamp information that allows this data to be time-locked to scan onset or offset. Thus, it is possible to temporally link peripheral physiological responses to functional task timings and parameters, to observe subject responses during a functional task of interest. Even if physiological responses are not of inherent interest to you, this data can also be used as a variable of non-interest during general linear modeling to increase the signal-to-noise ratio for task regressors.

How To Record Data

Outlined below are the steps required to perform the logging process, and some common questions about physiological recording.

1. To set up the scanner for logging, the recording device must be plugged into the scanner itself, in the round plug to the left of the head coil plugs.


2. The scanner console computer must also be set to enable logging. This is not the default configuration of this machine, so it is necessary to check whether logging is enabled before every scan session. If you plan to use physiological recording, contact the scan technician, Tammy Moran, to obtain the special log-in account information and instructions describing how to enable the recording process. Note: The process includes rebooting the computer which takes several minutes. It is advised that you build in 15 minutes prior to any series of scanning sessions to enable the logging process.

3. Once the computer and scanner are set up, a test-scan should be performed on the phantom ball to verify that data are being saved (see step 7 describing the location of saved files).

4. To set up a participant with the pulse oximeter, simply attach the finger clip to the subject's finger.


5. During scanning, on the lower left of the scanner console screen, set the display from 'Blank' to 'PPU' (e.g, Peripheral Physiology Unit) so you can observe the subject's physiological signals in real-time format. The image below is depicting the correct settings, but no one is attached to the pulse oximeter. If someone's finger were in the pulse oximeter at the time, the pink line would depict waveforms representing their heart beats, and a mean heart rate would be calculated and displayed in the lower right-hand box. This heart rate value is updated on the screen every 2 seconds, although it is of course sampled at a much higher rate.


6. Once steps 1-5 are completed, physiological response data should be saving 'behind-the-scenes'. In other words, during the actual scanning session, a text file is automatically being written for each individual scan that is performed, containing the physiological response data, sampled at 500Hz.

7. During or after scanning, navigate to the location of the saved files, to rename the files and retrieve the data. To access the main drives of the scanner console computer, hit the Windows button the keyboard, right-click on the Start menu, and choose 'Explore'.


The data are located in G:/log/scanphyslog.


In the 'scanphyslog' directory, physiological recording data from your scans will be represented as a series of '.log' files, one per scan. The files are initially saved with the naming convention 'SCANPHYSLOG_YEAR_MONTH_DAY_HOUR_MINUTE_SECOND.log' representing the day and time of the onset of that particular scan. Physiological recording data will be saved in the same temporal order as the scans were collected. You can use this timing information to determine which file corresponds to which scan. For example, if during a scan session, a scout was run followed by the SENSE reference scan, the physiological recording data corresponding to the scout will be saved first and the SENSE reference second. It may be useful to make notes during each scan session itself with end-time of each scan (according to the scanner console computer) to mitigate any ambiguity associated with which scan is which.


It is advisable to change this name to something meaningful, as the names are likely to be truncated during the transfer process, losing the precise timing information. You can do this by clicking on the current name, and typing in a new name.


8. After your scan session, it is important to immediately transfer the physiological recording data to an external location. Every time physiological logging is disabled, every log file in this directory is deleted and cannot be recovered (see FAQ1 for more information about this). The easiest way to transfer logging data is to plug a USB stick into the scanner console computer and transfer the files to it.

The scanner console computer is located in the gray cabinet on the floor to the right of the desk. Insert a USB stick, and send the data to it by right-clicking on the files of interest and sending them to the USB drive.


Congratulations! You have successfully logged physiological response data!

The Data

The physiological response data, in its raw format, is cumbersome and difficult to work with. There are 500 samples per second in the log file, creating hundreds of thousands of lines for a single functional run. The physiological response values are located in the fifth column of the .log file.

Log file.jpg

The onset of the file corresponds to 15 seconds prior to the start of the scan. There is a single line containing a hash mark (#) and no numbers that serves as a time-stamp of the onset of the actual scan. The last line of the file corresponds to the exact end of the scan. Note: For functional scans, the # mark corresponds to the onset of the template, not the onset of the functional run itself, and recording continues during any amount of time that passes between the end of the template scan and the onset of the actual functional run (which is variable). Therefore, it is advisable to time-lock physiological response data during functional scans based on when the scan ENDS.

In terms of pulse oximetry, the values represent the raw waveform of the heart beat, from which heart rate and heart rate variability can be calculated. Some tools exist to perform these analyses within Matlab 7.5 and are accessible in /afs/ ReadPhysiologyLog.m analyzes individual runs, and this process can be batched by executing read_physio_batch.m. You can view instructions on their use by typing help in matlab.

Frequently Asked Questions

1. Why does the physiological logging have to be enabled over and over again?

Physiological logging is disabled by several processes, including software reboots and scanner crashes, and other processes which have not yet been pinpointed. When you arrive for scanning, chances are it has been disabled by something that happened since last time you scanned. This is why it is so important to build in time prior to your participant arriving (I recommend 15 minutes) to alter the settings appropriately, fully reboot the scanner computer, and scan a phantom to verify data is being saved.

2. Does that mean that logging could be disabled while I'm scanning?

This is very unlikely. Once you enable logging and check that files are saving, it will continue to log during your scan sessions unless the scanner crashes.

3. If I don't transfer my data right away, can I come back and get it later?

Maybe, but don't count on it. Every time logging is disabled, the scanphyslog directory is emptied, so there is always a risk that the data will be lost. Also, the files are very large so the directory may be cleaned out to recover disk space.

4. Which finger is best to record from?

We haven't explicitly tested this but the middle finger seems to give consistent readings.

5. Are there other factors that influence data quality?

Subjects should be instructed to keep their hands very still during scanning, as hand movements can generate noise in data. Anecdotally it seems that people with very small fingers, and very cold fingers, produce noisier data than people with larger or warmer hands. It might be advisable to place a sheet or pillow case over the hand to keep the hand warm, although this should be done with caution as it may influence the dissipation of heat from the subject's body.

6. This seems so easy! Why wouldn't I want to record physiological response data?

Although it is fairly easy to collect this data, there are some associated drawbacks. First is the added set-up, particularly the fact that it takes 10-15 minutes each time you come down to scan to set up and test the logging. Second, if your subjects need both button boxes to make responses, it is probably not possible to hook up the pulse oximeter to their fingers. Third, the data are fairly difficult to work with as the files are huge and extracting the desired data requires fairly complex mathematical operations (although some of this has been automated in Matlab code written by Solomon Diamond, from Thayer School of Engineering, which is in /scratch/).

7. Are all study designs amenable to testing for differences physiological response across conditions?

If you are interested in finding out whether a given stimulus type or task leads to a change in physiological responding, some types of designs are more amenable to answering this question than others. Like the BOLD response, changes in heart rate are temporally slow, and therefore it would not be likely that you would observe heart rate fluctuations to an individual stimulus in an event-related design. Also, it not wholly clear what timescale heart rate changes operate on, so it may be difficult to set a time window within which you would look for a heart rate response. For these reasons, changes in physiological responding would be more clearly observable in blocked or state-item designs, where you could ask simple questions such as, "Does heart rate during block type A differ from block type B?"

Acknowledgments: This entire process was built from the ground up by Solomon Diamond, Tammy Moran, Leah Somerville and George Wolford, with additional assistance in programming from Dylan David Wagner and helpful advice from Catherine Norris.

--Leahs 13:23, 4 January 2008 (EST)