We are running a 3T MAGNETOM Tim Trio scanner on syngo MRB17 version.
According to the fMRI_Userguide.pdf which is written by Siemens, it states:
“A few different physiological signals may be monitored during an fMRI exam. Signals such as heart rate, breathing, and pulse may be measured and correlated with data acquisition and stimuli.”
“For details on how to set up the Siemens wireless ECG, respiratory cushion, and pulse oximeter, please refer to the System manual of the scanner.”
However, when we tested the pulse sensor with BOLD/EPI sequences we couldn’t find an input file where the physiological (pulse) data was recorded. Does anybody know what needs to be done to acquire heart rate during the fMRI scan?
I don’t have access to the full system manual. I found one on the internet but it appears to be incomplete. If anything when I ask the engineers in the facility they say they don’t know if it’s possible to record physiological data. The data can be viewed in real time as the scan goes on, but it is not recorded somehow. The local Siemens technician claims that it is not possible to record physiological data and the pulse sensor is only there to send triggers to the MRI scanner on when to take acquisitons/images during a scan.
However, the manual says it is possible. So I am stuck on my own trying to figure this out.
You can find some very useful information on this page:
Basically, you need to manually start and stop the recording of the PMU signals using the telnet command: ideacmdtool on the Siemens console.
It is not very convenient as it is not automatic and the format of output is also not very convenient to read. But it is possible to do so.
In our center, we do use the CMRR sequence (available through C2P collaboration) for fMRI where the recording of physiological signals is automatic which is much more easy to use.
If you are still stuck after reading these ressources, don’t hesitate to continue this thread, this may be useful to others.
We mainly need to record patient pulse because we have a physiological fMRI finding which we want to assess by having a measure of patient pulse. However, we can for sure use this data to improve our analysis in the future, as well.
What I gather from your reply is this:
It is possible to collect data, however I need to use the telnet command to save them, OR I need to use these custom sequences which automatically write them? Which will make the process more convenient. If I use the latter, I won’t need to use the telnet command to save pulse.
And to make use of the pulse data generated by the PMU (to analyze it), I can use PhysIO library, did I understand correctly?
Once again, thanks a lot for your answers and help so far!
What I gather from your reply is this:
It is possible to collect data, however I need to use the telnet command to save them, OR I need to use these custom sequences which automatically write them? Which will make the process more convenient. If I use the latter, I won’t need to use the telnet command to save pulse.
Correct, correct and correct.
And to make use of the pulse data generated by the PMU (to analyze it), I can use PhysIO library, did I understand correctly?
I am not sure that the PhysIO library directly reads this file, you may need to re-format it for PhysIO to be able to use it.
I never worked with those files myself, but a quick search on the web made me found this code that may be useful for you: