Calculating heart rate and heart rate variability from Siemen's Scanner Log Files

AFNI Message Board
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Hello,

I realize this is likely an odd question to ask on the AFNI message board but thought I'd give it a shot.

I have Siemen's scanner log files containing the respiration and pulse data collected on the scanner.

I'd ultimately like to use those files to compute heart rate and heart rate variability to compare two groups on a task fMRI run.

Is this something that can potentially be computed with 3dretroicorr?

Happy to upload a Siemen's log file to get a sense of the data format (which uses Siemen's tics).

Thanks!

Emily

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Hi, Emily-

I don't think there is a ready-made solution per se, but we are getting near releasing an updated version of RetroTS.py that might be able to calculate some summary stats that would be of use for comparison some summary points. Getting the mean+spread or even frequency distribution of peak-to-peak times seems pretty reasonable to output. How does that seem for this project?

--pt

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Hi Paul,

That would be amazing!!! When do you think the RetroTS.py might be available?

Thanks again for your willingness to try and include these summary statistics!

Emily

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Just to note, it will be an update/replacement for RetroTS.py.

I would say it should be pretty soon, though OHBM is happening now, so that will occupy a lot of time for the next week+. So perhaps in a couple/few weeks? (approximate estimate)

--pt

1 Like
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Sounds great! Thanks Paul! Enjoy OHBM!

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Hi Paul,

I wanted to check in and see if the updates have been made to RetroTS.py I was also wondering if it was possible to get those summary points including heart rate and heart rate variability we discussed was possible?: "Getting the mean+spread or even frequency distribution of peak-to-peak times seems pretty reasonable to output."

Thanks so much and hope you had a great time at OHBM!

Emily

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Sorry one additional follow-up. I wanted to see if I needed to reformat my log files generated from a Siemen's 3T Prisma scanner for import to RetroTS.py. Would it be possible to possibly attach those files and have you take a look?

Thanks so much!

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Hi Paul,

Hope you had a great time at OHBM!

I wanted to check in and see if the updates have been made to RetroTS.py I was also wondering if it was possible to get those summary points including heart rate and heart rate variability we discussed was possible?: "Getting the mean+spread or even frequency distribution of peak-to-peak times seems pretty reasonable to output."

I wanted to see if I needed to reformat my log files generated from a Siemen's 3T Prisma scanner for import to RetroTS.py. Would it be possible to possibly attach those files and have you take a look?

Thanks so much and hope you had a great time at OHBM!

Emily

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Hi, Emily-

Sorry for the delay in replying.

It is preetttty close. There is an early version which is now in a github branch, getting closer to readiness.

No reformatting would be needed.

Sure, sending the files to me might be easiest at present---I will send you a message for doing so.

--pt