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MRI physiological signal processing

Source: vignettes/mri-physiology.Rmd
mri-physiology.Rmd

Philips MRI scanners record cardiac, respiratory, and motion signals alongside the BOLD acquisition via the Physiological Monitoring Unit (PMU). mrpheus can read these .log files, detect QRS complexes with the Pan-Tompkins algorithm, and compute instantaneous heart rate — producing cardiac regressors ready for RETROICOR or HRV analysis.

Reading a Philips PMU log

read_philips_physlog() parses any Philips PMU .log file and returns a mrpheus_physlog object containing the signal matrix, event markers, and recording metadata.

path <- system.file("extdata", "example_physlog.log", package = "mrpheus")
rec  <- read_philips_physlog(path)
rec
#> 
#> ── mrpheus Philips PMU recording ───────────────────────────────────────────────
#> ℹ Path: /home/runner/work/_temp/Library/mrpheus/extdata/example_physlog.log
#> ℹ System: wBTU (496 Hz)
#> ℹ Channels: v1raw, v2raw, v1, v2, ppu, resp, gx, gy, gz, mark
#> ℹ Samples: 9920 (0.3 min)
#> ℹ Markers: 52 events

The system argument sets the hardware preset:

# Wireless VCG (Achieva/Ingenia dStream) — default
rec <- read_philips_physlog(path, system = "wBTU")

# Older wired ECG system (500 Hz)
rec <- read_philips_physlog(path, system = "wired")

# Site-specific sampling rate
rec <- read_philips_physlog(path, system = "custom", sfreq = 400)

The resolved sampling frequency is always at rec$HDR$sfreq so nothing downstream needs to hardcode it.

Signal channels 

ecg  <- as.double(rec$C[, "v1raw"])
ppu  <- as.double(rec$C[, "ppu"])
resp <- as.double(rec$C[, "resp"])

The wBTU layout provides ten channels:

Channel Contents
v1raw, v2raw Raw VCG electrode voltages
v1, v2 Processed VCG signals
ppu Peripheral pulse unit (PPG, foot)
resp Respiratory belt
gx, gy, gz 3-axis accelerometer
mark Bit-encoded event marker

Event markers 

rec$I$ScannerStart
#> [1] 496
rec$I$ScannerStop
#> [1] 9466
head(rec$I$VcgOnset)
#> [1]  198  396  594  792  990 1188

QRS detection

detect_qrs() implements the Pan-Tompkins (1985) algorithm and returns a mrpheus_qrs object.

qrs <- detect_qrs(ecg, fs = rec$HDR$sfreq)
qrs
#> 
#> ── mrpheus QRS detection ───────────────────────────────────────────────────────
#> ℹ R-peaks detected: 50
#> ℹ Mean HR: 150 bpm
#> ℹ Filter delay: 37 samples (0.075 s)
#> ℹ Sampling rate: 496 Hz

R-peak indices are in qrs$qrs_i. Account for qrs$delay if you need indices aligned to the raw (pre-filter) ECG.

rr_ms <- diff(qrs$qrs_i) / rec$HDR$sfreq * 1000
cat("Mean RR :", round(mean(rr_ms)), "ms\n")
#> Mean RR : 399 ms
cat("SDNN    :", round(sd(rr_ms)), "ms\n")
#> SDNN    : 1 ms

PPU as an alternative

In neonates, PPU often gives a cleaner signal than the ECG electrodes. detect_qrs() accepts any pulsatile channel:

qrs_ppu <- detect_qrs(as.double(rec$C[, "ppu"]), fs = rec$HDR$sfreq)

Heart rate signal

compute_hr_signal() converts R-peak indices into a sample-by-sample instantaneous HR trace (bpm). It reads fs from the mrpheus_qrs object directly:

Epoch extraction

To extract the physiology aligned to the fMRI scan, use the scanner-stop marker. This is more reliable than the start marker because the exact recording onset varies but the stop is always clean:

sfreq    <- rec$HDR$sfreq
enddelay <- 42L
tr       <- 0.392
vols     <- 47L

stopidx  <- tail(rec$I$ScannerStop, 1L) - enddelay
startidx <- max(1L, stopidx - round(vols * tr * sfreq))
epoch    <- rec$C[startidx:stopidx, ]
cat("Epoch:", nrow(epoch), "samples /", round(nrow(epoch) / sfreq, 1), "s\n")
#> Epoch: 9139 samples / 18.4 s

RR intervals per TR 

qrs_epoch <- detect_qrs(as.double(epoch[, "v1raw"]), fs = sfreq)

rr_t <- qrs_epoch$qrs_i[-1] / sfreq
rr_s <- diff(qrs_epoch$qrs_i) / sfreq

tr_times <- seq(0, vols * tr, by = tr)
rr_tr    <- approx(rr_t, rr_s, xout = tr_times, method = "constant")$y

cat("RR per TR (first 5):", round(rr_tr[1:5] * 1000), "ms\n")
#> RR per TR (first 5): NA NA 399 399 399 ms

rr_tr is a length-vols vector ready for RETROICOR phase computation or inclusion as a nuisance regressor in a GLM.

Full pipeline 

library(mrpheus)

rec      <- read_philips_physlog("sub-01_ses-01_physlog.log")
sfreq    <- rec$HDR$sfreq
stopidx  <- tail(rec$I$ScannerStop, 1L) - 42L
startidx <- stopidx - round(2300L * 0.392 * sfreq)
epoch    <- rec$C[startidx:stopidx, ]
qrs      <- detect_qrs(as.double(epoch[, "v1raw"]), fs = sfreq)
hr       <- compute_hr_signal(qrs)
rr_tr    <- approx(
  x      = qrs$qrs_i[-1] / sfreq,
  y      = diff(qrs$qrs_i) / sfreq,
  xout   = seq(0, 2300 * 0.392, by = 0.392),
  method = "constant"
)$y

References

Pan J, Tompkins WJ. A real-time QRS detection algorithm. IEEE Trans Biomed Eng. 1985;32(3):230–236. https://doi.org/10.1109/TBME.1985.325532

Groot PFC. ReadPhilipsScanPhysLog (MATLAB). AMC Amsterdam. 2010.

Glover GH, Li TQ, Ress D. Image-based method for retrospective correction of physiological motion effects in fMRI: RETROICOR. Magn Reson Med. 2000;44(1):162–167.