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BrainVoyager Available Tools Matlab Tools Physiological Noise Correction

Physiological Noise Correction

Physiological fluctuations from heartbeat and respiration are a common source of noise in fMRI data.

Here we provide a Matlab script (CreatePhysioPredictors_BIDS.m) that will use pulse and/or respiratory recordings, saved in BIDS compatible format (_physio.tsv.gz and _physio.json) (see for more information on BIDS) as well as a BrainVoyager .fmr file to create volume-based (filtered) predictors of the physiological recordings as well as volume-based physiological noise predictors saved in separate .sdm files. These include, but are not limited to, RETROICOR (Glover et al., 2000), the cardiac rate convolved with the cardiac response function (HR*CRF, Chang et al., 2009), the envelope of the respiratory signal, respiration variation (RV) and the respiratory volume per time (RVT) convolved with the respiratory response function (RVT*RRF, Birn et al., 2008).
Furthermore, by providing a task design matrix in the form of BrainVoyager's SDM file (optional input), all task regressors will be correlated with the derived physiological noise regressors.

Please note that the Matlab toolbox Neuroelf ( needs to be installed.

PhysioStructure 20220408


Respiration 20220408

TaskNoiseCorr 20220408

Mean heartrate and breathingrate values per protocol condition can be computed and saved to disk using an additional script (Extract_HR_BR_ForPRT.m together with ReadPRT.m) which takes as input a stimulation protocol (.prt file) and the resulting cardiacrespiratory.mat file of the script CreatePhysioPredictors_BIDS.m. 


PhysioStructure inclPRT 20220408

For more background information, please see this presentation.

The scripts can be downloaded using this link.


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