AbstractPurposeExternal physiological monitoring is the primary approach to measure and remove effects of low‐frequency respiratory variation from BOLD‐fMRI signals. However, the acquisition of clean external respiratory data during fMRI is not always possible, so recent research has proposed using machine learning to directly estimate respiratory variation (RV), potentially obviating the need for external monitoring. In this study, we propose an extended method for reconstructing RV waveforms directly from resting state BOLD‐fMRI data in healthy adult participants with the inclusion of both BOLD signals and derived head motion parameters.MethodsIn the proposed method, 1D convolutional neural networks (1D‐CNNs) used BOLD signals and head motion parameters to reconstruct the RV waveform for the whole fMRI scan time. Resting‐state fMRI data and associated respiratory records from the Human Connectome Project in Young Adults (HCP‐YA) dataset are used to train and test the proposed method.ResultsCompared to using only BOLD‐fMRI data for a CNN input, this approach yielded improvements of 14% in mean absolute error, 24% in mean square error, 14% in correlation, and 12% in dynamic time warping. When tested on independent datasets, the method demonstrated generalizability, even in data with different TRs and physiological conditions.ConclusionThis study shows that the respiratory variations could be reconstructed from BOLD‐fMRI data in the young adult population, and its accuracy could be improved using supportive data such as head motion parameters. The method also performed well on independent datasets with different experimental conditions.