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Within the last decade, great strides have been made to change this by improving multiple aspects of neonatal fMRI data analysis and acquisition. Despite these structural, functional, and behavioural differences, infant MRI studies often rely on data acquisition and analytical approaches that have been developed and refined to optimise spatial specificity and sensitivity to signal in adults. Features such as the high water and low myelin content lead to a reduction in contrast and an inversion of MRI signal between tissue types ( Paus et al., 2001), and data quality can be highly influenced by infant movement ( Power et al., 2012 Reuter et al., 2015 Satterthwaite et al., 2012 Siegel et al., 2017 Yendiki et al., 2014). During early development, the composition, size, and morphology of the human brain changes rapidly ( Dubois et al., 2014 Dubois and Dehaene-Lambertz, 2015), and neurodynamic and haemodynamic activity differs dramatically from that observed in adults ( André et al., 2010 Arichi et al., 2012). The infant brain is not a miniature replica of the adult brain. The improved sensitivity and specificity, made possible with this extended dHCP pipeline, will be paramount in making further progress in our understanding of the development of sensory processing in the infant brain. We demonstrate that a substantial increase in spatial specificity and sensitivity to signal can be attained with a bespoke neonatal preprocessing pipeline through optimised motion and distortion correction, ICA-based denoising, and haemodynamic modelling. We compare the results obtained from this extended dHCP pipeline to results obtained from a typical FSL FEAT-based analysis pipeline, evaluating the pipelines' outputs using a wide range of tests. We describe and validate this extended dHCP fMRI preprocessing pipeline to analyse changes in brain activity evoked following an acute noxious stimulus applied to the infant's foot. Here, in an independent neonatal dataset we have extended and optimised the dHCP fMRI preprocessing pipeline for the analysis of stimulus-response fMRI data. As the majority of current MRI analysis tools were designed for use in adults, a primary objective of the Developing Human Connectome Project (dHCP) is to develop optimised methodological pipelines for the analysis of neonatal structural, resting state, and diffusion MRI data. The infant brain is unlike the adult brain, with considerable differences in morphological, neurodynamic, and haemodynamic features.