Hi @mattcieslak and @oesteban,
Thanks for your response. Our lab has been using a custom fMRI preprocessing workflow for quite some time now, but we wanted to make a switch to fmriprep, given its reproducibility. Before doing so however, we wanted to see if the time series returned by the two pipelines are more or less comparable.
The voxels were combined into regions of interest (ROI) using the AAL atlas. On comparing time series of the corresponding ROIs of the preprocessed bold outputs, of both the lab pipeline and fmriprep, we noticed that though most ROIs were correlated, there were still visible differences in the time series.
Consequently, we are trying to re-order our pipeline in the same order as fmriprep, to compare the outputs at each stage of the pipeline, to see which stage contributes maximally to the differences between the pipelines. On going through the fmriprep documentation, I saw that slice timing correction is applied first to the BOLD image and then computed mappings (head motion correction, SDC, BOLD to T1 registration, T1 to MNI space registration) are concatenated and applied to the image in in one go.
This suggests that there will be two intermediate BOLD files to which changes have been applied - one after slice timing correction, and one after the concatenated mapping is applied. These are the two files I’m looking for. If the files after each individual step - HMC, SDC, T1 to BOLD registration etc. - do exist, it would be great if you could direct me to those.