I am in the process of writing my own preprocessing pipeline in nipype/niworkflows, which is inspired by fMRIPrep. I have to do so because we have BOLD data with a lot of artefacts and T1 with really poor gm/wm contrast and fMRIPrep fails to coregister the EPI to T1w frequently. With my own pipeline, I use the T2 for wm mask estimation, which works better and coregistration seems to work rather well.
My question now is: fMRIPrep concatenates the xforms from head motion correction and EPI to T1w registration in one step. Is that something that is necessary and yields better results? Or is it done purely for convenience?
@oesteban, maybe you can quickly enlighten me on this matter
Thanks in advance!