Hi, I found some severe distortion, especially in the medial wall of the brain, when using fmriprep. The fmriprep version that I used is 1.0.0-rc2. The MRIQC version that I used is 0.9.8-1. I can only attach the MRIQC image in this post because new user only allows to post one image. I also tried my old way of preprocessing by spm8 with one-step normalization (EPI to EPI template provided by spm). It looks like there is less distortion by using spm8. However, the location of ventricle is less accurate by using spm8 than using fmriprep. I am not sure why there is a huge difference between preprocessing by spm and fmriprep. One possibility is that our TE is pretty low (22.2 ms), which is lower than most of the studies (30ms). It is likely the image contrast in our EPI is lower than other studies. Please let me know if there is any good suggestions about using fmriprep. Please also let me know if you guys need info because I can not post more than one image.