Is there a problem with nuisance regression or registration?

[Berit Singer]

Hello,

I am a newbie in preprocessing and fMRI analysis. I tried to set up a preprocessing pipeline with C-pac following the instructions for Dataset1 in the method section of this paper. I used your browser-interface to "design a pipeline" to create my configuration file. 

The quality control looks fine. And also the results "functional_preprocessed" look okay (see the pic in attachment). But when I load the "functional_to_standard" nifti files with nilearn and plot them it looks wrong (see the pic in attachment). Now, I don't know where the problem lies. 

Do you have any ideas what went wrong?

What do you recommend doing?

Thank you very much!

Kind regards,

Berit Singer