fMRIprep output files

I am running fmriprep-docker for preprocessing of resting-state fMRI data, but I just need the motion corrected and brain extracted output file. I tried the “-w” option and set a path for intermediate files, but all of the files in the func folder are in pklz format. I am not sure how I can use these files for further processes as I need nii files.
Is there any way to get access the output of each step of fmriprep so that it can be used in FSL?
The other question is that how I can use fmriprep with the sole purpose of performing registration stage.

Hi Fatima,

Could you share your full command?

I’m not entirely sure what you mean, but @Jeanette_Mumford has posted a video on using fMRIPrep outputs with FSL, which may be useful, if not exactly what you’re looking for.

Could you clarify this question? What would you like to register to what, and which stages are you proposing to skip?