How to run preprocessed fmriprep data in SPM12

Summary of what happened:

Hi! I have preprocessed my fmri data using fmriprep as well as SPM12. I now want to compare the outputs of each data set from the two different softwares. I am going to run my first-level analysis for both using SPM12. How do i use my fmriprep data for SPM12 analysis?

When I load a batch into SPM12, I cannot select the fmriprep func data. Do I have to do something first to the fmriprep data to make it compatiable with SPM12? Will the outputs of each software be in different MNI space?



Environment (Docker, Singularity, custom installation):

I used Docker for fmriprep and Matlab for SPM12

Data formatted according to a validatable standard? Please provide the output of the validator:

Relevant log outputs (up to 20 lines):

Screenshots / relevant information:

I suspect this is because the images are gunzipped and that’s why you the SPM batch won’t run with those. You need to unzip the data first.

If that’s the case consider unzipping using bids-matlab copying and unzip function: Function description — bids-matlab v0.1.0dev documentation