Hi @Shannon_Cahalan,
The length of time for 1st level FEAT to complete with fMRIPrep-generated data depends on several factors, including data size, complexity of design matrix, etc. That being said, here are a few things to consider based on your initial post:
I would recommend the space-MNI152NLin6Asym fMRIPrep outputs if you have them, this space is equivalent to FSL’s MNI152 space (see here). This allows you to skip FEAT’s registration step (performed at the 2nd-level, see here for details). Additionally, FEAT enables smoothing via the “Spatial smoothing FWHM (mm)” option in the “Pre-stats” tab. You can select the amount of smoothing (in mm) that you prefer. This negates the need to smooth the data outside FEAT with fslmaths. I would also recommend you turn off “Motion correction”, "B0 unwarping, and “Slice timing correction”, as these have already been completed by fMRIPrep.
The confounds file(s) generated by fMRIPrep contain a wide variety of potential confound variables which can be used for different analysis pipelines (e.g., aroma denosing, CompCor, etc). However, as the fMRIPrep documentation warns, you should not use the entire confounds file in your analysis, simply specify the individual confounds you want into a separate .txt file and use that in FSL FEAT. I suspect this is what is what’s causing your FEAT to stall. However, you may still need to wait an hour (or two) for FEAT to finish, depending on the size of your data.
Hope this helps.