Thanks Paul, I'll have a look at these resources :)

And thank you Rick for your feedback :) that makes sense.

I realize now that the errts files are the final output for resting state from uber_subject.py .

The reason I was running my data through subject_proc.py first is because I wanted to preprocess my functional data with afni prior to applying ICA (with FSL) on my data.

I know this might sound like an FSL issue but it has more to do with AFNI's output in question.

I wanted to incorporate it into my pipeline by take the output of AFNI (the preprocessed data) and use it as input for FSL's ICA analysis.
I wanted to do this by converting my brik files (errts files) into nifti files and use it as input for fsl's ICA analysis, MELODIC. The problem is that the ICA analysis crashes when inputting the afni preprocessed data as input. I took a look at one of the issues and it had to do with registration of my data. One of the steps for MELODIC (fsl) involves registration of my funtional data to standard space and I get something that looks really funky. I've attached an image to show you what I mean. Naturally in the registration step I'd see my functional brain registered nicely to the standard space, in the case where I use errts I get this box image that is trying to be warped into standard space. I don't see a cleaned up functional brain (it has noise in the background it seems).
Looking at past literature it seems that this is what errts outputs look like, but I can't seem to understand how to integrate it into my pipeline after preprocessing.

Thank you so much for your help I appreciate it.