Ciao, Dante-

Q0: "[what] is the difference between the different *.FT.r* versions within each pb* version? For example, what is the difference between these files:"
FT.results/pb00.FT.r01.tcat+orig.HEAD
FT.results/pb00.FT.r02.tcat+orig.HEAD
FT.results/pb00.FT.r03.tcat+orig.HEAD ?"

To start, pb = "processing block", so when you specify major blocks of processing in afni_proc.py (such as volreg, blur, align, etc.), the main outputs of each one get a corresponding "pb.*" in the output files. I am guess that you have input 3 runs of EPI data (that is, 3 files of EPI time series), because I see *r01*, *r02*, *r03* in the file names. I can also tell that the pb00* output is part of the (implicit) "tcat" block, because of the helpful naming convention: basically, the files are copied into the directory here.

The processing blocks (automatic, default and optional ones) are described in the help here:
[afni.nimh.nih.gov]

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Q1: "[Where] can I find an explanation of the FT.results output files or generally the contents of the afni_proc.py results directory?"

A good, general question! (I hope I provide a good, specific answer...)

++ In the online tutorial videos, the afni_proc.py "start to finish: hands-on example" series starts looking at output here, and viewing/discussing/describing the results/ directory contents:
[www.youtube.com]
(Watching this detailed playlist from the video is recommended for afni_proc.py'ing-- might be a good Thanksgiving Day treat for the whole family?)

++ The HTML output in QC_${subj}/index.html provides a good review of the main files, in both informative quantities and useful pictures. The file names of relevant files are provided in many cases, for further investigation.
(Hopefully, you include the afni_proc.py option "-html_review_style python" in your real analyses, because this output will look much nicer; it just requires that you have Python+Matplotlib installed on your computer. For an example of this nicer output in the Bootcamp directory where s05* lives, open up the file results.QC_FT.05/index.html in your browser.)

++ To know a bit more about what the outputs are, there is a "dictionary" of keywords and output file names, stored in a text file:
out.ss_review_uvars.json
such as this excerpt:

"df_info_dset": "out.df_info.txt",
   "enorm_dset": "motion_FT_enorm.1D",
   "errts_dset": "errts.FT+tlrc.HEAD",
   "final_anat": "anat_final.FT+tlrc.HEAD",
   "final_epi_dset": "final_epi_vr_base_min_outlier+tlrc.HEAD",

... and to see (terse) descriptions of what each keyword represents, you can run "gen_ss_review_scripts.py -show_uvar_dict", of which this is a corresponding excerpt:

enorm_dset           : set motion_enorm file
   errts_dset           : set residual dataset
   final_anat           : anat aligned with stats dataset
   final_epi_dset       : set final EPI base dataset

++ the proc script itself is actually a useful resource for knowing what is what-- it is magically commented, as well as being organized by processing block. Because it is commented, searching for something like "motion" or the name of a block is useful; if you see an intriguing-looking file, you can also see where it appears in here with searching (subject ID might be a variable ${subj}, though, so avoid that part in search). This script shows *exactly* what each file is, because it includes the exact command used to make it.

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... and if you have any more questions after checking out some of these, we're always here to help!

--pt