Hi, Jonas-

Glad you enjoyed the Bootcamp!

Re. Q1a: Yes, this has been a roller coaster of an issue. After good discussions with the FreeSurfer folks, we discovered that the (mis)alignment issue that we thought was happening was due to our own way of viewing the before/after datasets. Somewhat humbling for us.... but that is life. So, the check_dset_for_fs.py is no longer active nor needed. Proceed directly onwards with your recon-all commands.

Re. Q1b: re. skullstripping before or after recon-all---I haven't looked at this systematically myself, so I couldn't say definitely one way or the other (to date, I have typically just run FS's recon-all on a non-skullstripped dataset). However, @SSwarper does a pretty darn nice job of skullstripping (typically), so I can see this being reasonable. I guess you could run @SSwarper, see if you like the results, and then decide if you want to use that as input to recon-all? (It would be great to have your feedback here, if you do decide to do that; this might be something I will try on some test data, as well, comparing results in both cases.)
Either way, I typically load the "anatSS.${subj}.nii" dataset from @SSwarper into afni_proc.py with "-copy_anat", and then do, indeed, add "-anat_has_skull no".

Re. Q2: No real shame in using WSL---at least you are using Linux! Re. your whereami woes: could you doublecheck if there is text in the terminal that shows any complaint that might point to the problem?
I have noticed that sometimes the problem is internet connection, because by default the "whereami" will try to connect to NeuroSynth, and if it can't it breaks down. You can try checking yoru internet connection from the commandline, and make sure it is OK ("wget www.nytimes.com" or something to see if you can pull down an HTML page). You can also edit your ~/.afnirc file to add the environment variable to turn off using neurosynth: put this line at the bottom of that text file (you should be able to open it with any text editor, such as "gedit ~/.afnirc"), for example:

AFNI_WEBBY_WAMI = NO

... and then see if things go better for you.

If your setup is different than the default, it might be that your AFNI can't find some atlas file; to check that, does the following return anything if you copy+paste it into a terminal?

@FindAfniDsetPath TTatlas+tlrc

Bonus response: you didn't ask, but I note that the afni_system_check.py found that you did *not* have matplotlib.pyplot on your system---that means that you won't be able to use the muuuuuch nicer "pythonic" form of QC HTML from afni_proc.py ("-html_review_style pythonic"). I would strongly encourage you to put Python's matplotlib library on your system (I like using Conda via miniconda for being able to have multiple Python setups cleanly on one machine, but you can also just "sudo apt-get install python-matplotlib" to install it on your system default, with Aptitude.)

--pt