Hi Paul,

thanks for your elaborate answer!
I certainly enjoyed bootcamp more than the people videocalling in from Norman campus... but I think that's partly due to not a single person attending the bootcamp from over there.

Q1a: Seems reasonable, I will just do that then. And people desperate for finding an answer to the question I had will now be able to find it through the power of Google. Yeih!

Q1b: I just started processing the subject I had FS skull-stripped earlier with @SSwarper - I'll keep you posted after comparing the two versions!
But I guess a good habit for me would be to script the analysis in a way that it does @SSwarper Skull Stripping --> recon_all with no skull strip option --> @SUMA_Make_Spec_FS ---> eternal happiness.

Q2: In an ideal world I will just run AFNI on a all-linux machine. Maybe someday...
The terminal doesn't show any complaints - it does give out the information that there might be other areas nearby etc that would normally pop-up in the GUI
Internet connection in the terminal is not an issue, I can download a .html site no problem.
I talked to other people in the lab and they have the same issue.

Buuuuut: Adding AFNI_WEBBY_WAMI = NO to my .afnirc does the trick. I don't pretend to comprehend what consequences it will have if it can't connect to NeuroSynth anymore but hey - at least it's not crashing now!

It does find the TTatlas+tlrc in the bin ~/abin directory like it should.

Bonus answer:
Well good that you pointed that out - I would have run into that issue as soon as I had executed the created afni_proc.py script. I don't want to live without this review ever again.
Over are the days of command line opening processed SPM images and clicking through all the slices manuallly! ... that is, if I convince my home lab in Germany to switch to AFNI once my internship here finishes and I have to go back.

Does look a lot better:
------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib/python2.7/dist-packages/PyQt4/__init__.pyc

++ module loaded: matplotlib.pyplot
module file : /usr/lib/python2.7/dist-packages/matplotlib/pyplot.pyc


Well, anyhow, thanks for your time and I'll keep you posted on the Skull Stripping comparison.

Best
Jonas

//EDIT you guys are faster at sending out answers than I can type my response!
What Daniel suggested made it work - our internal guidelines still recommend Xming but I installed VcXSrv as you suggested, removed the entry from ~/.afnirc again and it works like a charm. Legends!



Edited 2 time(s). Last edit at 03/18/2020 07:17PM by Jonas_St.