Thanks Paul!

This got a bit messy and turned into two questions:

1) InstaCorr:
It works. The problem was something else, which is strange. When setting up Instacorr, and mask is checked an automask = on, it turns out it makes an inverted mask! I get voxels/correlations if I place the marker outside the brain. If I turn off auto-mask, then I get values in the brain (and they make sense, e.g. DMN). What could cause this? Basically there is nothing in the brain with auto-mask.

2) 3dGroupInCorr
I tried your commands but something seems off. The server is on a secure network, so the firewall is off and should allow traffic:

sudo ufw status verbose
Status: inactive

But when running your command I get that no ports are available (it should be larger than 0 and less than 23 (I think) so the returned port is not valid:

afni -available_npb

First available npb: 0

I also looked into existing AFNI sessions:

ps aux | grep afni
robka    35837  0.0  0.0  15984  1024 pts/2    S+   02:18   0:00 grep --color=auto afni

I guess it finds the grep command I did?

Then I try the whole afni-niml + 3dgroupIncorr again:
Once I start 3dGrouIncor I see in

sudo netstat -tcp | grep afni
tcp        0      0 localhost:53213         localhost:41928         ESTABLISHED 37770/afni          
tcp        0      0 localhost:53213         localhost:41928         ESTABLISHED 37770/afni          
tcp        0      0 localhost:53213         localhost:41928         ESTABLISHED 37770/afni          
tcp        0      0 localhost:53213         localhost:41928         ESTABLISHED 37770/afni 
,,,

Before I ran 3dGroupIncorr it was empty. So, that seems to work?
But I don't get any information in the afni-viewer that it is connected..