Hello!
1) Yes, you are correct thank you! And thanks! I figured that more complex designs may lead to messier looking output but wanted to make sure. This is an event related design with many different things going on so I would expect it to be a bit less clear than in the example. And I do see visual cortex here which is comforting.
2) Here is the output from that command. I'd be happy to send along that html file once I get your email!
tue50988@cla19097:~$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 5.15.0-46-generic
version: #49~20.04.1-Ubuntu SMP Thu Aug 4 19:15:44 UTC 2022
distribution: ubuntu 20.04 focal
number of CPUs: 48
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Aug 25 2022
: AFNI_22.2.08 'Marcus Aurelius'
AFNI_version.txt : AFNI_22.2.08, linux_ubuntu_16_64, Aug 25 2022
which python : /usr/bin/python
python version : 3.8.10
which R : /usr/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/usr/local/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python3.8)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.8)
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : success
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
oo Warning:
These packages are not installed on the computer: paran!
These packages are not installed on the computer: psych!
These packages are not installed on the computer: brms!
These packages are not installed on the computer: corrplot!
These packages are not installed on the computer: metafor!
R RHOME : /usr/lib/R
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
++ module loaded: matplotlib.pyplot
module file : /usr/lib/python3/dist-packages/matplotlib/pyplot.py
matplotlib version : 3.1.2
-------------------------------- env vars --------------------------------
PATH = /home/local/TU/tue50988/.local/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/abin:/usr/local/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /usr/local/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.0.9 (amd64)
have Ubuntu system: ubuntu 20.04 focal
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Aug 25 2022
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
