AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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heffjos
December 31, 2022 02:24AM
Quote
ptaylor
Are you using precompiled binaries, or building on your own system (I'm guessing the latter, from the version info)?
I was using an fmriprep singularity image. I realized the version was old, so I built my own singularity container using @update.afni.binaries to install afni. This is the version I am using now: 
Precompiled binary linux_ubuntu_16_64: Dec  2 2022 (Version AFNI_22.3.07 'Lucius Verus')
Here is the output of `afni_system_check.py -check_all` now: 
-------------------------------- general ---------------------------------
architecture:         64bit ELF
cpu type:             x86_64
system:               Linux
release:              3.10.0-1160.15.2.el7.x86_64
version:              #1 SMP Wed Feb 3 15:06:38 UTC 2021
distribution:         Ubuntu 22.04.1 LTS
number of CPUs:       56
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /opt/afni/afni
afni version         : Precompiled binary linux_ubuntu_16_64: Dec  2 2022 
                     : AFNI_22.3.07 'Lucius Verus'
AFNI_version.txt     : AFNI_22.3.07, linux_ubuntu_16_64, Dec 02 2022
which python         : /usr/local/miniconda/bin/python
python version       : 3.10.8
which R              : /usr/bin/R
R version            : R version 4.1.2 (2021-11-01) -- "Bird Hippie"
which tcsh           : /usr/bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/opt/afni/afni)
    R       : 1   (/usr/bin/R)
    python  : 1   (/usr/local/miniconda/bin/python3.10)
    python2 : 0 
    python3 : 2 
      /usr/local/miniconda/bin/python3.10
      /usr/bin/python3.10

** have python3 but not python2

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: phia!
        These packages are not installed on the computer: snow!
        These packages are not installed on the computer: paran!
        These packages are not installed on the computer: brms!
        

R RHOME : /usr/lib/R

checking for $HOME files...
    .afnirc                   : found
    .sumarc                   : missing
    .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/local/miniconda/lib/python3.10/site-packages/matplotlib/pyplot.py
   matplotlib version : 3.6.2

-------------------------------- env vars --------------------------------
PATH = /usr/local/miniconda/bin:/opt/workbench/bin_linux64:/opt/fsl-v6.0.6.1/share/fsl/bin:/opt/fsl-v6.0.6.1/share/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/afni

PYTHONPATH = 
R_LIBS = 
LD_LIBRARY_PATH = /opt/workbench/lib_linux64::/.singularity.d/libs

DYLD_LIBRARY_PATH = 
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 /opt/afni

------------------------------ OS specific -------------------------------
which apt-get        : /usr/bin/apt-get
apt-get version      : apt 2.4.8 (amd64)

have Ubuntu system: Ubuntu 22.04.1 LTS
have Ubuntu afni  : Precompiled binary linux_ubuntu_16_64: Dec  2 2022 

=========================  summary, please fix:  =========================
*  just be aware: login shell 'bash', but our code examples use 'tcsh'
*  missing R packages (see rPkgsInstall)
*  please run: "suma -update_env" for .sumarc
*  insufficient data for AFNI bootcamp
   (see "Prepare for Bootcamp" on install pages)
The update fixed the problem I was having.



Edited 1 time(s). Last edit at 12/31/2022 02:28AM by heffjos.
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Subject Author Posted

Surf commands and singularity

heffjos December 29, 2022 04:45PM

Re: Surf commands and singularity

ptaylor December 30, 2022 11:33AM

Re: Surf commands and singularity

heffjos December 30, 2022 08:48PM

Re: Surf commands and singularity

ptaylor December 30, 2022 10:59PM

Re: Surf commands and singularity

heffjos December 31, 2022 02:24AM

Re: Surf commands and singularity

ptaylor December 31, 2022 07:59AM