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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Simone Cauzzo
October 10, 2018 08:32AM
I installed AFNI on my pc, following the instructions on the website, more than a year ago, and everything was going well. Today it was the first time that I tried 3dSkullStrip, so I don't know if the problem has always been present or if it new. Yesterday I installed ANTs, I don't know if this may have messed up something. Anyway, if I perform sudo apt-get install -y gsl-bin, it just says that everything is already installed 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
gsl-bin is already the newest version (2.4+dfsg-6).
The following packages were automatically installed and are no longer required:
  linux-headers-4.15.0-32 linux-headers-4.15.0-32-generic
  linux-image-4.15.0-32-generic linux-modules-4.15.0-32-generic
  linux-modules-extra-4.15.0-32-generic
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.

here's the output of "afni_system_check.py -check_all" 

-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Linux
release:              4.15.0-36-generic
version:              #39-Ubuntu SMP Mon Sep 24 16:19:09 UTC 2018
distribution:         Ubuntu 18.04 bionic
number of CPUs:       4
apparent login shell: tcsh
shell RC file:        .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /home/cauzzo_s/abin/afni
afni version         : Precompiled binary linux_ubuntu_16_64: Apr 28 2018 
                     : AFNI_18.1.08
AFNI_version.txt     : AFNI_18.1.08, linux_ubuntu_16_64, Apr 28 2018
which python         : /usr/bin/python
python version       : 2.7.15rc1
which R              : /usr/bin/R
R version            : R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
which tcsh           : /usr/bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/home/cauzzo_s/abin/afni)
    R       : 1   (/usr/bin/R)
    python  : 1   (/usr/bin/python2.7)
    python2 : 1   (/usr/bin/python2.7)
    python3 : 1   (/usr/bin/python3.6)


testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : FAILURE
        3dSkullStrip: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
    uber_subject.py      : success
    3dAllineate          : success
    3dRSFC               : FAILURE
        3dRSFC: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
    SurfMesh             : success
    3dClustSim           : success

checking for R packages...
    rPkgsInstall -pkgs ALL -check : success

checking for $HOME files...
    .afnirc                   : found
    .sumarc                   : found
    .afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
++ module 'PyQt4' found at /usr/lib/python2.7/dist-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /home/cauzzo_s/bin:/home/cauzzo_s/.local/bin:/home/cauzzo_s/code/antsbin/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/cauzzo_s/abin

PYTHONPATH = 
R_LIBS = /home/cauzzo_s/R

LD_LIBRARY_PATH = 
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 /home/cauzzo_s/abin

------------------------------ OS specific -------------------------------
which apt-get        : /usr/bin/apt-get
apt-get version      : apt 1.6.3ubuntu0.1 (amd64)

have Ubuntu system: Ubuntu 18.04 bionic
have Ubuntu afni  : Precompiled binary linux_ubuntu_16_64: Apr 28 2018 

=========================  summary, please fix:  =========================
*  AFNI programs show FAILURE
*  insufficient data for AFNI bootcamp
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Subject Author Posted

Missing lib with 3dSkullStrip

Simone Cauzzo October 10, 2018 07:58AM

Re: Missing lib with 3dSkullStrip

ptaylor October 10, 2018 08:20AM

Re: Missing lib with 3dSkullStrip

Simone Cauzzo October 10, 2018 08:32AM

Re: Missing lib with 3dSkullStrip

ptaylor October 10, 2018 08:49AM

Re: Missing lib with 3dSkullStrip

Simone Cauzzo October 10, 2018 08:59AM

Re: Missing lib with 3dSkullStrip

ptaylor October 10, 2018 09:37AM