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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jbursley
December 23, 2014 08:18PM
When I run afni_system_check.py with my newer version of AFNI (from November) I get this:

-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 2.6.32-358.11.1.el6.x86_64
version: #1 SMP Wed Jun 12 03:34:52 UTC 2013
distribution: CentOS 6.4 Final
number of CPUs: 64
apparent login shell: bash

--------------------- AFNI and related program tests ---------------------
which afni : /ncf/tools/current/apps/arch/linux_x86_64/afni/2014_12_13_1200/afni
afni version : Precompiled binary linux_gcc32: Nov 21 2014
which python : /ncf/tools/current/apps/arch/linux_x86_64/python/2.7.3/bin/python
python version : 2.7.3
which R : which: no R in (/ncf/tools/current/apps/arch/linux_x86_64/afni/2014_12_13_1200:/ncf/tools/current/code/bin:/ncf/tools/current/code/bin/linux_x86_64:/ncf/tools/current/code/lib/perl/Common:/ncf/tools/current/code/lib/shell:/ncf/tools/current/apps/arch/linux_x86_64/fsl/4.0.3/bin:/ncf/tools/current/apps/arch/linux_x86_64/mongodb/2.2.0/bin:/ncf/tools/current/apps/arch/linux_x86_64/php/5.4.3/bin:/ncf/tools/current/apps/arch/linux_x86_64/freesurfer/4.0.2/bin:/ncf/tools/current/apps/arch/linux_x86_64/freesurfer/4.0.2/fsfast/bin:/ncf/tools/current/apps/arch/linux_x86_64/freesurfer/4.0.2/mni/bin:/ncf/tools/current/apps/arch/linux_x86_64/dcmtk/3.6/bin:/ncf/tools/current/apps/arch/linux_x86_64/xjview/8.4:/ncf/tools/current/apps/arch/linux_x86_64/caret/5.0:/ncf/tools/current/apps/arch/linux_x86_64/mricron/2009_12:/ncf/tools/current/apps/arch/linux_x86_64/python/2.7.3/bin:/ncf/tools/current/apps/arch/linux_x86_64/java/1.6.0_24/bin:/ncf/tools/current/code/lib/c/linux_x86_64:/ncf/tools/current/code/bin/.package_loaders:/usr/local/bin:/usr/lib64/qt-3.3/bin:/lsf/7.0/linux2.6-glibc2.3-x86_64/etc:/lsf/7.0/linux2.6-glibc2.3-x86_64/bin:/bin:/usr/bin:/opt/dell/srvadmin/bin)

which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/ncf/tools/apps/arch/linux_x86_64/afni/2014_12_13_1200/afni)
R : 0
python : 2
/ncf/tools/apps/arch/linux_x86_64/python/2.7.3/bin/python2.7
/usr/bin/python

testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : FAILURE
SurfMesh: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory

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

------------------------------ python libs -------------------------------
---------------------------------------------------------
** python module not found: PyQt4

-> please see the output of "uber_subject.py -help_install"


------------------------------- path vars --------------------------------
PATH = /ncf/tools/current/apps/arch/linux_x86_64/afni/2014_12_13_1200:/ncf/tools/current/code/bin:/ncf/tools/current/code/bin/linux_x86_64:/ncf/tools/current/code/lib/perl/Common:/ncf/tools/current/code/lib/shell:/ncf/tools/current/apps/arch/linux_x86_64/fsl/4.0.3/bin:/ncf/tools/current/apps/arch/linux_x86_64/mongodb/2.2.0/bin:/ncf/tools/current/apps/arch/linux_x86_64/php/5.4.3/bin:/ncf/tools/current/apps/arch/linux_x86_64/freesurfer/4.0.2/bin:/ncf/tools/current/apps/arch/linux_x86_64/freesurfer/4.0.2/fsfast/bin:/ncf/tools/current/apps/arch/linux_x86_64/freesurfer/4.0.2/mni/bin:/ncf/tools/current/apps/arch/linux_x86_64/dcmtk/3.6/bin:/ncf/tools/current/apps/arch/linux_x86_64/xjview/8.4:/ncf/tools/current/apps/arch/linux_x86_64/caret/5.0:/ncf/tools/current/apps/arch/linux_x86_64/mricron/2009_12:/ncf/tools/current/apps/arch/linux_x86_64/python/2.7.3/bin:/ncf/tools/current/apps/arch/linux_x86_64/java/1.6.0_24/bin:/ncf/tools/current/code/lib/c/linux_x86_64:/ncf/tools/current/code/bin/.package_loaders:/usr/local/bin:/usr/lib64/qt-3.3/bin:/lsf/7.0/linux2.6-glibc2.3-x86_64/etc:/lsf/7.0/linux2.6-glibc2.3-x86_64/bin:/bin:/usr/bin:/opt/dell/srvadmin/bin

PYTHONPATH = /ncf/nrg/sw/lib/pylib/2.0:/ncf/tools/current/code/lib/python/Neuroinfo_Toolkit/1.5.2

LD_LIBRARY_PATH = /lsf/7.0/linux2.6-glibc2.3-x86_64/lib

DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing suma_demo
atlas : found TT_N27+tlrc under /ncf/tools/current/apps/arch/linux_x86_64/afni/2014_12_13_1200

------------------------------ OS specific -------------------------------

---------------------------- general comments ----------------------------
* consider copying AFNI.afnirc to ~/.afnirc
* consider running "apsearch -update_all_afni_help"
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Subject Author Posted

3dAttribute exec failure

bursley December 15, 2014 03:18PM

Re: 3dAttribute exec failure

bursley December 16, 2014 05:06PM

Re: 3dAttribute exec failure

Isaac Schwabacher December 16, 2014 05:24PM

Re: 3dAttribute exec failure

Peter Molfese December 16, 2014 06:34PM

Re: 3dAttribute exec failure

jbursley December 23, 2014 02:33PM

Re: 3dAttribute exec failure

Peter Molfese December 23, 2014 04:23PM

Re: 3dAttribute exec failure

jbursley December 23, 2014 08:18PM

Re: 3dAttribute exec failure

ziad December 24, 2014 09:20AM

Re: 3dAttribute exec failure

jbursley December 28, 2014 03:06PM

Re: 3dAttribute exec failure

bursley January 14, 2015 10:46AM

Re: 3dAttribute exec failure

rick reynolds December 17, 2014 11:48AM