AFNI crashes from terminal!

Hi all,

I just installed AFNI on my MacBook (Mac OS Mojave 10.14), and when I try to load the GUI by typing afni in the terminal, it crashes. I’ve posted the output below. Any help would be GREATLY appreciated! Thank you!

-Lauren

Precompiled binary macos_10.12_local: Aug 19 2019 (Version AFNI_19.2.14 ‘Claudius’)

** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to B Feige for useful feedback

Initializing: X11
++ If you are using XQuartz 2.7.10 (or later), and AFNI crashes when

  • opening windows, or you cannot type text into AFNI popup windows,
  • you might need to set an environment variable to solve this problem:
  • setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace
  • This command is best put in your startup ~/.cshrc file, so that
  • it will be invoked for every (t)csh shell you open.

++ AFNI is detached from terminal.
(base) Laurens-MacBook-Pro-2:~ laurennelson$ [The X.Org Foundation v 11804000].
Fatal Signal 11 (SIGSEGV) received
ISQ_record_button
open_MCW_imseq
SPLASH_popup_image
AFNI_splashup
MAIN_workprocess
AFNI:main
Bottom of Debug Stack
** AFNI version = AFNI_19.2.14 Compile date = Aug 19 2019
** [[Precompiled binary macos_10.12_local: Aug 19 2019]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /Users/laurennelson/.afni.crashlog
afni
Precompiled binary macos_10.12_local: Aug 19 2019 (Version AFNI_19.2.14 ‘Claudius’)

** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to LR Frank for “quick” questions

Initializing: X11
++ If you are using XQuartz 2.7.10 (or later), and AFNI crashes when

  • opening windows, or you cannot type text into AFNI popup windows,
  • you might need to set an environment variable to solve this problem:
  • setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace
  • This command is best put in your startup ~/.cshrc file, so that
  • it will be invoked for every (t)csh shell you open.

[The X.Org Foundation v 11804000].
Fatal Signal 11 (SIGSEGV) received
ISQ_record_button
open_MCW_imseq
SPLASH_popup_image
AFNI_splashup
MAIN_workprocess
AFNI:main
Bottom of Debug Stack
** AFNI version = AFNI_19.2.14 Compile date = Aug 19 2019
** [[Precompiled binary macos_10.12_local: Aug 19 2019]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /Users/laurennelson/.afni.crashlog
++ AFNI is detached from terminal.

Hi-

I think the crash message gives a suggestion of what is happening:


++ If you are using XQuartz 2.7.10 (or later), and AFNI crashes when
+ opening windows, or you cannot type text into AFNI popup windows,
+ you might need to set an environment variable to solve this problem:
+ setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace
+ This command is best put in your startup ~/.cshrc file, so that
+ it will be invoked for every (t)csh shell you open.

Can you please run:


afni_system_check.py -check_all

… and paste the output here, to be more sure?

thanks,
pt

Here’s the output:

(base) Laurens-MacBook-Pro-2:~ laurennelson$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.7.0
version: Darwin Kernel Version 18.7.0: Thu Jun 20 18:42:21 PDT 2019; root:xnu-4903.270.47~4/RELEASE_X86_64
distribution: 10.14.6 x86_64
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/laurennelson/abin/afni
afni version : Precompiled binary macos_10.12_local: Aug 19 2019
: AFNI_19.2.14 ‘Claudius’
AFNI_version.txt : AFNI_19.2.14, macos_10.12_local, Aug 19 2019
which python : /Applications/anaconda2/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 3.5.2 (2018-12-20) – “Eggshell Igloo”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/laurennelson/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 2
/Applications/anaconda2/bin/python2.7
/usr/bin/python
python2 : 1 (/Applications/anaconda2/bin/python2.7)
python3 : 1 (/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
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 -------------------------------
** failed to load module PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
module file : /Applications/anaconda2/lib/python2.7/site-packages/matplotlib/pyplot.pyc

-------------------------------- env vars --------------------------------
PATH = /Applications/anaconda2/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurennelson/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: …2019 [ptaylor]: updated FT_analysis/results.QC_FT.05
data dir : found AFNI_demos under $HOME
top history: 29 Apr 2019 [rickr]: AFNI_pamenc command newline
data dir : found suma_demo under $HOME
top history: …s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/laurennelson/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.10

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
– consider installing gcc under homebrew
– consider installing glib under homebrew
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
– recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell ‘bash’…
++ found evar DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace
– recent OS X, cheating to check DYLD_LIBRARY_PATH in shell ‘tcsh’…
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace

========================= summary, please fix: =========================

  • login shell ‘bash’, trusting user to translate code examples from ‘tcsh’
  • shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile

If you copy+paste this in the terminal:


echo "" >> ~/.bash_profile
echo "source ~/.bashrc" >> ~/.bash_profile
echo "" >> ~/.bash_profile

… and then open up a new terminal, does the AFNI GUI still crash?

-pt

It worked! Yay!!! Thank you so much for your help!

Rockin’, glad that sorted it.

Happy AFNIing…

–pt

I am getting a similar error, when I follow these steps it will open a GUI, but won’t let me connect and open my data into it–each time i try that it recrashes and detached from the terminal. Any suggestions?

Please copy+paste the output of:


afni_system_check.py -check_all

That will show necessary pieces of information like your OS, what version of AFNI you have, what things you have installed, etc.

–pt

[spower48@node37 ShP_PastDep]$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-1062.9.1.el7.x86_64
version: #1 SMP Mon Dec 2 08:31:54 EST 2019
distribution: Red Hat Enterprise Linux Server 7.7 Maipo
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/afni/19.2.04/afni
afni version : Precompiled binary linux_openmp_64: Jul 19 2019
: AFNI_19.2.04 ‘Claudius’
AFNI_version.txt : AFNI_19.2.04, linux_openmp_64, Jul 19 2019
which python : /usr/bin/python
python version : 2.7.5
which R : /usr/local/R/3.6.1/bin/R
R version : R version 3.6.1 (2019-07-05) – “Action of the Toes”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/usr/local/afni/19.2.04/afni)
R : 1 (/usr/local/R/3.6.1/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 : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success

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

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

------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /usr/lib64/python2.7/site-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /usr/local/afni/19.2.04:/usr/local/R/3.6.1/bin:/usr/local/curl/7.64.1/bin:/usr/local/proj/6.0.0/bin:/usr/local/jags/4.3.0/bin:/usr/local/gdal/2.4.1/bin:/usr/local/geos/3.7.1/bin:/usr/local/udunits2/2.2.26/bin:/usr/local/gsl/2.5/bin:/usr/local/openmpi/4.0.1/ib-gcc8.3.0/bin:/usr/local/gcc/8.3.0/bin:/usr/local/Modules/3.2.10/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/spower48/.local/bin:/home/spower48/bin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH = /usr/local/afni/19.2.04:/usr/local/R/3.6.1/lib64:/usr/local/curl/7.64.1/lib:/usr/local/proj/6.0.0/lib:/usr/local/jags/4.3.0/lib:/usr/local/gdal/2.4.1/lib:/usr/local/geos/3.7.1/lib:/usr/local/udunits2/2.2.26/lib:/usr/local/gsl/2.5/lib:/usr/local/lapack/3.8.0/lib64:/usr/local/blas/3.8.0/lib:/usr/local/openmpi/4.0.1/ib-gcc8.3.0/lib:/usr/local/gcc/8.3.0/lib64:/opt2/amd-opencl/lib

DYLD_LIBRARY_PATH = :/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/afni/19.2.04

------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3

========================= summary, please fix: =========================

  • login shell ‘bash’, trusting user to translate code examples from ‘tcsh’
  • shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
  • please run: “suma -update_env” for .sumarc
  • insufficient data for AFNI bootcamp

Hi-

Please copy+paste this into a terminal:


echo "" >> ~/.bash_profile
echo "source ~/.bashrc" >> ~/.bash_profile
echo "" >> ~/.bash_profile

Then, if you open a new terminal, does the behavior with the GUI improve?

Also, based on the output of that system check, you can also copy+paste this:


suma -update_env

to set up your SUMA behavior.

Finally, you AFNI is quite old-- nearly a year now, nearly a lifetime in AFNI-land. It might be a good idea to update it:


@update.afni.binaries -d

–pt

PT,

Thank you so much! That worked–I will update afni as well!

Shan

Rockin’.

–pt

Hello!

Sadly, I am still getting this error. I’ve done everything from the previous thread we talked about–thoughts? It also says I don’t have permission to update. See below! I also, thought I hadn’t downloaded suma but I did so you can ignore that portion!

spower48@node37 ~]$ module load apps/afni-19.2.04
[spower48@node37 ~]$ afni
Precompiled binary linux_openmp_64: Jul 19 2019 (Version AFNI_19.2.04 ‘Claudius’)

** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to SJ Li for much encouragement

Initializing: X11Error: Can’t open display:
++ AFNI is detached from terminal.
[spower48@node37 ~]$ ^C
[spower48@node37 ~]$
[spower48@node37 ~]$ afni
Precompiled binary linux_openmp_64: Jul 19 2019 (Version AFNI_19.2.04 ‘Claudius’)

** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to KM Donahue for useful feedback

Initializing: X11Error: Can’t open display:
++ AFNI is detached from terminal.
[spower48@node37 ~]$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-1062.9.1.el7.x86_64
version: #1 SMP Mon Dec 2 08:31:54 EST 2019
distribution: Red Hat Enterprise Linux Server 7.7 Maipo
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/afni/19.2.04/afni
afni version : Precompiled binary linux_openmp_64: Jul 19 2019
: AFNI_19.2.04 ‘Claudius’
AFNI_version.txt : AFNI_19.2.04, linux_openmp_64, Jul 19 2019
which python : /usr/bin/python
python version : 2.7.5
which R : /usr/local/R/3.6.1/bin/R
R version : R version 3.6.1 (2019-07-05) – “Action of the Toes”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/usr/local/afni/19.2.04/afni)
R : 1 (/usr/local/R/3.6.1/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 : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success

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

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

------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /usr/lib64/python2.7/site-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /usr/local/afni/19.2.04:/usr/local/R/3.6.1/bin:/usr/local/curl/7.64.1/bin:/usr/local/proj/6.0.0/bin:/usr/local/jags/4.3.0/bin:/usr/local/gdal/2.4.1/bin:/usr/local/geos/3.7.1/bin:/usr/local/udunits2/2.2.26/bin:/usr/local/gsl/2.5/bin:/usr/local/openmpi/4.0.1/ib-gcc8.3.0/bin:/usr/local/gcc/8.3.0/bin:/usr/local/Modules/3.2.10/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/spower48/.local/bin:/home/spower48/bin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH = /usr/local/afni/19.2.04:/usr/local/R/3.6.1/lib64:/usr/local/curl/7.64.1/lib:/usr/local/proj/6.0.0/lib:/usr/local/jags/4.3.0/lib:/usr/local/gdal/2.4.1/lib:/usr/local/geos/3.7.1/lib:/usr/local/udunits2/2.2.26/lib:/usr/local/gsl/2.5/lib:/usr/local/lapack/3.8.0/lib64:/usr/local/blas/3.8.0/lib:/usr/local/openmpi/4.0.1/ib-gcc8.3.0/lib:/usr/local/gcc/8.3.0/lib64:/opt2/amd-opencl/lib

DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/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/afni/19.2.04

------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3

========================= summary, please fix: =========================

  • login shell ‘bash’, trusting user to translate code examples from ‘tcsh’
  • please run: “suma -update_env” for .sumarc
  • insufficient data for AFNI bootcamp

[spower48@node37 ~]$ suma -update_env
++ Notice suma (SUMA_suma.c:745 @10:12:54):
Environment update done.
[spower48@node37 ~]$ @update.afni.binaries -d
– running @update.afni.binaries version 3.9, June 14, 2019
– have AFNI binaries under /usr/local/afni/19.2.04
– install dir: using existing /usr/local/afni/19.2.04
– any downloads will be from https://afni.nimh.nih.gov via wget

– attempting to install package linux_openmp_64 under
install dir: /usr/local/afni/19.2.04…
– have install dir
** you do not have write permissions in the install directory
(install dir = /usr/local/afni/19.2.04)
[spower48@node37 ~]$

Hello,

There are 2 things to note here. One is that you do not own the AFNI binary directory on that server (which seems like it might be a high-performance cluster, since you start with “module load apps/afni-19.2.04”). Perhaps a newer version is available with a different “module load” call.

In any case, you are getting “Can’t open display” error. If X11 is not set up, the afni and suma graphical interfaces will not work.

It seems likely that you are doing a remote login session to that HPC server, but that needs to be via “ssh -X” or “ssh -Y” instead of simply “ssh” (the -X or -Y allow X11 forwarding).

Anyway, how are you logging onto “node37”? Is it via “ssh”? What operating system are you logging into it from?

  • rick

Hi Im also having the problem to open AFNI from terminal,

lbohorquez@PSYC-CRI-10822:~$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.2.0
version: Darwin Kernel Version 19.2.0: Sat Nov 9 03:47:04 PST 2019; root:xnu-6153.61.1~20/RELEASE_X86_64
distribution: unknown Darwin
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (does not exist)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/lbohorquez/abin/afni
afni version : Precompiled binary macos_10.12_local: May 4 2020
: AFNI_20.1.06 ‘Otho’
AFNI_version.txt : AFNI_20.1.06, macos_10.12_local, May 04 2020
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 3.5.3 (2019-03-11) – “Great Truth”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/lbohorquez/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 2
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/bin/python3.7
/usr/bin/python3

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 : success

R RHOME : /Library/Frameworks/R.framework/Resources

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 : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc

– python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python3.7 (sym link to /usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/bin/python3.7)

-------------------------------- env vars --------------------------------
PATH = /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/lbohorquez/abin

PYTHONPATH =
R_LIBS =
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 /Users/lbohorquez/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11

which brew : /usr/local/bin/brew
brew version : Homebrew 2.2.15

++ found PyQt4 under /usr/local/lib/python2.7/site-packages
** warning: have brew? PyQt4, but non-brew python /usr/bin/python
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
** env var DYLD_LIBRARY_PATH is not set to contain /opt/X11/lib/flat_namespace
(so afni and suma may fail)

========================= summary, please fix: =========================

  • login shell ‘bash’, trusting user to translate code examples from ‘tcsh’
  • shell bash: MISSING non-login setup file .bashrc
  • shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
  • insufficient data for AFNI bootcamp
  • OS X version might be old
  • consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace

The DYLD_LIBRARY_PATH variable does not seem to be set (according to the system test output). Test this using:

export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace
afni

Does that work?

If so, add that line to .bash_profile in your home directory (.bashrc does not seem to exist), open a new terminal window, and try ‘afni’ again. Your dot files might need some extra work.

  • rick

Thank you Rick!!

It works when I type
export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace
afni

The funny part is that I have this line saved in my bash_profile, so I don’t understand why each time I open a new terminal I have to type it again

That’s good. The dot file (.bashrc/.bash_profile) that gets used depends on the circumstance. We generally find it easier to populate .bashrc and then to have .bash_profile source .bashrc. For example, you could:

cd
cp .bash_profile .bash_profile.save
mv .bash_profile .bashrc
echo ". ~/.bashrc' > .bash_profile

Be careful and slow with these commands, making sure you get that “.save” copy of .bash_profile, in case it gets accidentally overwritten.

How does that seem?

  • rick

Rick,

Thank you for the quick reply! Sorry for the delay.

Yes, you are correct in that I am logging into an HPC server to do my analysis through that cluster.

I log on as the following:

X2go to access HPC, once I am there in the terminal as follows: ssh -x node37 (then in I cd into the folder with my information). I am logging into the HPC from my Mac (update Catalina unfortunately which causes so many issues elsewhere).

Thanks,

Shannon

Hi Shannon,

I think a lower-case x might actually disable X11 forwarding. Trying using:

ssh -X node37

  • rick