unfortunately i failed to open afni gui by running: "afni"
the output:
Precompiled binary macos_10.12_local: Aug 25 2023 (Version AFNI_23.2.08 'Marcus Didius Severus Julianus')
** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to JA Butman 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 # tcsh
- export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace # bash
- This command is best put in your startup ~/.cshrc file, so that
- it will be invoked for every (t)csh shell you open (mutatis mutandis
- for the bash shell, of course).
- If things are OK and you want to avoid having this warning message
- pollute your terminal, use this:
- setenv AFNI_SKIP_DYLD_WARNING YES # tcsh
- export AFNI_SKIP_DYLD_WARNING=YES # bash
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
[The X.Org Foundation v 12101006].
++++++++ IMAGE SAVE SETUP WARNINGS ++++++++
++ Can't find program ffmpeg for Save to MPEG-1
++ To disable these warnings, set environment
++ variable AFNI_IMSAVE_WARNINGS to 'NO'.
+++++++++++++++++++++++++++++++++++++++++++++
Warning: Widget must be a VendorShell.
Fatal Signal 11 (SIGSEGV) received
open_MCW_imseq
SPLASH_popup_image
AFNI_splashup
MAIN_workprocess
AFNI:main
Bottom of Debug Stack
** AFNI version = AFNI_23.2.08 Compile date = Aug 25 2023
** [[Precompiled binary macos_10.12_local: Aug 25 2023]]
** 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/lianqi/.afni.crashlog
++ AFNI is detached from terminal.
addition: I installed XQuartz (X11) and set an environment variable on bash_profile.
Crash log:
------ CRASH LOG ------------------------------**
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=31) from open_MCW_imseq {6898 ms}
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=40) to open_MCW_imseq {6898 ms}
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=31) from open_MCW_imseq {6898 ms}
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=43) to open_MCW_imseq {6898 ms}
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=31) from open_MCW_imseq {6898 ms}
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=40) to open_MCW_imseq {6898 ms}
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=31) from open_MCW_imseq {6898 ms}
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=40) to open_MCW_imseq {6898 ms}
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=31) from open_MCW_imseq {6898 ms}
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=40) to open_MCW_imseq {6899 ms}
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=31) from open_MCW_imseq {6899 ms}
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=40) to open_MCW_imseq {6899 ms}
+++++++SPLASH_imseq_getim [7]: {ENTRY (file=afni_splash.c line=442) from open_MCW_imseq {6899 ms}
-------SPLASH_imseq_getim [7]: EXIT} (file=afni_splash.c line=464) to open_MCW_imseq {6899 ms}
+++++++SPLASH_imseq_getim [7]: {ENTRY (file=afni_splash.c line=442) from open_MCW_imseq {6899 ms}
++++++++mri_valpad_2D [8]: {ENTRY (file=mri_zeropad.c line=28) from SPLASH_imseq_getim {6899 ms}
+++++++++mri_new_7D_generic [9]: {ENTRY (file=mri_new.c line=48) from mri_valpad_2D {6899 ms}
---------mri_new_7D_generic [9]: EXIT} (file=mri_new.c line=143) to mri_valpad_2D {6899 ms}
+++++++++mri_add_name [9]: {ENTRY (file=mri_add_name.c line=19) from mri_valpad_2D {6899 ms}
---------mri_add_name [9]: EXIT} (file=mri_add_name.c line=24) to mri_valpad_2D {6899 ms}
--------mri_valpad_2D [8]: EXIT} (file=mri_zeropad.c line=138) to SPLASH_imseq_getim {6899 ms}
-------SPLASH_imseq_getim [7]: EXIT} (file=afni_splash.c line=484) to open_MCW_imseq {6899 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from open_MCW_imseq {6899 ms}
mri_free -- call killpurge {6899 ms}
++++++++mri_killpurge [8]: {ENTRY (file=mri_purger.c line=259) from mri_free {6899 ms}
mri_killpurge -- check if im==NULL ptr=0x7fa95d6066c0
mri_killpurge -- can't killpurge NULL fname! {6899 ms}
--------mri_killpurge [8]: EXIT} (file=mri_purger.c line=270) to mri_free {6899 ms}
mri_free -- free ptr {6899 ms}
mri_free -- free im {6899 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=69) to open_MCW_imseq {6899 ms}
............................................................................
open_MCW_imseq
SPLASH_popup_image
AFNI_splashup
MAIN_workprocess
AFNI:main
** AFNI compile date = Aug 25 2023
** [[Precompiled binary macos_10.12_local: Aug 25 2023]]
** Program Crash **
Output of afni_system_check.py:
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm
system: Darwin
release: 22.5.0
version: Darwin Kernel Version 22.5.0: Thu Jun 8 22:29:35 PDT 2023; root:xnu-8796.121.3~8/RELEASE_ARM64_T6020
distribution: 13.4.1
number of CPUs: 12
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/lianqi/abin/afni
afni version : Precompiled binary macos_10.12_local: Aug 25 2023
: AFNI_23.2.08 'Marcus Didius Severus Julianus'
AFNI_version.txt : AFNI_23.2.08, macos_10.12_local, Aug 25 2023, official
which python : /Users/lianqi/anaconda3/bin/python
python version : 3.11.3
which R : /Library/Frameworks/R.framework/Resources/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
instances of various programs found in PATH:
afni : 1 (/Users/lianqi/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 2
/Users/lianqi/anaconda3/bin/python3.11
/opt/homebrew/Cellar/python@3.11/3.11.5/Frameworks/Python.framework/Versions/3.11/bin/python3.11
python2 : 0
python3 : 3
/opt/homebrew/Cellar/python@3.11/3.11.5/Frameworks/Python.framework/Versions/3.11/bin/python3.11
/Users/lianqi/anaconda3/bin/python3.11
/usr/bin/python3
** have python3 but not python2
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : success
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /bin/tcsh
which Xvfb : /opt/X11/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: phia!
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 : /Library/Frameworks/R.framework/Resources
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /Users/lianqi/anaconda3/lib/python3.11/site-packages/matplotlib/pyplot.py
matplotlib version : 3.7.1
-------------------------------- env vars --------------------------------
PATH = /Users/lianqi/fsl/share/fsl/bin:/Users/lianqi/fsl/share/fsl/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/Users/lianqi/anaconda3/bin:/Users/lianqi/anaconda3/condabin:/usr/local/gfortran/bin:/Library/Frameworks/R.framework/Resources:/opt/homebrew/opt/python/libexec/bin:/Users/lianqi/abin:/Users/lianqi/ants-2.4.4/bin:/Library/Java/JavaVirtualMachines/jdk-20.jdk/Contents/Home/bin:/Users/lianqi/MATLAB_R2023a.app/bin:/Users/lianqi/freesurfer/bin:/Users/lianqi/freesurfer/fsfast/bin:/Users/lianqi/freesurfer/mni/bin:/Users/lianqi/anaconda3/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:.
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : missing
.afni/help/all_progs.COMP : missing
--------- shell startup files ----------
-- good: .cshrc seems to contain 'source .tcshrc'
-- considered operations: path, flatdir, apsearch
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
dot file test : want 3 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 0 1
.tcshrc 1 1 1 0
.bashrc 0 0 0 0
------------------------------ 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/lianqi/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.1.9
-- 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'...
** env var DYLD_LIBRARY_PATH not set to contain /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
- just be aware: login shell 'bash', but our code examples use 'tcsh'
- shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
- missing R packages (see rPkgsInstall)
- please run: "suma -update_env" for .sumarc
- please run: apsearch -update_all_afni_help
- dot file test : want 3 modifications across 3 files:
- insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
- please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in tcsh