Hi experts,
I open the afni GUI, set the underlay to TT_N27, then select the Draw Dataset option. The GUI suddenly crash and show some errors. By the way, I've seen the same error messages when I use "where am I" in GUI, but I can still get the information about the location.
Thanks a lot for the help!
Best,
Xin
These are messages popped up in the terminal and in .afni.crash.log.
Error in terminal
** ERROR: No atlas named AFNI_ATLAS_COLORS found in global atlas list
** ERROR: No atlases given were found in global atlas list
Please see whereami help and AFNI_atlas_spaces.niml for information
on how to add atlases to AFNI
.afni.crashlog
*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
+++++AV_assign_ival [5]: {ENTRY (file=bbox.c line=1921) from new_MCW_optmenu_orig {10892 ms}
AV_assign_ival -- adjust text {10892 ms}
-----AV_assign_ival [5]: EXIT} (file=bbox.c line=1977) to new_MCW_optmenu_orig {10892 ms}
+++++AV_assign_ival [5]: {ENTRY (file=bbox.c line=1921) from new_MCW_optmenu_orig {10892 ms}
AV_assign_ival -- adjust text {10892 ms}
AV_assign_ival -- adjust optmenu history {10892 ms}
-----AV_assign_ival [5]: EXIT} (file=bbox.c line=1977) to new_MCW_optmenu_orig {10892 ms}
----new_MCW_optmenu_orig [4]: EXIT} (file=bbox.c line=1116) to PLUG_startup_plugin_CB {10892 ms}
++++new_MCW_arrowval [4]: {ENTRY (file=bbox.c line=544) from PLUG_startup_plugin_CB {10892 ms}
new_MCW_arrowval -- creating wrowcol {10892 ms}
new_MCW_arrowval -- creating wlabel {10892 ms}
new_MCW_arrowval -- getting label height {10892 ms}
new_MCW_arrowval -- freeing xstr {10892 ms}
new_MCW_arrowval -- creating item labels {10892 ms}
new_MCW_arrowval -- creating wtext2 {10892 ms}
+++++AV_assign_ival [5]: {ENTRY (file=bbox.c line=1921) from new_MCW_arrowval {10892 ms}
AV_assign_ival -- adjust text {10892 ms}
-----AV_assign_ival [5]: EXIT} (file=bbox.c line=1977) to new_MCW_arrowval {10892 ms}
----new_MCW_arrowval [4]: EXIT} (file=bbox.c line=787) to PLUG_startup_plugin_CB {10892 ms}
++++Atlas_With_Trimming [4]: {ENTRY (file=thd_ttatlas_query.c line=7180) from PLUG_startup_plugin_CB {10892 ms}
+++++get_Atlas_Named [5]: {ENTRY (file=thd_ttatlas_query.c line=6947) from Atlas_With_Trimming {10892 ms}
-----get_Atlas_Named [5]: EXIT} (file=thd_ttatlas_query.c line=6960) to Atlas_With_Trimming {10892 ms}
----Atlas_With_Trimming [4]: EXIT} (file=thd_ttatlas_query.c line=7324) to PLUG_startup_plugin_CB {10892 ms}
++++Atlas_With_Trimming [4]: {ENTRY (file=thd_ttatlas_query.c line=7180) from PLUG_startup_plugin_CB {10892 ms}
+++++get_Atlas_Named [5]: {ENTRY (file=thd_ttatlas_query.c line=6947) from Atlas_With_Trimming {10892 ms}
-----get_Atlas_Named [5]: EXIT} (file=thd_ttatlas_query.c line=6960) to Atlas_With_Trimming {10892 ms}
----Atlas_With_Trimming [4]: EXIT} (file=thd_ttatlas_query.c line=7324) to PLUG_startup_plugin_CB {10892 ms}
++++Atlas_Names_to_List [4]: {ENTRY (file=thd_ttatlas_query.c line=7083) from PLUG_startup_plugin_CB {10892 ms}
+++++get_Atlas_Named [5]: {ENTRY (file=thd_ttatlas_query.c line=6947) from Atlas_Names_to_List {10892 ms}
-----get_Atlas_Named [5]: EXIT} (file=thd_ttatlas_query.c line=6964) to Atlas_Names_to_List {10892 ms}
----Atlas_Names_to_List [4]: EXIT} (file=thd_ttatlas_query.c line=7108) to PLUG_startup_plugin_CB {10892 ms}
............................................................................
PLUG_startup_plugin_CB
AFNI:main
** AFNI compile date = Oct 10 2019
** [[Precompiled binary macos_10.12_local: Oct 10 2019]]
** Program Crash **
Also, the afni_system_check.py if it will help
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.7.0
version: Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64
distribution: 10.14.6 x86_64
number of CPUs: 8
apparent login shell: csh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/xc363/abin/afni
afni version : Precompiled binary macos_10.12_local: Oct 10 2019
: AFNI_19.3.03 'Nero'
AFNI_version.txt : AFNI_19.3.03, macos_10.12_local, Oct 10 2019
which python : /usr/local/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/xc363/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 2
/usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/usr/bin/python
python2 : 1 (/usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/usr/local/Cellar/python/3.7.4_1/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
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 -------------------------------
++ module loaded: PyQt4
module file : /usr/local/lib/python2.7/site-packages/PyQt4/__init__.pyc
** have PyQt4, but cannot load QtCore, QtGui; error is:
**************************************************
**************************************************
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-- python binaries under /sw/bin:
/sw/bin/python (sym link to /sw/bin/python2.7)
-- python binaries under /usr/local/bin:
/usr/local/bin/python (sym link to /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python2 (sym link to /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
/usr/local/bin/python3.7 (sym link to /usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python2.7 (sym link to /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
-------------------------------- env vars --------------------------------
PATH = /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/laps:/opt/X11/bin:/Users/xc363/abin
PYTHONPATH = /usr/local/lib/python2.7/site-packages
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /Applications/freesurfer/lib/gcc/lib:/opt/X11/lib/flat_namespace:/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: ...ay 2019 [rickr]: AFNI_pamenc updates to global_*.txt
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/xc363/aglobal
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.12
++ found PyQt4 under /usr/local/lib/python2.7/site-packages
** consider linking /usr/local/Cellar/gcc/9.2.0/lib/gcc/9/libgomp.1.dylib under /usr/local/lib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.62.0/lib/libglib-2.0.dylib
++ 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 'csh'...
++ found evar DYLD_LIBRARY_PATH = /Applications/freesurfer/lib/gcc/lib:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* check for partial install of PyQt4
* consider adding /usr/local/lib/python2.7/site-packages to PYTHONPATH
Edited 1 time(s). Last edit at 10/24/2019 06:48PM by icupsy.
