AFNI GUI crash after click the Draw Dataset

AFNI Message Board
1

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.

[size=large]Error in terminal[/size]
** 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

[size=large].afni.crashlog[/size]
------ 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 **

[size=large]Also, the afni_system_check.py if it will help[/size]
-------------------------------- 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
2

That’s strange. Can you report the output of these commands?

@AfniEnv -get AFNI_ATLAS_LIST
@AfniEnv -get AFNI_ATLAS_COLORS

Also does “whereami -show_atlases” report the expected atlases?

3

Hi Daniel,
I checked my .afnirc file and I think the problem is caused by adding a template using the following commands:

AFNI_ATLAS_LIST “Haskins_Pediatric_Nonlinear_1.0,Haskins_Pediatric_Affine_1.0,CA_MPM_18_MNIA”
AFNI_ATLAS_COLORS Haskins_Pediatric_Nonlinear_1.0
AFNI_TEMPLATE_SPACE_LIST HaskinsPeds,MNI,TLRC[size=large]The output of AFNI_ATLAS_LIST:[/size]

After I remove these lines, the viewer works well. Is there any way to add templates without changing the default settings?
Thanks,
Xin

4

Something still strange:
When I click whereami in the Cluserize in the viewer, some warnings pop up in the terminal.

** Warning: Atlas CA_N27_PM could not be loaded.
** Warning: Atlas CA_PM_18_MNIA could not be loaded.
** Warning: Atlas DKD_Desai_PM could not be loaded.
** Warning: Atlas DD_Desai_PM could not be loaded.
** Warning: Atlas FS_Desai_PM could not be loaded.

[size=medium]The output of AFNI_ATLAS_LIST and AFNI_ATLAS_COLORS are both empty.
The output of “whereami -show_atlases”:[/size]
++ ----- Atlas list: -------
++ Name Space Dataset Description
++ __________________________________________________________
++ MNI_Glasser_HCP_v1.0 MNI /Users/xc363/abin//MNI_Glasser_HCP_v1.0.nii.gz Glasser HCP atlas 2016 surface-based parcellation
++ Brainnetome_1.0 MNI /Users/xc363/abin//BN_Atlas_246_1mm.nii.gz Brainnetome MPM
++ CA_MPM_22_MNI MNI /Users/xc363/abin//MNI_caez_mpm_22+tlrc Eickhoff-Zilles MPM atlas
++ CA_MPM_22_TT TT_N27 /Users/xc363/abin//TT_caez_mpm_22+tlrc Eickhoff-Zilles MPM atlas - Talairach space
++ CA_N27_ML TT_N27 /Users/xc363/abin//TT_caez_ml_18+tlrc Macro Labels (N27)
++ CA_N27_MPM TT_N27 /Users/xc363/abin//TT_caez_mpm_18+tlrc Cytoarch. Max. Prob. Maps
++ CA_N27_PM TT_N27 TT_caez_pmaps_18+tlrc Cytoarch. Probabilistic Maps
++ CA_N27_GW TT_N27 /Users/xc363/abin//TT_caez_gw_18+tlrc Cytoarch. Prob. Maps for gray/white matter
++ CA_N27_LR TT_N27 /Users/xc363/abin//TT_caez_lr_18+tlrc Left/Right (N27)
++ CA_ML_18_MNI MNI /Users/xc363/abin//MNI_caez_ml_18+tlrc Macro Labels (N27-MNI)
++ CA_MPM_18_MNI MNI /Users/xc363/abin//MNI_caez_mpm_18+tlrc Cytoarch. Max. Prob. Maps (MNI)
++ CA_LR_18_MNI MNI /Users/xc363/abin//MNI_caez_lr_18+tlrc Left/Right (N27-MNI)
++ CA_ML_18_MNIA MNI_ANAT /Users/xc363/abin//MNIa_caez_ml_18+tlrc Macro Labels (N27)
++ CA_MPM_18_MNIA MNI_ANAT /Users/xc363/abin//MNIa_caez_mpm_18+tlrc Cytoarch. Max. Prob. Maps
++ CA_PM_18_MNIA MNI_ANAT MNIa_caez_pmaps_18+tlrc Cytoarch. Probabilistic Maps
++ CA_GW_18_MNIA MNI_ANAT /Users/xc363/abin//MNIa_caez_gw_18+tlrc Cytoarch. Prob. Maps for gray/white matter
++ CA_LR_18_MNIA MNI_ANAT /Users/xc363/abin//MNIa_caez_lr_18+tlrc Left/Right (N27)
++ DKD_Desai_PM TT_N27 TT_desai_dkpmaps+tlrc Probability maps of 35 cortical areas (gyri)
++ DD_Desai_PM TT_N27 TT_desai_ddpmaps+tlrc Probability maps of 75 cortical areas
++ FS_Desai_PM TT_N27 TT_desai_fspmaps+tlrc Contains 40 subcortical areas
++ DD_Desai_MPM TT_N27 /Users/xc363/abin//TT_desai_dd_mpm+tlrc Contains the maximum probability maps of Desai DD and FS maps
++ DKD_Desai_MPM TT_N27 /Users/xc363/abin//TT_desai_dk_mpm+tlrc Contains the maximum probability maps of Desai DKD and FS maps
++ MNI_VmPFC MNI /Users/xc363/abin//MNI_VmPFC+tlrc Ventromedial Prefrontal Cortex
++ TT_Daemon TLRC /Users/xc363/abin//TTatlas+tlrc Talairach-Tournoux Atlas
++ Haskins_Pediatric_Nonline HaskinsPeds /Users/xc363/abin//HaskinsPeds_NL_atlas1.0+tlrc.HEAD Version 1.0
++
++ MNI_Glasser_HCP_v1.0: Glasser, et al,A multi-modal parcellation of human cerebral cortex,
Nature,2016.
Atlas was constructed from surface analysis in Contee grayordinates.
Use with caution on volumetric analysis. Transformed to MNI space
via FreeSurfer and then to a standard mesh in AFNI.
More details on this implementation in Atlas_notes.txt and here:
https://openwetware.org/wiki/Beauchamp:CorticalSurfaceHCP
++ Brainnetome_1.0: Please cite Fan, L. et al., The Human Brainnetome Atlas:
A New Brain Atlas Based on Connectional Architecture.
Cerebral Cortex, 26 (8): 3508-3526,(2016).
++ CA_MPM_22_MNI: Eickhoff-Zilles maximum probability map from cytoarchitectonic probabilistic atlas
SPM ANATOMY TOOLBOX v2.2
For full list of references,
http://www.fz-juelich.de/inm/inm-1/EN/Forschung/_docs/SPMAnatomyToolbox/SPMAnatomyToolbox_node.html
Primary references:
Contact: Simon Eickhoff (s.eickhoff@fz-juelich.de)
Eickhoff SB et al.: A new SPM toolbox… (2005) NeuroImage 25(4): 1325-1335
Eickhoff SB et al.: Testing anatomically specified hypotheses… (2006) NeuroImage 32(2): 570-82
Eickhoff SB et al.: Assignment of functional activations… (2007) NeuroImage 36(3): 511-521
Publications describing included probabilistic maps:
TE 1.0, TE 1.1, TE 1.2------------------------------------------ Morosan et al., NeuroImage 2001
BA 44, BA 45---------------------------------------------------- Amunts et al., J Comp Neurol 1999
BA 4a, BA 4p BA 6----------------------------------------------- Geyer et al., Nature 1996 S. Geyer,
Springer press 2003
BA 3a, BA 3b, BA 1 BA 2----------------------------------------- Geyer et al., NeuroImage, 1999, 2000
Grefkes et al., NeuroImage 2001
OP 1, OP 2, OP 3, OP 4------------------------------------------ Eickhoff et al., Cerebral Cortex 2006a,b
PFt, PF, PFm, PFcm, PFop, PGa, PGp 5Ci, 5L, 5M, 7A, 7M, 7P, 7PC- Caspers et al., Neuroimage 2007, BSF 2008
Scheperjans et al., Cerebral Cortex 2008a,b
hIP1, hIP2 hIP3------------------------------------------------- Choi et al., J Comp Neurol 2006
Scheperjans et al., Cerebral Cortex 2008a,b
Ig1, Ig2, Id1--------------------------------------------------- Kurth et al., Cerebral Cortex 2010
CM/LB/SF FD/CA/SUB/EC/HATA-------------------------------------- Amunts et al., Anat Embryol 2005
Amunts et al., Anat Embryol 2005
BA 17, BA 18 hOC5 hOC3v / hOC4v--------------------------------- Amunts et al., NeuroImage 2000
Malikovic et al., Cerebral Cortex 2006
Rottschy et al., Hum Brain Mapp 2007
13 structures--------------------------------------------------- Burgel et al., NeuroImage 1999, 2006
18 structures--------------------------------------------------- Diedrichsen et al., NeuroImage 2009
Dorsal extrastriate cortex (hOC3d / hOC4d)---------------------- Kujovic et al., Brain Struct Funct 2012
Gyrus fusiformis (FG1, FG2)------------------------------------- Caspers et al., Brain Struct Funct 2012
Frontal pole (Fp1, Fp2)----------------------------------------- Bludau et al., Neuroimage, 2014
Other areas may only be used with authors’ permission !

AFNI adaptation by
Ziad S. Saad and Daniel Glen (SSCC/NIMH/NIH)
no comment
++ CA_N27_ML: Eickhoff-Zilles macro labels from N27 in Talairach TT_N27 space
SPM ANATOMY TOOLBOX v1.8
Primary references:
Contact: Simon Eickhoff (s.eickhoff@fz-juelich.de)
Eickhoff SB et al.: A new SPM toolbox… (2005) NeuroImage 25(4): 1325-1335
Eickhoff SB et al.: Testing anatomically specified hypotheses… (2006) NeuroImage 32(2): 570-82
Eickhoff SB et al.: Assignment of functional activations… (2007) NeuroImage 36(3): 511-521
Publications describing included probabilistic maps:
TE 1.0, TE 1.1, TE 1.2------------------------------------------ Morosan et al., NeuroImage 2001
BA 44, BA 45---------------------------------------------------- Amunts et al., J Comp Neurol 1999
BA 4a, BA 4p BA 6----------------------------------------------- Geyer et al., Nature 1996 S. Geyer,
Springer press 2003
BA 3a, BA 3b, BA 1 BA 2----------------------------------------- Geyer et al., NeuroImage, 1999, 2000
Grefkes et al., NeuroImage 2001
OP 1, OP 2, OP 3, OP 4------------------------------------------ Eickhoff et al., Cerebral Cortex 2006a,b
PFt, PF, PFm, PFcm, PFop, PGa, PGp 5Ci, 5L, 5M, 7A, 7M, 7P, 7PC- Caspers et al., Neuroimage 2007, BSF 2008
Scheperjans et al., Cerebral Cortex 2008a,b
hIP1, hIP2 hIP3------------------------------------------------- Choi et al., J Comp Neurol 2006
Scheperjans et al., Cerebral Cortex 2008a,b
Ig1, Ig2, Id1--------------------------------------------------- Kurth et al., Cerebral Cortex 2010
CM/LB/SF FD/CA/SUB/EC/HATA-------------------------------------- Amunts et al., Anat Embryol 2005
Amunts et al., Anat Embryol 2005
BA 17, BA 18 hOC5 hOC3v / hOC4v--------------------------------- Amunts et al., NeuroImage 2000
Malikovic et al., Cerebral Cortex 2006
Rottschy et al., Hum Brain Mapp 2007
13 structures--------------------------------------------------- Burgel et al., NeuroImage 1999, 2006
18 structures--------------------------------------------------- Diedrichsen et al., NeuroImage 2009
Other areas may only be used with authors’ permission !

AFNI adaptation by
Ziad S. Saad and Daniel Glen (SSCC/NIMH/NIH)
++ CA_N27_MPM: Eickhoff-Zilles maximum probability map on TT_N27 from post-mortem analysis
++ CA_N27_PM: Eickhoff-Zilles probablity maps on TT_N27 from post-mortem analysis
++ CA_N27_GW: Eickhoff-Zilles probablity maps on MNI-152 from post-mortem analysis
++ CA_N27_LR: Simple left, right hemisphere segmentation
++ CA_ML_18_MNI: Eickhoff-Zilles macro labels from N27 (MNI space)
++ CA_MPM_18_MNI: Eickhoff-Zilles maximum probability map on MNI-152 from post-mortem analysis (MNI space)
++ CA_LR_18_MNI: Simple left, right hemisphere segmentation (MNI space)
++ CA_ML_18_MNIA: Eickhoff-Zilles macro labels from N27 (MNI_ANAT space)
++ CA_MPM_18_MNIA: Eickhoff-Zilles maximum probability map on MNI-152 from post-mortem analysis (MNI_ANAT space)
++ CA_PM_18_MNIA: Eickhoff-Zilles probablity maps on MNI-152 from post-mortem analysis (MNI_ANAT space)
++ CA_GW_18_MNIA: Eickhoff-Zilles probablity maps on MNI-152 from post-mortem analysis (MNI_ANAT space)
++ CA_LR_18_MNIA: Simple left, right hemisphere segmentation (MNI_ANAT space)
++ DKD_Desai_PM:
Please cite:
Desikan et al., Neuroimage 2006 (31) pp. 968-980.
++ DD_Desai_PM:
For each hemisphere,including both gyri and sulci.
Please cite:
Destrieux et al., Neuroimage 2010 (53) pp. 1-15.
++ FS_Desai_PM: 15 in left & right hemispheres,10 midline structures parcellated by freesurfer
++ DD_Desai_MPM: Smoothed maximum maps masked by unsmoothed maximum map
++ DKD_Desai_MPM: Smoothed maximum maps masked by unsmoothed maximum map
++ MNI_VmPFC: Mackey, S. and Petrides, M. (2014), Architecture and morphology
of the human ventromedial prefrontal cortex. European Journal
of Neuroscience, 40: 2777-796. doi: 10.1111/ejn.12654
++ TT_Daemon: The standard talaraich atlas
++ Haskins_Pediatric_Nonlinear_1.0: Haskins Atlas 1.0. Ref: Molfese, Glen, Mesite, Pugh, & Cox (2015, June). The Haskins Pediatric Brain Atlas.
Poster session presented at the Organization for Human Brain Mapping, Honolulu, HI
++ --------------------------

5

The PMap atlases are no longer distributed with AFNI by default, but they are still available on our site if you want to download them. The AFNI_ATLAS_LIST setting you had before was probably the cause of this because the affine version of the Haskins pediatric atlas is also no longer distributed by default.

6

Thanks for the help!