Hello!
I got a new machine and installed AFNI using the new App. I’ve having an issue with a script that still runs on a machine that hasn’t been updated in a while. The new machine is running:
Mojave 10.14.5
X11- 2.7.11
AFNI_19.1.26 Compile date June 26, 2019
Below are the script, the error message and the output of my .cshrc file, which is where I’m suspicious the problem is.
thanks!
Stu
Script:
##############################################################################
Make a jpg (montage) of all the identified contrast in the
axial direction
and moves this to a directory you specify
##############################################################################
export ssid=“378”
#give a name for all the contrasts you are interested in
export contrast=" Cue_App Cue_Avo Fdb_Rew Fdb_Pun "
#set the subbrick identifier. For most purposes you would use the identifier to the T
#subbrick, as this is how the image is being thresholded.
declare -a subbrick=( 2 5 8 11 )
export datadir=“/Volumes/MILLER/PA_DATA/”
export picdir=“/Users/whistu/Desktop/fMRI/MILLER_PA/Check_images”
#identifier that will be part of the output filename, used to move pictures to your
#identified folder. Make sure this ID is unique in your results directory, otherwise
#more file will be moved than you would like
export ID=“PA”
export anat=“anat_final.PA.0+tlrc”
export stats=“stats.PA_IND.3+tlrc”
#Xvfb (The X Windows Virtual Frame Buffer).
#Xvfb allows you to launch X windows (of which AFNI is one)
#without actually displaying the contents to your screen
which Xvfb :1 -screen 0 1024x768x24 &
for ssid_index in $ssid
do
let SubbrickIndex=0
for contrast_index in $contrast
do
let SubbrickIndex=SubbrickIndex+1
export FileName=$ssid_index$ID$contrast_index
echo "************************************"
echo the FileName = $FileName
echo the SubbrickIndex = $SubbrickIndex
echo the subbrick is ${subbrick[$SubbrickIndex-1]}
echo the contrast is $contrast_index
echo "************************************"
cd "$datadir$ssid_index"/PA.0.results
pwd
DISPLAY=:1 afni -com "OPEN_WINDOW A.axialimage mont=6x6:3 " \
-com "SWITCH_UNDERLAY A.$anat" \
-com 'SET_VIEW A.tlrc' \
-com "SWITCH_OVERLAY A.$stats" \
-com 'SET_XHAIRS A.OFF' \
-com "SET_SUBBRICKS A 0 ${subbrick[$SubbrickIndex-1]} ${subbrick[$SubbrickIndex-1]} " \
-com "SET_DICOM_XYZ A 0 0 0 " \
-com 'SET_THRESHNEW A 0.05 *p' \
-com 'SET_PBAR_NUMBER A.8' \
-com 'SEE_OVERLAY A.+' \
-com "SAVE_JPEG A.axialimage $FileName" \
-com "QUIT"
done
sleep 5
mv *"$ID"* "$picdir"
done
killall Xvfb
Error Message:
[NERC134684:~/Desktop/fMRI/MILLER_PA] whistu% sh PullImages_Functional.sh
the FileName = 378_PA_Cue_App
the SubbrickIndex = 1
the subbrick is 2
the contrast is Cue_App
/Volumes/MILLER/PA_DATA/378/PA.0.results
Precompiled binary macos_10.12_local: Jun 26 2019 (Version AFNI_19.1.26 ‘Caligula’)
** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to E Leibenluft for much encouragement
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_19.1.26 Compile date = Jun 26 2019
** [[Precompiled binary macos_10.12_local: Jun 26 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/whistu/.afni.crashlog
++ AFNI is detached from terminal.
AFNI Crash log:
------ CRASH LOG ------------------------------**
Fatal Signal 11 (SIGSEGV) received
… recent internal history …
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=39) to open_MCW_imseq {327 ms}
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=27) from open_MCW_imseq {327 ms}
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=36) to open_MCW_imseq {327 ms}
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=27) from open_MCW_imseq {327 ms}
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=36) to open_MCW_imseq {328 ms}
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=27) from open_MCW_imseq {328 ms}
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=36) to open_MCW_imseq {328 ms}
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=27) from open_MCW_imseq {328 ms}
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=36) to open_MCW_imseq {328 ms}
+++++++THD_find_executable [7]: {ENTRY (file=thd_getpathprogs.c line=27) from open_MCW_imseq {328 ms}
-------THD_find_executable [7]: EXIT} (file=thd_getpathprogs.c line=36) to open_MCW_imseq {328 ms}
+++++++SPLASH_imseq_getim [7]: {ENTRY (file=afni_splash.c line=442) from open_MCW_imseq {328 ms}
-------SPLASH_imseq_getim [7]: EXIT} (file=afni_splash.c line=464) to open_MCW_imseq {328 ms}
+++++++SPLASH_imseq_getim [7]: {ENTRY (file=afni_splash.c line=442) from open_MCW_imseq {328 ms}
++++++++mri_valpad_2D [8]: {ENTRY (file=mri_zeropad.c line=28) from SPLASH_imseq_getim {328 ms}
+++++++++mri_new_7D_generic [9]: {ENTRY (file=mri_new.c line=48) from mri_valpad_2D {328 ms}
---------mri_new_7D_generic [9]: EXIT} (file=mri_new.c line=142) to mri_valpad_2D {328 ms}
+++++++++mri_add_name [9]: {ENTRY (file=mri_add_name.c line=19) from mri_valpad_2D {328 ms}
---------mri_add_name [9]: EXIT} (file=mri_add_name.c line=24) to mri_valpad_2D {328 ms}
--------mri_valpad_2D [8]: EXIT} (file=mri_zeropad.c line=138) to SPLASH_imseq_getim {328 ms}
-------SPLASH_imseq_getim [7]: EXIT} (file=afni_splash.c line=484) to open_MCW_imseq {328 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from open_MCW_imseq {328 ms}
mri_free – call killpurge {328 ms}
++++++++mri_killpurge [8]: {ENTRY (file=mri_purger.c line=259) from mri_free {328 ms}
mri_killpurge – check if im==NULL ptr=0x7ff8d9501a00
mri_killpurge – can’t killpurge NULL fname! {328 ms}
--------mri_killpurge [8]: EXIT} (file=mri_purger.c line=270) to mri_free {328 ms}
mri_free – free ptr {328 ms}
mri_free – free im {328 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=67) to open_MCW_imseq {328 ms}
+++++++ISQ_record_button [7]: {ENTRY (file=imseq.c line=10962) from open_MCW_imseq {333 ms}
…
ISQ_record_button
open_MCW_imseq
SPLASH_popup_image
AFNI_splashup
MAIN_workprocess
AFNI:main
** AFNI compile date = Jun 26 2019
** [[Precompiled binary macos_10.12_local: Jun 26 2019]]
** Program Crash **
.cshrc file
if ( $?DYLD_LIBRARY_PATH ) then
setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace
else
setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace
endif
set path = ( $path /Users/whistu/abin )
if ( -f $HOME/.afni/help/all_progs.COMP ) then
source $HOME/.afni/help/all_progs.COMP
endif
set filec
set autolist
set nobeep
alias ls ls -G
alias ll ls -lG
I’m definitely missing Harma.