I get this error when running my group’s fMRI processing pipeline:
3ddot -dodice full_mask.p249+orig mask_anat.p249+orig
tee out.mask_ae_dice.txt
dyld: Library not loaded: /sw/lib/libjpeg.9.dylib
Referenced from: /Users/witherscp/abin/3ddot
Reason: image not found
Abort
When I run “afni_system_check.py -check_all”, this is my output:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Mon Apr 18 21:50:40 PDT 2022; root:xnu-6153.141.62~1/RELEASE_X86_64
distribution: 10.15.7
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/witherscp/abin/afni
afni version : Precompiled binary macos_10.12_local: Jun 24 2022
: AFNI_22.1.14 'Antoninus Pius'
AFNI_version.txt : AFNI_22.1.14, macos_10.12_local, Jun 24 2022
which python : /Users/witherscp/anaconda3/bin/python
python version : 3.8.12
which R : /usr/local/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/witherscp/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 2
/Users/witherscp/anaconda3/bin/python3.8
/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
/Users/witherscp/anaconda3/bin/python3.8
/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 : /Users/witherscp/anaconda3/lib/python3.8/site-packages/matplotlib/pyplot.py
matplotlib version : 3.3.4
-------------------------------- env vars --------------------------------
PATH = /opt/local/bin:/opt/local/sbin:/Users/witherscp/anaconda3/bin:/Users/witherscp/anaconda3/condabin:/Users/witherscp/TORTOISE_V3.2.0/DRTAMASV320/bin:/Users/witherscp/TORTOISE_V3.2.0/DRBUDDIV320/bin:/Users/witherscp/TORTOISE_V3.2.0/DIFFCALC/DIFFCALCV320:/Users/witherscp/TORTOISE_V3.2.0/DIFFPREPV320/bin/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/Users/witherscp/abin:/Applications/MATLAB_R2021a.app/bin
PYTHONPATH = :/Volumes/shares/NEU/Users/price
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH = /Applications/freesurfer/lib/gcc/lib::/opt/X11/lib/flat_namespace:/Users/witherscp/TORTOISE_V3.2.0/DRBUDDIV320/bin
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (954004M Avail)
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: ...ct 2020 [taylorp]: updated scripts under FATCAT_DEMO
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/witherscp/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.1
which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.16
which port : /opt/local/bin/port
port version : Version: 2.7.2
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
-- consider installing gcc under homebrew
** consider linking /usr/local/Cellar/glib/2.58.3/lib/libglib-2.0.dylib under /usr/local/lib
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
++ yay, env var DYLD_LIBRARY_PATH contains /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
I have never encountered this problem before. Do you know how to fix this?