Hello,
I am trying to run 3dLME on our local lab mac machine that has had various versions of afni installed on it throughout the years. I recently updated the software to allow for needed R version and packages to be installed and updated our afni binaries. I also updated all other programs, such as homebrew, xcode, and x11. When I run the code, it doesn't produce an error, just returns a new command line.
I believe I've narrowed it down to this error:
When I run afni_system_check.py -check_all to see what's gone wrong, I consistently get the following error:
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 : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/Users/DSNLab/abin/R_io.so':
dlopen(/Users/DSNLab/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/DSNLab/abin/R_io.so
Reason: image not found
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted
I've gone through prior message board posts and have tried different versions of the update afni binaries (and made sure other programs associated with afni were updated, but the error remains. Do you have other recommendations of what could be going wrong? Since this is a shard computer, could there be issues of multiple afni copies or things I'm not seeing/knowing to look for?
I'm also attaching the top of our 3dLME script below incase there is another issue as to why the script won't run. (As for the F test, I just made an example one quickly to see if I could get the script to run, not necessarily interested in that f test. )
Thank you so much for your help!
#!/bin/bash
#---------------------------
#
cd /Volumes/DSNLab/NeuroTeen/analysis/Shapes/Shapes_3dLME_test \
3dLME -prefix 3dLME_v1 \
-model "reward*punishment*grade" \
-resid grade_resids \
-ranEff '~1+grade_c' \
-SS_type 3 \
-qVars "grade_c" \
-qVarsCenters "0,0" \
-mask \
-num_glf 1 \
-glfLabel 1 'Ant_grade' -glfCode 1 'Ant : 1*rew & 1*pun grade_c :' \
-dataTable \
Subj Ant grade_c age wave Inputfile \
001 rew 1 12.96 wave1 /Volume/DSNLab/NeuroTeen/subs/wave1/NT1001/con_001.nii \
001 pun 1 12.96 wave1 /Volume/DSNLab/NeuroTeen/subs/wave1/NT1001/con_002.nii \
001 neu 1 12.96 wave1 /Volume/DSNLab/NeuroTeen/subs/wave1/NT1001/con_003.nii \
003 rew 1 12.76 wave1 /Volume/DSNLab/NeuroTeen/subs/wave1/NT1003/con_001.nii \
003 pun 1 12.76 wave1 /Volume/DSNLab/NeuroTeen/subs/wave1/NT1003/con_002.nii \
003 neu 1 12.76 wave1 /Volume/DSNLab/NeuroTeen/subs/wave1/NT1003/con_003.nii \
003 rew 3 15.16 wave3 /Volume/DSNLab/NeuroTeen/subs/wave3/NT3003/con_001.nii \
003 pun 3 15.16 wave3 /Volume/DSNLab/NeuroTeen/subs/wave3/NT3003/con_002.nii \
003 neu 3 15.16 wave3 /Volume/DSNLab/NeuroTeen/subs/wave3/NT3003/con_003.nii \
004 rew 1 13.07 wave1 /Volume/DSNLab/NeuroTeen/subs/wave1/NT1004/con_001.nii \
004 pun 1 13.07 wave1 /Volume/DSNLab/NeuroTeen/subs/wave1/NT1004/con_002.nii \
004 neu 1 13.07 wave1 /Volume/DSNLab/NeuroTeen/subs/wave1/NT1004/con_003.nii \
005 rew 1 12.50 wave1 /Volume/DSNLab/NeuroTeen/subs/wave1/NT1005/con_001.nii \
005 pun 1 12.50 wave1 /Volume/DSNLab/NeuroTeen/subs/wave1/NT1005/con_002.nii \
005 neu 1 12.50 wave1 /Volume/DSNLab/NeuroTeen/subs/wave1/NT1005/con_003.nii \
005 rew 2 13.47 wave2 /Volume/DSNLab/NeuroTeen/subs/wave2/NT2005/con_001.nii \
005 pun 2 13.47 wave2 /Volume/DSNLab/NeuroTeen/subs/wave2/NT2005/con_002.nii \
005 neu 2 13.47 wave2 /Volume/DSNLab/NeuroTeen/subs/wave2/NT2005/con_003.nii \
005 rew 3 14.58 wave3 /Volume/DSNLab/NeuroTeen/subs/wave3/NT3005/con_001.nii \
005 pun 3 14.58 wave3 /Volume/DSNLab/NeuroTeen/subs/wave3/NT3005/con_002.nii \
