Dear AFNI expert,
I'm still struggling with the error during runing of SEM script on FC-7 64bit
After change shell from bash to tcsh, the error message was slightly changed. But fatal error still showed up.
Please give me any kind of comment.
thanks,
Sean
This below is the error message.
[root@gwd TimeSeries]# tcsh -x AFNI_SEM_script_treegrowth.csh subj1.1D subj2.1D thetas3.1D
-------- freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.5 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
SUBJECTS_DIR /usr/local/freesurfer/subjects
MNI_DIR /usr/local/freesurfer/mni
GSL_DIR /usr/local/freesurfer/lib/gsl
FSL_DIR /usr/local/fsl
@ last = 3 - 1
set minModel = thetas3.1D
set subj_dsets = ( subj1.1D subj2.1D )
set NSUBJS = 2
glob subj1.1D subj2.1D
subj1.1Dsubj2.1Decho
set NVALS = `1dcat ${subj_dsets[1]}'[0]' | wc -l`
1dcat subj1.1D[0]
wc -l
set NROIS = `1dcat ${subj_dsets[1]}'{0}' | wc -w`
1dcat subj1.1D{0}
wc -w
@ NP = 250 + 2
@ NVM1 = 250 - 2
rm: No match.
rm: No match.
rm -i -f SEM_svd_roi0001.txt SEM_svd_roi0002.txt SEM_svd_roi0003.txt
rm -i -f SEM_eigents_roi0001.1D SEM_eigents_roi0002.1D SEM_eigents_roi0003.1D
rm -i -f SEM_sv_roi0001.1D SEM_sv_roi0002.1D SEM_sv_roi0003.1D
rm -i -f SEM_sv2_roi0001.1D SEM_sv2_roi0002.1D SEM_sv2_roi0003.1D
rm -i -f SEM_resvar.1D
rm -i -f SEM_resvarcorr.1D
rm: No match.
rm -i -f SEM_ts_mean_roi0001.1D SEM_ts_mean_roi0002.1D SEM_ts_mean_roi0003.1D
rm -i -f SEM_eigentsc_roi0001.1D SEM_eigentsc_roi0002.1D SEM_eigentsc_roi0003.1D
rm -i -f SEM_autocorr.1D
rm -i -f SEM_cov.1D
rm -i -f SEM_corr.1D
rm -i -f SEM_temp.1D
rm -i -f SEM_DF.1D
foreach roi ( `count 1 $NROIS` )
count 1 3
@ roi_index = 0001 - 1
foreach subj ( `count 1 $NSUBJS` )
count 1 2
1dcat subj1.1D[0]
end
1dcat subj2.1D[0]
end
1dcat SEM_roi0001_subj0001_extract.1D SEM_roi0001_subj0002_extract.1D
1dsvd SEM_roi0001_allsubjs.1D
grep -A 252 -m 1 ++ Left Vectors SEM_svd_roi0001.txt
tail -250
tr -d :
1dcat SEM_temp.1D[1]
grep -A 1 -m 1 ++ Left Vectors SEM_svd_roi0001.txt
tail -1
1dtranspose SEM_temp.1D
1deval -a SEM_sv_roi0001.1D -expr a*a
3dTstat -sum -prefix SEM_resvar_roi0001 SEM_sv2_roi0001.1D{1..$}'
++ 3dTstat: AFNI version=AFNI_2007_05_29_1644 (Aug 10 2007) [64-bit]
++ Authored by: KR Hammett & RW Cox
** FATAL ERROR: Can't use dataset with < 2 values per voxel!
1dcat SEM_resvar_roi0001.1D
** Can't read input file SEM_resvar_roi0001.1D
set s1 = `1dcat SEM_sv2_roi${roi}.1D'{0}'`
1dcat SEM_sv2_roi0001.1D{0}
set ssum = `1dcat SEM_resvar_roi${roi}.1D`
1dcat SEM_resvar_roi0001.1D
** Can't read input file SEM_resvar_roi0001.1D
ccalc -expr 1- 0.113707/ (+0.113707)
3dMean -prefix SEM_ts_mean_roi0001 SEM_roi0001_subj0001_extract.1D SEM_roi0001_subj0002_extract.1D
++ 3dMean: AFNI version=AFNI_2007_05_29_1644 (Aug 10 2007) [64-bit]
set dotp = `3ddot -dodot SEM_eigents_roi${roi}.1D SEM_ts_mean_roi${roi}.1D`
3ddot -dodot SEM_eigents_roi0001.1D SEM_ts_mean_roi0001.1D
1deval -a SEM_eigents_roi0001.1D -expr step(-0.154167)*(-a)+step(0.154167)*a
3ddot -demean SEM_eigentsc_roi0001.1D{0..248} SEM_eigentsc_roi0001.1D{1..$}
end
@ roi_index = 0002 - 1
foreach subj ( `count 1 $NSUBJS` )
count 1 2
1dcat subj1.1D[1]
end
1dcat subj2.1D[1]
end
1dcat SEM_roi0002_subj0001_extract.1D SEM_roi0002_subj0002_extract.1D
1dsvd SEM_roi0002_allsubjs.1D
grep -A 252 -m 1 ++ Left Vectors SEM_svd_roi0002.txt
tail -250
tr -d :
1dcat SEM_temp.1D[1]
grep -A 1 -m 1 ++ Left Vectors SEM_svd_roi0002.txt
tail -1
1dtranspose SEM_temp.1D
1deval -a SEM_sv_roi0002.1D -expr a*a
3dTstat -sum -prefix SEM_resvar_roi0002 SEM_sv2_roi0002.1D{1..$}'
++ 3dTstat: AFNI version=AFNI_2007_05_29_1644 (Aug 10 2007) [64-bit]
++ Authored by: KR Hammett & RW Cox
** FATAL ERROR: Can't use dataset with < 2 values per voxel!
1dcat SEM_resvar_roi0002.1D
** Can't read input file SEM_resvar_roi0002.1D
set s1 = `1dcat SEM_sv2_roi${roi}.1D'{0}'`
1dcat SEM_sv2_roi0002.1D{0}
set ssum = `1dcat SEM_resvar_roi${roi}.1D`
1dcat SEM_resvar_roi0002.1D
** Can't read input file SEM_resvar_roi0002.1D
ccalc -expr 1- 0.0559729/ (+0.0559729)
3dMean -prefix SEM_ts_mean_roi0002 SEM_roi0002_subj0001_extract.1D SEM_roi0002_subj0002_extract.1D
++ 3dMean: AFNI version=AFNI_2007_05_29_1644 (Aug 10 2007) [64-bit]
set dotp = `3ddot -dodot SEM_eigents_roi${roi}.1D SEM_ts_mean_roi${roi}.1D`
3ddot -dodot SEM_eigents_roi0002.1D SEM_ts_mean_roi0002.1D
1deval -a SEM_eigents_roi0002.1D -expr step(-0.167292)*(-a)+step(0.167292)*a
3ddot -demean SEM_eigentsc_roi0002.1D{0..248} SEM_eigentsc_roi0002.1D{1..$}
end
@ roi_index = 0003 - 1
foreach subj ( `count 1 $NSUBJS` )
count 1 2
1dcat subj1.1D[2]
end
1dcat subj2.1D[2]
end
1dcat SEM_roi0003_subj0001_extract.1D SEM_roi0003_subj0002_extract.1D
1dsvd SEM_roi0003_allsubjs.1D
grep -A 252 -m 1 ++ Left Vectors SEM_svd_roi0003.txt
tail -250
tr -d :
1dcat SEM_temp.1D[1]
grep -A 1 -m 1 ++ Left Vectors SEM_svd_roi0003.txt
tail -1
1dtranspose SEM_temp.1D
1deval -a SEM_sv_roi0003.1D -expr a*a
3dTstat -sum -prefix SEM_resvar_roi0003 SEM_sv2_roi0003.1D{1..$}'
++ 3dTstat: AFNI version=AFNI_2007_05_29_1644 (Aug 10 2007) [64-bit]
++ Authored by: KR Hammett & RW Cox
** FATAL ERROR: Can't use dataset with < 2 values per voxel!
1dcat SEM_resvar_roi0003.1D
** Can't read input file SEM_resvar_roi0003.1D
set s1 = `1dcat SEM_sv2_roi${roi}.1D'{0}'`
1dcat SEM_sv2_roi0003.1D{0}
set ssum = `1dcat SEM_resvar_roi${roi}.1D`
1dcat SEM_resvar_roi0003.1D
** Can't read input file SEM_resvar_roi0003.1D
ccalc -expr 1- 0.0095925/ (+0.0095925)
3dMean -prefix SEM_ts_mean_roi0003 SEM_roi0003_subj0001_extract.1D SEM_roi0003_subj0002_extract.1D
++ 3dMean: AFNI version=AFNI_2007_05_29_1644 (Aug 10 2007) [64-bit]
set dotp = `3ddot -dodot SEM_eigents_roi${roi}.1D SEM_ts_mean_roi${roi}.1D`
3ddot -dodot SEM_eigents_roi0003.1D SEM_ts_mean_roi0003.1D
1deval -a SEM_eigents_roi0003.1D -expr step(-0.0660108)*(-a)+step(0.0660108)*a
3ddot -demean SEM_eigentsc_roi0003.1D{0..248} SEM_eigentsc_roi0003.1D{1..$}
end
1ddot -dem -cov -terse SEM_eigentsc_roi0001.1D SEM_eigentsc_roi0002.1D SEM_eigentsc_roi0003.1D
1ddot -dem -terse SEM_eigentsc_roi0001.1D SEM_eigentsc_roi0002.1D SEM_eigentsc_roi0003.1D
1deval -a SEM_autocorr.1D -expr (250 / 3) * (1-a)/(1+a)
3dTstat -prefix SEM_DF -sum SEM_temp.1D'
++ 3dTstat: AFNI version=AFNI_2007_05_29_1644 (Aug 10 2007) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
++ Output dataset ./SEM_DF.1D
set DF = `1dcat SEM_DF.1D`
1dcat SEM_DF.1D
1dSEM -theta thetas3.1D -C SEM_corr.1D -DF 75.0068 -psi SEM_resvarcorr.1D -tree_growth -limits -2 2
++ 1dSEM: AFNI version=AFNI_2007_05_29_1644 (Aug 10 2007) [64-bit]
++ Authored by: Daniel Glen, Gang Chen
** FATAL ERROR: Can not compute inverse of variance vector
rm -i -f SEM_temp.1D
rm -i -f SEM_roi0001_subj0001_extract.1D SEM_roi0001_subj0002_extract.1D SEM_roi0002_subj0001_extract.1D SEM_roi0002_subj0002_extract.1D SEM_roi0003_subj0001_extract.1D SEM_roi0003_subj0002_extract.1D
rm -i -f SEM_roi0001_allsubjs.1D SEM_roi0002_allsubjs.1D SEM_roi0003_allsubjs.1D
