Hello,
I am using z shell (zsh) on a Mac. I am trying to run 3dISC after computing pairwise correlations between subjects using 3dTcorrelate.
The problem is that 3dISC prints the following error after I try running it.
Processing Interoception ...
updating R_LD_LIBRARY_PATH ...
** Error:
The content under -dataTable is not rectangular ! 761 3
Processing Exteroception ...
updating R_LD_LIBRARY_PATH ...
** Error:
The content under -dataTable is not rectangular ! 761 3
Processing Cognitive ...
updating R_LD_LIBRARY_PATH ...
** Error:
The content under -dataTable is not rectangular ! 761 3
The error has nothing to do with the for loop that I apply in my script, since when I remove the for loop, the error [quote=“The content under -dataTable is not rectangular ! 761 3”][/quote] remains.
I also ran
file_tool -test -infile ...
on my script. The result of that was
isc_list.txt has 0 bad characters
Here is my full script:
directory_rois=/volumes/sandisk2/fmri/dataset_1/processed/rois
directory_results=/volumes/sandisk2/fmri/dataset_1/processed/ISC
directory_data=/volumes/sandisk2/fmri/dataset_1/processed/ISC/Subject_correlation_pairs
cd $directory_data
rois=(Interoception Exteroception Cognitive)
for roi in $rois
do
echo "Processing $roi ..."
3dISC \
-jobs 12 \
-mask $directory_rois/$roi+tlrc \
-model "1+(1|Subj1)+(1|Subj2)" \
-prefix $directory_results/ISC_${roi} \
-dataTable \
Subj1 Subj2 InputFile \
s1 s2 Correlation_Subject1_Subject2+tlrc \
s1 s4 Correlation_Subject1_Subject4+tlrc \
s1 s5 Correlation_Subject1_Subject5+tlrc \
s1 s6 Correlation_Subject1_Subject6+tlrc \
s1 s7 Correlation_Subject1_Subject7+tlrc \
s1 s8 Correlation_Subject1_Subject8+tlrc \
s1 s9 Correlation_Subject1_Subject9+tlrc \
s1 s10 Correlation_Subject1_Subject10+tlrc \
s1 s11 Correlation_Subject1_Subject11+tlrc \
s1 s12 Correlation_Subject1_Subject12+tlrc \
s1 s13 Correlation_Subject1_Subject13+tlrc \
s1 s14 Correlation_Subject1_Subject14+tlrc \
s1 s15 Correlation_Subject1_Subject15+tlrc \
s1 s16 Correlation_Subject1_Subject16+tlrc \
s1 s17 Correlation_Subject1_Subject17+tlrc \
s1 s18 Correlation_Subject1_Subject18+tlrc \
s1 s19 Correlation_Subject1_Subject19+tlrc \
s1 s20 Correlation_Subject1_Subject20+tlrc \
s1 s22 Correlation_Subject1_Subject22+tlrc \
s1 s23 Correlation_Subject1_Subject23+tlrc \
s1 s24 Correlation_Subject1_Subject24+tlrc \
s1 s25 Correlation_Subject1_Subject25+tlrc \
s2 s4 Correlation_Subject2_Subject4+tlrc \
s2 s5 Correlation_Subject2_Subject5+tlrc \
s2 s6 Correlation_Subject2_Subject6+tlrc \
s2 s7 Correlation_Subject2_Subject7+tlrc \
s2 s8 Correlation_Subject2_Subject8+tlrc \
s2 s9 Correlation_Subject2_Subject9+tlrc \
s2 s10 Correlation_Subject2_Subject10+tlrc \
s2 s11 Correlation_Subject2_Subject11+tlrc \
s2 s12 Correlation_Subject2_Subject12+tlrc \
s2 s13 Correlation_Subject2_Subject13+tlrc \
s2 s14 Correlation_Subject2_Subject14+tlrc \
s2 s15 Correlation_Subject2_Subject15+tlrc \
s2 s16 Correlation_Subject2_Subject16+tlrc \
s2 s17 Correlation_Subject2_Subject17+tlrc \
s2 s18 Correlation_Subject2_Subject18+tlrc \
s2 s19 Correlation_Subject2_Subject19+tlrc \
s2 s20 Correlation_Subject2_Subject20+tlrc \
s2 s22 Correlation_Subject2_Subject22+tlrc \
s2 s23 Correlation_Subject2_Subject23+tlrc \
s2 s24 Correlation_Subject2_Subject24+tlrc \
s2 s25 Correlation_Subject2_Subject25+tlrc \
s4 s5 Correlation_Subject4_Subject5+tlrc \
s4 s6 Correlation_Subject4_Subject6+tlrc \
s4 s7 Correlation_Subject4_Subject7+tlrc \
s4 s8 Correlation_Subject4_Subject8+tlrc \
s4 s9 Correlation_Subject4_Subject9+tlrc \
s4 s10 Correlation_Subject4_Subject10+tlrc \
s4 s11Correlation_Subject4_Subject11+tlrc \
s4 s12 Correlation_Subject4_Subject12+tlrc \
s4 s13 Correlation_Subject4_Subject13+tlrc \
s4 s14 Correlation_Subject4_Subject14+tlrc \
s4 s15 Correlation_Subject4_Subject15+tlrc \
s4 s16 Correlation_Subject4_Subject16+tlrc \
s4 s17 Correlation_Subject4_Subject17+tlrc \
s4 s18 Correlation_Subject4_Subject18+tlrc \
s4 s19 Correlation_Subject4_Subject19+tlrc \
s4 s20 Correlation_Subject4_Subject20+tlrc \
s4 s22 Correlation_Subject4_Subject22+tlrc \
s4 s23 Correlation_Subject4_Subject23+tlrc \
s4 s24 Correlation_Subject4_Subject24+tlrc \
s4 s25 Correlation_Subject4_Subject25+tlrc \
s5 s6 Correlation_Subject5_Subject6+tlrc \
s5 s7 Correlation_Subject5_Subject7+tlrc \
s5 s8 Correlation_Subject5_Subject8+tlrc \
s5 s9 Correlation_Subject5_Subject9+tlrc \
s5 s10 Correlation_Subject5_Subject10+tlrc \
s5 s11 Correlation_Subject5_Subject11+tlrc \
s5 s12 Correlation_Subject5_Subject12+tlrc \
s5 s13 Correlation_Subject5_Subject13+tlrc \
s5 s14 Correlation_Subject5_Subject14+tlrc \
s5 s15 Correlation_Subject5_Subject15+tlrc \
s5 s16 Correlation_Subject5_Subject16+tlrc \
s5 s17 Correlation_Subject5_Subject17+tlrc \
s5 s18 Correlation_Subject5_Subject18+tlrc \
s5 s19 Correlation_Subject5_Subject19+tlrc \
s5 s20 Correlation_Subject5_Subject20+tlrc \
s5 s22 Correlation_Subject5_Subject22+tlrc \
s5 s23 Correlation_Subject5_Subject23+tlrc \
s5 s24 Correlation_Subject5_Subject24+tlrc \
s5 s25 Correlation_Subject5_Subject25+tlrc \
s6 s7 Correlation_Subject6_Subject7+tlrc \
s6 s8 Correlation_Subject6_Subject8+tlrc \
s6 s9 Correlation_Subject6_Subject9+tlrc \
s6 s10 Correlation_Subject6_Subject10+tlrc \
s6 s11 Correlation_Subject6_Subject11+tlrc \
s6 s12 Correlation_Subject6_Subject12+tlrc \
s6 s13 Correlation_Subject6_Subject13+tlrc \
s6 s14 Correlation_Subject6_Subject14+tlrc \
s6 s15 Correlation_Subject6_Subject15+tlrc \
s6 s16 Correlation_Subject6_Subject16+tlrc \
s6 s17 Correlation_Subject6_Subject17+tlrc \
s6 s18 Correlation_Subject6_Subject18+tlrc \
s6 s19 Correlation_Subject6_Subject19+tlrc \
s6 s20 Correlation_Subject6_Subject20+tlrc \
s6 s22 Correlation_Subject6_Subject22+tlrc \
s6 s23 Correlation_Subject6_Subject23+tlrc \
s6 s24 Correlation_Subject6_Subject24+tlrc \
s6 s25 Correlation_Subject6_Subject25+tlrc \
s7 s8 Correlation_Subject7_Subject8+tlrc \
s7 s9 Correlation_Subject7_Subject9+tlrc \
s7 s10 Correlation_Subject7_Subject10+tlrc \
s7 s11 Correlation_Subject7_Subject11+tlrc \
s7 s12 Correlation_Subject7_Subject12+tlrc \
s7 s13 Correlation_Subject7_Subject13+tlrc \
s7 s14 Correlation_Subject7_Subject14+tlrc \
s7 s15 Correlation_Subject7_Subject15+tlrc \
s7 s16 Correlation_Subject7_Subject16+tlrc \
s7 s17 Correlation_Subject7_Subject17+tlrc \
s7 s18 Correlation_Subject7_Subject18+tlrc \
s7 s19 Correlation_Subject7_Subject19+tlrc \
s7 s20 Correlation_Subject7_Subject20+tlrc \
s7 s22 Correlation_Subject7_Subject22+tlrc \
s7 s23 Correlation_Subject7_Subject23+tlrc \
s7 s24 Correlation_Subject7_Subject24+tlrc \
s7 s25 Correlation_Subject7_Subject25+tlrc \
s8 s9 Correlation_Subject8_Subject9+tlrc \
s8 s10 Correlation_Subject8_Subject10+tlrc \
s8 s11 Correlation_Subject8_Subject11+tlrc \
s8 s12 Correlation_Subject8_Subject12+tlrc \
s8 s13 Correlation_Subject8_Subject13+tlrc \
s8 s14 Correlation_Subject8_Subject14+tlrc \
s8 s15 Correlation_Subject8_Subject15+tlrc \
s8 s16 Correlation_Subject8_Subject16+tlrc \
s8 s17 Correlation_Subject8_Subject17+tlrc \
s8 s18 Correlation_Subject8_Subject18+tlrc \
s8 s19 Correlation_Subject8_Subject19+tlrc \
s8 s20 Correlation_Subject8_Subject20+tlrc \
s8 s22 Correlation_Subject8_Subject22+tlrc \
s8 s23 Correlation_Subject8_Subject23+tlrc \
s8 s24 Correlation_Subject8_Subject24+tlrc \
s8 s25 Correlation_Subject8_Subject25+tlrc \
s9 s10 Correlation_Subject9_Subject10+tlrc \
s9 s11 Correlation_Subject9_Subject11+tlrc \
s9 s12 Correlation_Subject9_Subject12+tlrc \
s9 s13 Correlation_Subject9_Subject13+tlrc \
s9 s14 Correlation_Subject9_Subject14+tlrc \
s9 s15 Correlation_Subject9_Subject15+tlrc \
s9 s16 Correlation_Subject9_Subject16+tlrc \
s9 s17 Correlation_Subject9_Subject17+tlrc \
s9 s18 Correlation_Subject9_Subject18+tlrc \
s9 s19 Correlation_Subject9_Subject19+tlrc \
s9 s20 Correlation_Subject9_Subject20+tlrc \
s9 s22 Correlation_Subject9_Subject22+tlrc \
s9 s23 Correlation_Subject9_Subject23+tlrc \
s9 s24 Correlation_Subject9_Subject24+tlrc \
s9 s25 Correlation_Subject9_Subject25+tlrc \
s10 s11 Correlation_Subject10_Subject11+tlrc \
s10 s12 Correlation_Subject10_Subject12+tlrc \
s10 s13 Correlation_Subject10_Subject13+tlrc \
s10 s14 Correlation_Subject10_Subject14+tlrc \
s10 s15 Correlation_Subject10_Subject15+tlrc \
s10 s16 Correlation_Subject10_Subject16+tlrc \
s10 s17 Correlation_Subject10_Subject17+tlrc \
s10 s18 Correlation_Subject10_Subject18+tlrc \
s10 s19 Correlation_Subject10_Subject19+tlrc \
s10 s20 Correlation_Subject10_Subject20+tlrc \
s10 s22 Correlation_Subject10_Subject22+tlrc \
s10 s23 Correlation_Subject10_Subject23+tlrc \
s10 s24 Correlation_Subject10_Subject24+tlrc \
s10 s25 Correlation_Subject10_Subject25+tlrc \
s11 s12 Correlation_Subject11_Subject12+tlrc \
s11 s13 Correlation_Subject11_Subject13+tlrc \
s11 s14 Correlation_Subject11_Subject14+tlrc \
s11 s15 Correlation_Subject11_Subject15+tlrc \
s11 s16 Correlation_Subject11_Subject16+tlrc \
s11 s17 Correlation_Subject11_Subject17+tlrc \
s11 s18 Correlation_Subject11_Subject18+tlrc \
s11 s19 Correlation_Subject11_Subject19+tlrc \
s11 s20 Correlation_Subject11_Subject20+tlrc \
s11 s22 Correlation_Subject11_Subject22+tlrc \
s11 s23 Correlation_Subject11_Subject23+tlrc \
s11 s24 Correlation_Subject11_Subject24+tlrc \
s11 s25 Correlation_Subject11_Subject25+tlrc \
s12 s13 Correlation_Subject12_Subject13+tlrc \
s12 s14 Correlation_Subject12_Subject14+tlrc \
s12 s15 Correlation_Subject12_Subject15+tlrc \
s12 s16 Correlation_Subject12_Subject16+tlrc \
s12 s17 Correlation_Subject12_Subject17+tlrc \
s12 s18 Correlation_Subject12_Subject18+tlrc \
s12 s19 Correlation_Subject12_Subject19+tlrc \
s12 s20 Correlation_Subject12_Subject20+tlrc \
s12 s22 Correlation_Subject12_Subject22+tlrc \
s12 s23 Correlation_Subject12_Subject23+tlrc \
s12 s24 Correlation_Subject12_Subject24+tlrc \
s12 s25 Correlation_Subject12_Subject25+tlrc \
s13 s14 Correlation_Subject13_Subject14+tlrc \
s13 s15 Correlation_Subject13_Subject15+tlrc \
s13 s16 Correlation_Subject13_Subject16+tlrc \
s13 s17 Correlation_Subject13_Subject17+tlrc \
s13 s18 Correlation_Subject13_Subject18+tlrc \
s13 s19 Correlation_Subject13_Subject19+tlrc \
s13 s20 Correlation_Subject13_Subject20+tlrc \
s13 s22 Correlation_Subject13_Subject22+tlrc \
s13 s23 Correlation_Subject13_Subject23+tlrc \
s13 s24 Correlation_Subject13_Subject24+tlrc \
s13 s25 Correlation_Subject13_Subject25+tlrc \
s14 s15 Correlation_Subject14_Subject15+tlrc \
s14 s16 Correlation_Subject14_Subject16+tlrc \
s14 s17 Correlation_Subject14_Subject17+tlrc \
s14 s18 Correlation_Subject14_Subject18+tlrc \
s14 s19 Correlation_Subject14_Subject19+tlrc \
s14 s20 Correlation_Subject14_Subject20+tlrc \
s14 s22 Correlation_Subject14_Subject22+tlrc \
s14 s23 Correlation_Subject14_Subject23+tlrc \
s14 s24 Correlation_Subject14_Subject24+tlrc \
s14 s25 Correlation_Subject14_Subject25+tlrc \
s15 s16 Correlation_Subject15_Subject16+tlrc \
s15 s17 Correlation_Subject15_Subject17+tlrc \
s15 s18 Correlation_Subject15_Subject18+tlrc \
s15 s19 Correlation_Subject15_Subject19+tlrc \
s15 s20 Correlation_Subject15_Subject20+tlrc \
s15 s22 Correlation_Subject15_Subject22+tlrc \
s15 s23 Correlation_Subject15_Subject23+tlrc \
s15 s24 Correlation_Subject15_Subject24+tlrc \
s15 s25 Correlation_Subject15_Subject25+tlrc \
s16 s17 Correlation_Subject16_Subject17+tlrc \
s16 s18 Correlation_Subject16_Subject18+tlrc \
s16 s19 Correlation_Subject16_Subject19+tlrc \
s16 s20 Correlation_Subject16_Subject20+tlrc \
s16 s22 Correlation_Subject16_Subject22+tlrc \
s16 s23 Correlation_Subject16_Subject23+tlrc \
s16 s24 Correlation_Subject16_Subject24+tlrc \
s16 s25 Correlation_Subject16_Subject25+tlrc \
s17 s18 Correlation_Subject17_Subject18+tlrc \
s17 s19 Correlation_Subject17_Subject19+tlrc \
s17 s20 Correlation_Subject17_Subject20+tlrc \
s17 s22 Correlation_Subject17_Subject22+tlrc \
s17 s23 Correlation_Subject17_Subject23+tlrc \
s17 s24 Correlation_Subject17_Subject24+tlrc \
s17 s25 Correlation_Subject17_Subject25+tlrc \
s18 s19 Correlation_Subject18_Subject19+tlrc \
s18 s20 Correlation_Subject18_Subject20+tlrc \
s18 s22 Correlation_Subject18_Subject22+tlrc \
s18 s23 Correlation_Subject18_Subject23+tlrc \
s18 s24 Correlation_Subject18_Subject24+tlrc \
s18 s25 Correlation_Subject18_Subject25+tlrc \
s19 s20 Correlation_Subject19_Subject20+tlrc \
s19 s22 Correlation_Subject19_Subject22+tlrc \
s19 s23 Correlation_Subject19_Subject23+tlrc \
s19 s24 Correlation_Subject19_Subject24+tlrc \
s19 s25 Correlation_Subject19_Subject25+tlrc \
s20 s22 Correlation_Subject20_Subject22+tlrc \
s20 s23 Correlation_Subject20_Subject23+tlrc \
s20 s24 Correlation_Subject20_Subject24+tlrc \
s20 s25 Correlation_Subject20_Subject25+tlrc \
s22 s23 Correlation_Subject22_Subject23+tlrc \
s22 s24 Correlation_Subject22_Subject24+tlrc \
s22 s25 Correlation_Subject22_Subject25+tlrc \
s23 s24 Correlation_Subject23_Subject24+tlrc \
s23 s25 Correlation_Subject22_Subject25+tlrc \
s24 s25 Correlation_Subject24_Subject25+tlrc
done
Any ideas where the mistake could be? And why does it always try to run
updating R_LD_LIBRARY_PATH …
?
The r packages lme4 and snow are installed, both via the terminal and in R.