Hello,
I am trying to run my 3dISC script that includes my covariates and group factor levels. It keeps returning the following error:
updating R_LD_LIBRARY_PATH ...
Read 19956 items
Error in `[.data.frame`(lop$dataStr, , jj) : undefined columns selected
Calls: process.ISC.opts -> [ -> [.data.frame
In addition: Warning messages:
1: In process.ISC.opts(lop, verb = lop$verb) : NAs introduced by coercion
2: In FUN(X[[i]], ...) : NAs introduced by coercion
Execution halted
I have been doing some research on this and so far the only thing I have come across is this older topic: https://afni.nimh.nih.gov/afni/community/board/read.php?1,137476,137483 where the problem was fixed by changing the , in the qVars specification to a +. I have tried this but to no avail – it still returns the same error. I have also tried to run the file_tool to see if there are any bugs in my code, and there doesn’t seem to be, as I get this output:
file_tool -test -infile ./ISC_C_run.sh
file './ISC_C_run.sh': missing final newline
./ISC_C_run.sh has 0 bad characters
./ISC_C_run.sh file type: UNIX
I am not sure what the first line of the file_tool output means, so maybe it has to do with the “missing final newline”? In any case, I am have looked around again and I am not sure how to fix that, either.
This is my code from my script:
#!/bin/bash
3dISC -prefix ISC_C_nov24 -jobs 12 \
-r2z \
-model '0+grp+Age+Sex+(1|Subj1)+(1|Subj2)' \
-qVars 'Age,Sex' \
-gltCode ave '1/6 1/6 1/6 1/6 1/6 1/6' \
-gltCode G11 '1 0 0 0 0 0' \
-gltCode G12 '0 1 0 0 0 0' \
-gltCode G13 '0 0 1 0 0 0' \
-gltCode G22 '0 0 0 1 0 0' \
-gltCode G23 '0 0 0 0 1 0' \
-gltCode G33 '0 0 0 0 0 1' \
-gltCode G11vG22 '1 0 0 -1 0 0' \
-gltCode G11vG33 '1 0 0 0 0 -1' \
-gltCode G22vG33 '0 0 0 1 0 -1' \
-gltCode G11vG12+G13 '1 -0.5 -0.5 0 0 0' \
-gltCode G22vG12+G23 '0 -0.5 0 1 -0.5 0' \
-gltCode G33vG13+G23 '0 0 -0.5 0 -0.5 1' \
-dataTable @ISC_C_table.txt
and this is the header + first/last few lines from my dataTable (there is a total of 2850 pairs, for 76 subjects):
Subj1 Subj2 InputFile Age Sex grp \
1089001 1089002 TCorr1089001_1089002+orig 2.06 1 G12 \
1089001 1089004 TCorr1089001_1089004+orig 0.31 1 G12 \
1089001 1089005 TCorr1089001_1089005+orig 0.06 1 G22 \
...
1089682 1089685 TCorr1089682_1089685+orig 1.36 -1 G23 \
1089684 1089685 TCorr1089684_1089685+orig 2.04 -1 G33
Thanks!
Ryann