Hello, my 3dLME .txt file contains the following lines of code (this is a shorter version of my full dataset):

3dLME -prefix Example4 -jobs 24 \
-mask myMask+tlrc \
-model "cond*group" \
-ranEff '~1' \
-SS_type 3 \
-num_glt 2 \
-gltLabel 1 'neg-pos' -gltCode 1 'cond : 1*neg -1*pos' \
-gltLabel 2 'pat_neg-pos' -gltCode 2 'cond : 1*neg -1*pos group : 1*pat' \
-dataTable \
Subj cond group InputFile \
s10058 pos ctr ctlNeutral_10058_Larea11.z.nii \
s10058 neg ctr ctlStrong_10058_Larea11.z.nii \
s10210 pos ctr ctlNeutral_10210_Larea11.z.nii \
s10210 neg ctr ctlStrong_10210_Larea11.z.nii \
s14061 pos ctr ctlNeutral_14061_Larea11.z.nii \
s14061 neg ctr ctlStrong_14061_Larea11.z.nii \
s11366 pos pat ocdNeutral_11366_Larea11.z.nii \
s11366 neg pat ocdStrong_11366_Larea11.z.nii \
s18526 pos pat ocdNeutral_18526_Larea11.z.nii \
s18526 neg pat ocdStrong_18526_Larea11.z.nii \
s20718 pos pat ocdNeutral_20718_Larea11.z.nii \
s20718 neg pat ocdStrong_20718_Larea11.z.nii \
...


When running the code using tcsh -x [myfile].txt I'm receiving the following error:
3dLME -prefix Example4 -jobs 24
Error in if (len%%wd != 0) errex.AFNI(paste("The content under -dataTable is not rectangular !", :
argument is of length zero
Calls: process.LME.opts
Execution halted
-mask myMask+tlrc
-mask: Command not found.
-model cond*group
-model: Command not found.
-ranEff ~1
-ranEff: Command not found.
-SS_type 3
-SS_type: Command not found.
-num_glt 2
-num_glt: Command not found.
-gltLabel 1 pos-neg -gltCode 1 cond : 1*pos -1*neg
-gltLabel: Command not found.
-gltLabel 2 pat_pos-neg -gltCode 2 cond : 1*pos -1*neg group : 1*pat
-gltLabel: Command not found.
-dataTable
-dataTable: Command not found.
Subj cond group InputFile
Subj: Command not found.
s10058 pos ctr ctlNeutral_10058_Larea11.z.nii
s10058: Command not found.
s10058 neg ctr ctlStrong_10058_Larea11.z.nii
s10058: Command not found.
s10210 pos ctr ctlNeutral_10210_Larea11.z.nii
s10210: Command not found.
s10210 neg ctr ctlStrong_10210_Larea11.z.nii
s10210: Command not found.
s14061 pos ctr ctlNeutral_14061_Larea11.z.nii
s14061: Command not found.
s14061 neg ctr ctlStrong_14061_Larea11.z.nii
s14061: Command not found.
s11366 pos pat ocdNeutral_11366_Larea11.z.nii
s11366: Command not found.
s11366 neg pat ocdStrong_11366_Larea11.z.nii
s11366: Command not found.
s18526 pos pat ocdNeutral_18526_Larea11.z.nii
s18526: Command not found.
s18526 neg pat ocdStrong_18526_Larea11.z.nii
s18526: Command not found.
s20718 pos pat ocdNeutral_20718_Larea11.z.nii
s20718: Command not found.
s20718 neg pat ocdStrong_20718_Larea11.z.nii
s20718: Command not found.
...


I suppose the main error is that my data table is not rectangular.

To get more insight I've used file_tool -test -infile [myfile].txt which showed me I had bad backslashes. I fixed these bad backslashes using

file_tool -show_file_type -infile [old_file].txt -prefix [fixed_file].txt

However, after running the new fixed file, I'm still getting an error:

#3dLME -prefix Example4 -jobs 24 -mask myMask+tlrc -model cond*group -ranEff ~1 -SS_type 3 -num_glt 2 -gltLabel 1 neg-pos -gltCode 1 cond : 1*neg -1*pos -gltLabel 2 pat_neg-pos -gltCode 2 cond : 1*neg -1*pos group : 1*pat -dataTable Subj cond group InputFile s10058 pos ctr ctlNeutral_10058_Larea11.z.nii s10058 neg ctr ctlStrong_10058_Larea11.z.nii s10210 pos ctr ctlNeutral_10210_Larea11.z.nii s10210 neg ctr ctlStrong_10210_Larea11.z.nii s14061 pos ctr ctlNeutral_14061_Larea11.z.nii s14061 neg ctr ctlStrong_14061_Larea11.z.nii s11366 pos pat ocdNeutral_11366_Larea11.z.nii s11366 neg pat ocdStrong_11366_Larea11.z.nii s18526 pos pat ocdNeutral_18526_Larea11.z.nii s18526 neg pat ocdStrong_18526_Larea11.z.nii s20718 pos pat ocdNeutral_20718_Larea11.z.nii s20718 neg pat ocdStrong_20718_Larea11.z.nii ...

** Error:
The content under -dataTable is not rectangular ! 53 4

: Command not found.

: Command not found.

Any advice for an issue like this? Maybe I missed something else in my code? Thanks.



Edited 1 time(s). Last edit at 03/10/2022 05:11AM by leyamarz.