[b]EDIT: Never mind, I found the problem. The file was indeed empty… I was looking at the wrong file. Sorry, and thank you again.[/b]
I’m running 3dDeconvolve, and it fails to read the Motion time series file.
The File is not empty and doesn’t have weird characters in it (I checked).
Any idea what the problem is?
Here is the script, looping over a few subjects:
foreach i ("S02" "S03" "S04" "S05")
set j=$i"_DATA"
cd /home/user/Desktop/fMRI_AFNI/$j
3dDeconvolve \
-input $i"_Run1.data.tshift.alignedCenters.deobl.motion_correct.despiked.PSC.BlurToFWHM6+orig.BRIK" $i"_Run2.data.tshift.alignedCenters.deobl.motion_correct.despiked.PSC.BlurToFWHM6+orig.BRIK" \
-mask ./brainmask.d1.res+orig -censor ./$i"_Motion".All.censor.1D -polort A \
-xout \
-num_stimts 8 \
-local_times \
-stim_times 1 Words_timing.txt 'BLOCK(12,1)' -stim_label 1 Words \
-stim_times 2 Scrambled_timing.txt 'BLOCK(12,1)' -stim_label 2 Scrambled \
-stim_file 3 ./$i"_Motion".All.txt'[0]' -stim_label 3 Roll \
-stim_file 4 ./$i"_Motion".All.txt'[1]' -stim_label 4 Pitch \
-stim_file 5 ./$i"_Motion".All.txt'[2]' -stim_label 5 Yaw \
-stim_file 6 ./$i"_Motion".All.txt'[3]' -stim_label 6 SI \
-stim_file 7 ./$i"_Motion".All.txt'[4]' -stim_label 7 LR \
-stim_file 8 ./$i"_Motion".All.txt'[5]' -stim_label 8 PA \
-num_glt 1 \
-gltsym 'SYM: +Words -Scrambled' -glt_label 1 'Words-Scrambled' \
-xsave \
-errts $i"_residuals" \
-tout \
-xjpeg matrix \
-x1D matrix.1D \
-bout \
-noFDR \
-jobs 2 \
-bucket $i.single_subject_GLM
end
And here is the error:
3dDeconvolve dies: Unable to read time series file: ./S02_Motion.All.txt[0]
** Program compile date = Oct 12 2018