3dDeconvolve error when using -ortvec

AFNI Message Board
1

Dear AFNI experts,

I'm trying to run GLM analysis on a laminar-resolution fMRI dataset (3 runs, each having 300 time-points) with jittered event-related paradigm and varying trial duration. Since I want to include motion and other noise confounds (outputs of CompCor), I used "-ortvec" option instead of "-stim_file" but 3dDeconvolve crashed with the following error: "3dDeconvolve dies: Unrecognized command line option: 'SYM: new -old'. Here is my script and a screenshot of the confound file including 10 columns where the first 6 are motion estimates and the remaining 4 are CompCor principal components. There were 2 components estimated in run1 and 2 while run3 had 4 components, so I added two columns of zeros for the first two runs. Any help would be very much appreciated.

Kind regards,
Khazar

confounds
confounds1848×1053 222 KB

3dDeconvolve -input all-runs-smoothed.nii.gz -concat '1D: 0 300 600' -mask mask_averaged-bin.nii.gz -polort A -local_times -num_stimts 7 -stim_times_AM1 1 old_reg.txt 'dmUBLOCK(-4)' -stim_label 1 old -stim_times_AM1 2 lure_reg.txt 'dmUBLOCK(-4)' -stim_label 2 lure -stim_times_AM1 3 new_reg.txt 'dmUBLOCK(-4)' -stim_label 3 new -stim_times_AM1 4 incorr_reg.txt 'dmUBLOCK(-4)' -stim_label 4 incorr -stim_times_AM1 5 sceneCorr_reg.txt 'dmUBLOCK(-4)' -stim_label 5 sceneCorr -stim_times_AM1 6 sceneError_reg.txt 'dmUBLOCK(-4)' -stim_label 6 sceneError -stim_times_AM1 7 gabor_reg.txt 'dmUBLOCK(-4)' -stim_label 7 gabor -ortvec allConfounds.1D -gltsym 'SYM: new -old' -glt_label 1 new-old -gltsym 'SYM: old -lure' -glt_label 2 old-lure -gltsym 'SYM: old -gabor' -glt_label 3 old-gabor -gltsym 'SYM: new -gabor' -glt_label 4 new-gabor -gltsym 'SYM: new -lure' -glt_label 5 new-lure -gltsym 'SYM: new -incorr' -glt_label 6 new-incorr -gltsym 'SYM: old -incorr' -glt_label 7 old-incorr -gltsym 'SYM: lure -incorr' -glt_label 8 lure-incorr -gltsym 'SYM: lure -gabor' -glt_label 9 lure-gabor -gltsym 'SYM: sceneCorr -old' -glt_label 10 sceneCorr-old -tout -fout -x1D all_design.xmat.1D -xjpeg all_design.jpg -fitts Fitts_all.nii.gz -errts error.nii.gz -bucket all_runs -jobs 15

2

I figured out that -ortvec option requires 2 inputs , while I had provided one. Should have read 3dDeconvovle page more carefully! Thanks a lot for developing such great tools for the neuroscience community.

Best,
K.