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May 27, 2022 11:45AM
Hi Rick,

I really appreciate your help on this matter! I got closer this time, but still getting some errors. I concatenated the motion and confound files into one 1D file each (with 217 (number of TRs per run)*4 (number of runs) rows) and am getting the following error:

** error: option -regress_opts_3dD follows unknown arg #107 (-regress_extra_ortvec)

Here is the terminal output when I run the script to set up AFNI proc. If you need any other info from me please let me know!

set subjects = ( 1055 )
set GLM = PostfmriPrep
set topdir = /data/projects/STUDIES/LEARN/fMRI
set subjfmridata = /data/projects/STUDIES/LEARN/fMRI/derivatives/fmriPREP
set subjecttiming = /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData
set results = /data/projects/STUDIES/LEARN/fMRI/derivatives/afni/IndvlLvlAnalyses
cd /data/projects/STUDIES/LEARN/fMRI/derivatives/afni/IndvlLvlAnalyses
foreach subj ( 1055 )
mkdir 1055
cd 1055
set subj_dir = /data/projects/STUDIES/LEARN/fMRI/derivatives/fmriPREP/sub-1055
set stimdurmoddir = /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055
afni_proc.py -subj_id 1055 -dsets /data/projects/STUDIES/LEARN/fMRI/derivatives/fmriPREP/sub-1055/func/sub-1055_task-learn_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz /data/projects/STUDIES/LEARN/fMRI/derivatives/fmriPREP/sub-1055/func/sub-1055_task-learn_run-2_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz /data/projects/STUDIES/LEARN/fMRI/derivatives/fmriPREP/sub-1055/func/sub-1055_task-learn_run-3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz /data/projects/STUDIES/LEARN/fMRI/derivatives/fmriPREP/sub-1055/func/sub-1055_task-learn_run-4_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz -scr_overwrite -script /data/projects/STUDIES/LEARN/fMRI/derivatives/afni/IndvlLvlAnalyses/1055/proc.1055.PostfmriPrep -out_dir 1055.results.PostfmriPrep -blocks blur mask scale regress -copy_anat /data/projects/STUDIES/LEARN/fMRI/derivatives/fmriPREP/sub-1055/anat/sub-1055_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz -blur_size 6 -regress_run_clustsim yes -regress_stim_times_offset -0.870967741935484 -regress_stim_times /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/class.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/iti.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean60_fdkm.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean60_fdkn.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean60_pred.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean60_rsp.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean80_fdkm.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean80_fdkn.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean80_pred.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean80_rsp.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice60_fdkm.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice60_fdkn.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice60_pred.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice60_rsp.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice80_fdkm.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice80_fdkn.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice80_pred.1D /data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice80_rsp.1D -regress_stim_labels Class ITI FBM.Mean60 FBN.Mean60 Pred.Mean60 Resp.Mean60 FBM.Mean80 FBN.Mean80 Pred.Mean80 Resp.Mean80 FBM.Nice60 FBN.Nice60 Pred.Nice60 Resp.Nice60 FBM.Nice80 FBN.Nice80 Pred.Nice80 Resp.Nice80 -regress_stim_types AM1 AM1 AM1 AM1 AM1 AM1 AM1 AM1 AM1 AM1 AM1 AM1 AM1 AM1 AM1 AM1 AM1 AM1 -regress_basis_multi dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) dmBLOCK(0) -regress_make_ideal_sum IDEAL_sum.1D -regress_motion_file /data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/task-learn_rall_motion.1D -regress_motion_per_run -regress_extra_ortvec /data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/ortvec_rall_aCompCor6.1D /data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/ortvec_rall_cosine.1D /data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/ortvec_rall_fd.1D -regress_extra_ortvec_labels aCompcor6 cosine fd -regress_opts_3dD -num_glt 7 -gltsym SYM: +FBM.Mean60 +FBN.Mean60 +Pred.Mean60 +Resp.Mean60 +FBM.Mean80 +FBN.Mean80 +Pred.Mean80 +Resp.Mean80 +FBM.Nice60 +FBN.Nice60 +Pred.Nice60 +Resp.Nice60 +FBM.Nice80 +FBN.Nice80 +Pred.Nice80 +Resp.Nice80 -glt_label 1 Task.V.BL -gltsym SYM: +Pred.Mean60 +Pred.Mean80 +Pred.Nice60 +Pred.Nice80 -glt_label 2 Prediction.V.BL -gltsym SYM: +Pred.Mean60 +Pred.Mean80 -Pred.Nice60 -Pred.Nice80 -glt_label 3 Prediction.Mean.V.Nice -gltsym SYM: +FBM.Mean60 +FBN.Mean60 +FBM.Mean80 +FBN.Mean80 +FBM.Nice60 +FBN.Nice60 +FBM.Nice80 +FBN.Nice80 -glt_label 4 FB.V.BL -gltsym SYM: +FBM.Mean60 +FBM.Mean80 +FBM.Nice60 +FBM.Nice80 -glt_label 5 FBM.V.BL -gltsym SYM: +FBN.Mean60 +FBN.Mean80 +FBN.Nice60 +FBN.Nice80 -glt_label 6 FBN.V.BL -gltsym SYM: +FBM.Mean60 +FBM.Mean80 +FBM.Nice60 +FBM.Nice80 -FBN.Mean60 -FBN.Mean80 -FBN.Nice60 -FBN.Nice80 -glt_label 7 FBM.V.FBN -cbucket cbucket.stats.1055 -jobs 30
** error: option -regress_opts_3dD follows unknown arg #107 (-regress_extra_ortvec)
----------------------------------------------------------------------
** failed command (get_user_opts):

afni_proc.py -subj_id 1055 -dsets \
/data/projects/STUDIES/LEARN/fMRI/derivatives/fmriPREP/sub-1055/func/sub-1055_task-learn_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz \
/data/projects/STUDIES/LEARN/fMRI/derivatives/fmriPREP/sub-1055/func/sub-1055_task-learn_run-2_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz \
/data/projects/STUDIES/LEARN/fMRI/derivatives/fmriPREP/sub-1055/func/sub-1055_task-learn_run-3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz \
/data/projects/STUDIES/LEARN/fMRI/derivatives/fmriPREP/sub-1055/func/sub-1055_task-learn_run-4_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz \
-scr_overwrite -script \
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/IndvlLvlAnalyses/1055/proc.1055.PostfmriPrep \
-out_dir 1055.results.PostfmriPrep -blocks blur mask scale regress \
-copy_anat \
/data/projects/STUDIES/LEARN/fMRI/derivatives/fmriPREP/sub-1055/anat/sub-1055_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz \
-blur_size 6 -regress_run_clustsim yes -regress_stim_times_offset \
-0.870967741935484 -regress_stim_times \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/class.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/iti.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean60_fdkm.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean60_fdkn.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean60_pred.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean60_rsp.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean80_fdkm.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean80_fdkn.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean80_pred.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Mean80_rsp.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice60_fdkm.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice60_fdkn.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice60_pred.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice60_rsp.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice80_fdkm.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice80_fdkn.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice80_pred.1D \
/data/projects/STUDIES/LEARN/fMRI/code/afni/BehavData/sub-1055/Nice80_rsp.1D \
-regress_stim_labels Class ITI FBM.Mean60 FBN.Mean60 Pred.Mean60 \
Resp.Mean60 FBM.Mean80 FBN.Mean80 Pred.Mean80 Resp.Mean80 FBM.Nice60 \
FBN.Nice60 Pred.Nice60 Resp.Nice60 FBM.Nice80 FBN.Nice80 Pred.Nice80 \
Resp.Nice80 -regress_stim_types AM1 AM1 AM1 AM1 AM1 AM1 AM1 AM1 AM1 AM1 \
AM1 AM1 AM1 AM1 AM1 AM1 AM1 AM1 -regress_basis_multi 'dmBLOCK(0)' \
'dmBLOCK(0)' 'dmBLOCK(0)' 'dmBLOCK(0)' 'dmBLOCK(0)' 'dmBLOCK(0)' \
'dmBLOCK(0)' 'dmBLOCK(0)' 'dmBLOCK(0)' 'dmBLOCK(0)' 'dmBLOCK(0)' \
'dmBLOCK(0)' 'dmBLOCK(0)' 'dmBLOCK(0)' 'dmBLOCK(0)' 'dmBLOCK(0)' \
'dmBLOCK(0)' 'dmBLOCK(0)' -regress_make_ideal_sum IDEAL_sum.1D \
-regress_motion_file \
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/task-learn_rall_motion.1D \
-regress_motion_per_run -regress_extra_ortvec \
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/ortvec_rall_aCompCor6.1D \
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/ortvec_rall_cosine.1D \
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/ortvec_rall_fd.1D \
-regress_extra_ortvec_labels aCompcor6 cosine fd -regress_opts_3dD \
-num_glt 7 -gltsym 'SYM: +FBM.Mean60 +FBN.Mean60 +Pred.Mean60 \
+Resp.Mean60 +FBM.Mean80 +FBN.Mean80 +Pred.Mean80 +Resp.Mean80 \
+FBM.Nice60 +FBN.Nice60 +Pred.Nice60 +Resp.Nice60 +FBM.Nice80 \
+FBN.Nice80 +Pred.Nice80 +Resp.Nice80' -glt_label 1 Task.V.BL -gltsym \
'SYM: +Pred.Mean60 +Pred.Mean80 +Pred.Nice60 +Pred.Nice80' -glt_label 2 \
Prediction.V.BL -gltsym 'SYM: +Pred.Mean60 +Pred.Mean80 -Pred.Nice60 \
-Pred.Nice80' -glt_label 3 Prediction.Mean.V.Nice -gltsym 'SYM: \
+FBM.Mean60 +FBN.Mean60 +FBM.Mean80 +FBN.Mean80 +FBM.Nice60 +FBN.Nice60 \
+FBM.Nice80 +FBN.Nice80' -glt_label 4 FB.V.BL -gltsym 'SYM: +FBM.Mean60 \
+FBM.Mean80 +FBM.Nice60 +FBM.Nice80' -glt_label 5 FBM.V.BL -gltsym \
'SYM: +FBN.Mean60 +FBN.Mean80 +FBN.Nice60 +FBN.Nice80' -glt_label 6 \
FBN.V.BL -gltsym 'SYM: +FBM.Mean60 +FBM.Mean80 +FBM.Nice60 +FBM.Nice80 \
-FBN.Mean60 -FBN.Mean80 -FBN.Nice60 -FBN.Nice80' -glt_label 7 FBM.V.FBN \
-cbucket cbucket.stats.1055 -jobs 30
----------------------------------------------------------------------
Subject Author Posted

afniproc.py error -regress_motion_per_run follows unknown arg

MeganQ May 19, 2022 02:05PM

Re: afniproc.py error -regress_motion_per_run follows unknown arg

rick reynolds May 20, 2022 01:42PM

Re: afniproc.py error -regress_motion_per_run follows unknown arg

MeganQ May 23, 2022 08:26AM

Re: afniproc.py error -regress_motion_per_run follows unknown arg

MeganQ May 27, 2022 11:45AM

Re: afniproc.py error -regress_motion_per_run follows unknown arg

rick reynolds May 27, 2022 01:04PM

Re: afniproc.py error -regress_motion_per_run follows unknown arg

MeganQ May 27, 2022 04:11PM

Re: afniproc.py error -regress_motion_per_run follows unknown arg

rick reynolds May 27, 2022 07:44PM

Re: afniproc.py error -regress_motion_per_run follows unknown arg

MeganQ May 30, 2022 08:28AM



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