Welcome! Log In Create A New Profile

AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates

Previous Message Next Message

Message List New Topic Print View

MeganQ

May 27, 2022 11:45AM

Registered: 4 years ago
Posts: 53

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
----------------------------------------------------------------------

Reply Quote

RSS

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