afniproc.py error -regress_motion_per_run follows unknown arg

MeganQ · May 19, 2022, 6:05pm

Hello,

I’m trying to run AFNI proc using data that was preprocessed using fmriPREP. Because of this, I have a few different options and conditions than I typically have had with afni proc. I’m running into an error that states:

** error: option -regress_motion_per_run follows unknown arg #106 (/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-2_motion.tsv)

** failed command (get_user_opts):

I have pasted the script output below. I have double checked that the file /data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-2_motion.tsv exists and has the expected information included in it.

Any thoughts? Thank you!

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/sub-1055_task-learn_run-1_motion.tsv
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-2_motion.tsv
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-3_motion.tsv
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-4_motion.tsv
-regress_extra_ortvec_labels
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-1_aCompCor6.tsv
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-2_aCompCor6.tsv
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-3_aCompCor6.tsv
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-4_aCompCor6.tsv
-regress_extra_ortvec_labels
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-1_cosine.tsv
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-2_cosine.tsv
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-3_cosine.tsv
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-4_cosine.tsv
-regress_extra_ortvec_labels
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-1_fd.tsv
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-2_fd.tsv
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-3_fd.tsv
/data/projects/STUDIES/LEARN/fMRI/derivatives/afni/confounds/sub-1055/sub-1055_task-learn_run-4_fd.tsv
-regress_motion_per_run -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

rickr · May 20, 2022, 5:42pm

Hi Megan,

There are just a few things to note here, and the main one is that 1D (TSV) inputs should be concatenated across runs.

For example, the 4 sub-1055_task-learn_run-*_motion.tsv should be concatenated, with only the 1 input passed via -regress_motion_file. I could consider allowing 1 per run as an alternative, but it is not an option right now.

Also, -regress_extra_ortvec can take multiple files as input, but they should also be concatenated across runs. So if you were to :
cat sub-1055_task-learn_run-*_aCompCor6.tsv > ortvec_rall_aCompCor6.1D
(and similarly for cosine and fd), then the options might read:

-regress_extra_ortvec ortvec_rall_aCompCor6.1D   \
                      ortvec_rall_cosine.1D      \
                      ortvec_rall_fd.1D          \
-regress_extra_ortvec_labels aCompcor6 cosine fd \

Note that the “labels” option just names the ortvec files in some way.

Also, the -regress_stim_times_offset parameter is probably negated. If fmriprep has done 3dTshift to align to the middle(ish) of the TR, then it will be as if the EPI timing is later than the start of the TR, and so relatively, the task timing should be earlier. Consider using:

-regress_stim_times_offset -0.870967741935484

Also, just to make it easier, since the -regress_stim_types and -regress_basis_multi parameters are all the same, it is okay to use a single parameter, as in:

-regress_stim_types AM1           \
-regress_basis_multi 'dmBLOCK(0)' \

Does that seem reasonable?

rick

MeganQ · May 23, 2022, 12:26pm

Hi Rick,

Thank you so much for the feedback! That was very helpful. I will give those things a shot and let you know if I have any further problems.

Best,
Megan

MeganQ · May 27, 2022, 3:45pm

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

rickr · May 27, 2022, 5:04pm

Hi Megan,

I probably should have asked last time to be sure, what what does “afni -ver” show?
That -regress_extra_ortvec option was added Feb, 2021.

rick

MeganQ · May 27, 2022, 8:11pm

Ah, that could do it! Here’s the version:
Precompiled binary linux_ubuntu_16_64: Dec 7 2020 (Version AFNI_20.3.03 ‘Vespasian’)

So it looks like we need to update. Unless there’s an older version of the -regress_extra_ortvec option?

rickr · May 27, 2022, 11:44pm

No, that is the version needed for that option. You could pass a bunch of 1D files, but that is generally not as convenient.
To be sure, would it be problematic to update at this point? If you are still running the regression, I would expect that you would rather have the current version.
Consider: @update.afni.binaries -defaults

rick

MeganQ · May 30, 2022, 12:28pm

Nope updating would be great, thank you!