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History of AFNI updates  

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May 05, 2017 12:42PM
Hello AFNI experts,

I got the following "follows unknown arg" error when running afni_proc.py but could not figure out the reason. Could you please help.
(I am using AFNI 17.0.18 and afni_proc.py 5.13)

Thank you,
Duong

++++++++++++++++++++ SCRIPT +++++++++++++++++++++++++++++++++++++++++++++++++++++
#!/bin/tcsh -xef
# Include all sections, or some particular sections, of data here. Folder names are the same as those copied from '/Users/papageor/Desktop/data/indcm'
set datasets = ('20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917')
set dataset_num = (`count -digits 1 1 ${#datasets}`)
# Params - Make sure to check epi run indices. Defaults = runs 3 and 4
set inprefix = '001_'
set anat_run_ind = '000002_'
set epi_run_ind = ('000003_' '000004_')
set epi_run_num = (`count -digits 1 1 ${#epi_run_ind}`)
set dicomFolder = 'indcm'
set epiFolder = 'funcHeadBrik'
set anatFolder = 'anatHeadBrik'
set epi_outprefix = 'epi'
set anat_outprefix = 'anat'
# ---
set numSlices = 33
set sliceOrder = 'alt+z'
set TR = 2.0

# Afni_proc.py
foreach dat ($dataset_num)
foreach runInd ($epi_run_num)
set subj = $datasets[$dat]
afni_proc.py -subj_id $subj \
-script ./proc_r$runInd.sh \
-out_dir $subj.results \
-dsets ./$datasets[$dat]/$epiFolder/epi.r?+orig.HEAD \
-blocks despike tshift volreg align tlrc blur mask scale regress \
-anat_has_skull yes \
-tcat_remove_first_trs 6 \
-tcat_remove_last_trs 4 \
-tshift_opts_ts -tpattern $sliceOrder \
-tshift_align_to -slice 17 \
-copy_anat ./$datasets[$dat]/$anatFolder/anat.r1+orig \
-volreg_align_to first \
-volreg_align_e2a \
-volreg_tlrc_warp \
-align_opts_aea -giant_move \
-tlrc_opts_at -init_xform AUTO_CENTER \
-blur_size 7 \
-regress_stim_times ./stim_times/run$runInd/baseline.txt \
./stim_times/run$runInd/left.txt \
./stim_times/run$runInd/right.txt \
./stim_times/run$runInd/up.txt \
./stim_times/run$runInd/down.txt \
-regress_stim_labels b \
L \
R \
U \
D \
-regress_local_times \
-regress_reml_exec \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_basis 'BLOCK(12,1)' \
'BLOCK(30,1)' \
'BLOCK(30,1)' \
'BLOCK(30,1)' \
'BLOCK(30,1)' \
-regress_censor_outliers 0.1 \
-regress_censor_motion 0.3 \
-regress_opts_3dD \
-num_glt 4 \
-gltsym 'SYM: +L -b' -glt_label 1 L-b \
-gltsym 'SYM: +R -b' -glt_label 2 R-b \
-gltsym 'SYM: +L -R' -glt_label 3 L-R \
-gltsym 'SYM: +U -D' -glt_label 3 U-D \
-jobs 4 \
-execute
end
end
+++++++++++++++++++++++++++++++++ END SCRIPT ++++++++++++++++++++++++++++++++++++++++++++++++++


+++++++++++++++++++++++++++++++++ WHAT I GOT +++++++++++++++++++++++++++++++++++++++++++++++++
set datasets = ( 20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917 )
set dataset_num = ( `count -digits 1 1 ${#datasets}` )
count -digits 1 1 1
set inprefix = 001_
set anat_run_ind = 000002_
set epi_run_ind = ( 000003_ 000004_ )
set epi_run_num = ( `count -digits 1 1 ${#epi_run_ind}` )
count -digits 1 1 2
set dicomFolder = indcm
set epiFolder = funcHeadBrik
set anatFolder = anatHeadBrik
set epi_outprefix = epi
set anat_outprefix = anat
set numSlices = 33
set sliceOrder = alt+z
set TR = 2.0
foreach dat ( 1 )
foreach runInd ( 1 2 )
set subj = 20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917
afni_proc.py -subj_id 20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917 -script ./proc_r1.sh -out_dir 20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917.results -dsets ./20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917/funcHeadBrik/epi.r1+orig.HEAD ./20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917/funcHeadBrik/epi.r2+orig.HEAD -blocks despike tshift volreg align tlrc blur mask scale regress -anat_has_skull yes -tcat_remove_first_trs 6 -tcat_remove_last_trs 4 -tshift_opts_ts -tpattern alt+z -tshift_align_to -slice 17 -copy_anat ./20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917/anatHeadBrik/anat.r1+orig -volreg_align_to first -volreg_align_e2a -volreg_tlrc_warp -align_opts_aea -giant_move -tlrc_opts_at -init_xform AUTO_CENTER -blur_size 7 -regress_stim_times ./stim_times/run1/baseline.txt ./stim_times/run1/left.txt ./stim_times/run1/right.txt ./stim_times/run1/up.txt ./stim_times/run1/down.txt -regress_stim_labels b L R U D -regress_local_times -regress_reml_exec -regress_est_blur_epits -regress_est_blur_errts -regress_basis BLOCK(12,1) BLOCK(30,1) BLOCK(30,1) BLOCK(30,1) BLOCK(30,1) -regress_censor_outliers 0.1 -regress_censor_motion 0.3 -regress_opts_3dD -num_glt 4 -gltsym SYM: +L -b -glt_label 1 L-b -gltsym SYM: +R -b -glt_label 2 R-b -gltsym SYM: +L -R -glt_label 3 L-R -gltsym SYM: +U -D -glt_label 3 U-D -jobs 4 -execute
** error: option -regress_censor_outliers follows unknown arg #63 (BLOCK(30,1))
----------------------------------------------------------------------
** failed command (get_user_opts):

afni_proc.py -subj_id \
20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917 \
-script ./proc_r1.sh -out_dir \
20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917.results \
-dsets \
./20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917/funcHeadBrik/epi.r1+orig.HEAD \
./20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917/funcHeadBrik/epi.r2+orig.HEAD \
-blocks despike tshift volreg align tlrc blur mask scale regress \
-anat_has_skull yes -tcat_remove_first_trs 6 -tcat_remove_last_trs 4 \
-tshift_opts_ts -tpattern alt+z -tshift_align_to -slice 17 -copy_anat \
./20170309.pt001_rtfMRI_1Trn3Tst_GD_030917.pt001_rtfMRI_1Trn3Tst_GD_030917/anatHeadBrik/anat.r1+orig \
-volreg_align_to first -volreg_align_e2a -volreg_tlrc_warp \
-align_opts_aea -giant_move -tlrc_opts_at -init_xform AUTO_CENTER \
-blur_size 7 -regress_stim_times ./stim_times/run1/baseline.txt \
./stim_times/run1/left.txt ./stim_times/run1/right.txt \
./stim_times/run1/up.txt ./stim_times/run1/down.txt \
-regress_stim_labels b L R U D -regress_local_times -regress_reml_exec \
-regress_est_blur_epits -regress_est_blur_errts -regress_basis \
'BLOCK(12,1)' 'BLOCK(30,1)' 'BLOCK(30,1)' 'BLOCK(30,1)' 'BLOCK(30,1)' \
-regress_censor_outliers 0.1 -regress_censor_motion 0.3 \
-regress_opts_3dD -num_glt 4 -gltsym 'SYM: +L -b' -glt_label 1 L-b \
-gltsym 'SYM: +R -b' -glt_label 2 R-b -gltsym 'SYM: +L -R' -glt_label 3 \
L-R -gltsym 'SYM: +U -D' -glt_label 3 U-D -jobs 4 -execute
Subject Author Posted

"follows unknown arg"- error from afni_proc.py

dlhuynh May 05, 2017 12:42PM

Re: "follows unknown arg"- error from afni_proc.py

rick reynolds May 05, 2017 01:32PM

Re: "follows unknown arg"- error from afni_proc.py

dlhuynh May 05, 2017 03:23PM

Re: "follows unknown arg"- error from afni_proc.py

rick reynolds May 05, 2017 03:35PM

Re: "follows unknown arg"- error from afni_proc.py

dlhuynh May 05, 2017 03:41PM