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June 14, 2022 12:23PM
Sorry to bother you again, but a question about shifting my timing files!

I have a regressor of no interest (called "Class") that has an onset of 0.011 in run 1 for example.

Therefore, when I apply the stim time offset of -.831, my new class_offset.1D file reads as so

-0.82:5
-0.82:5
-0.815:5

This is I believe what is causing my script to error, however I have copied the output below. Is there a parameter that can be added to avoid shifting that "class" timing file? Or am I running into a separate issue? Thank you SO much! I really appreciate the help!

set subjects = ( s1562 s1571 s1577 s1585 s1591 s1603 s1610 s1614 s1622 s1629 s1671 s1693 s1712 )
set GLM = AggPM053122
set topdir = /data/projects/STUDIES/SEAT/fMRI
set results = /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/IndvlLvlAnalyses
cd /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/IndvlLvlAnalyses
foreach subj ( s1562 s1571 s1577 s1585 s1591 s1603 s1610 s1614 s1622 s1629 s1671 s1693 s1712 )
cd s1562
tcsh -xef proc.s1562.AggPM053122
echo auto-generated by afni_proc.py, Tue Jun 14 12:16:20 2022
echo (version 7.39, May 10, 2022)
echo execution started: `date`
date
afni -ver
afni_history -check_date 7 Mar 2022
if ( 0 ) then
if ( 0 > 0 ) then
set subj = s1562
endif
set output_dir = s1562.results.AggPM053122
if ( -d s1562.results.AggPM053122 ) then
set runs = ( `count -digits 2 1 3` )
count -digits 2 1 3
mkdir -p s1562.results.AggPM053122
mkdir s1562.results.AggPM053122/stimuli
timing_tool.py -add_offset -0.831 -timing /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/TimingFilesPM/sub-s1562/class_agg.1D -write_timing s1562.results.AggPM053122/stimuli/offset_class_agg.1D
timing_tool.py -add_offset -0.831 -timing /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/TimingFilesPM/sub-s1562/Mean_anticipation_agg.1D -write_timing s1562.results.AggPM053122/stimuli/offset_Mean_anticipation_agg.1D
timing_tool.py -add_offset -0.831 -timing /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/TimingFilesPM/sub-s1562/Mean_feedback_agg.1D -write_timing s1562.results.AggPM053122/stimuli/offset_Mean_feedback_agg.1D
timing_tool.py -add_offset -0.831 -timing /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/TimingFilesPM/sub-s1562/Mean_response_agg.1D -write_timing s1562.results.AggPM053122/stimuli/offset_Mean_response_agg.1D
timing_tool.py -add_offset -0.831 -timing /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/TimingFilesPM/sub-s1562/Nice_anticipation_agg.1D -write_timing s1562.results.AggPM053122/stimuli/offset_Nice_anticipation_agg.1D
timing_tool.py -add_offset -0.831 -timing /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/TimingFilesPM/sub-s1562/Nice_feedback_agg.1D -write_timing s1562.results.AggPM053122/stimuli/offset_Nice_feedback_agg.1D
timing_tool.py -add_offset -0.831 -timing /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/TimingFilesPM/sub-s1562/Nice_response_agg.1D -write_timing s1562.results.AggPM053122/stimuli/offset_Nice_response_agg.1D
timing_tool.py -add_offset -0.831 -timing /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/TimingFilesPM/sub-s1562/UnpMean_anticipation_agg.1D -write_timing s1562.results.AggPM053122/stimuli/offset_UnpMean_anticipation_agg.1D
timing_tool.py -add_offset -0.831 -timing /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/TimingFilesPM/sub-s1562/UnpMean_feedback_agg.1D -write_timing s1562.results.AggPM053122/stimuli/offset_UnpMean_feedback_agg.1D
timing_tool.py -add_offset -0.831 -timing /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/TimingFilesPM/sub-s1562/UnpMean_response_agg.1D -write_timing s1562.results.AggPM053122/stimuli/offset_UnpMean_response_agg.1D
timing_tool.py -add_offset -0.831 -timing /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/TimingFilesPM/sub-s1562/UnpNice_anticipation_agg.1D -write_timing s1562.results.AggPM053122/stimuli/offset_UnpNice_anticipation_agg.1D
timing_tool.py -add_offset -0.831 -timing /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/TimingFilesPM/sub-s1562/UnpNice_feedback_agg.1D -write_timing s1562.results.AggPM053122/stimuli/offset_UnpNice_feedback_agg.1D
timing_tool.py -add_offset -0.831 -timing /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/TimingFilesPM/sub-s1562/UnpNice_response_agg.1D -write_timing s1562.results.AggPM053122/stimuli/offset_UnpNice_response_agg.1D
timing_tool.py -add_offset -0.831 -timing /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/TimingFilesPM/sub-s1562/missing_agg.1D -write_timing s1562.results.AggPM053122/stimuli/offset_missing_agg.1D
cp /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/confounds/sub-s1562/sub-s1562_task-seat_allruns_aCompCor6.1D /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/confounds/sub-s1562/sub-s1562_task-seat_allruns_cosine.1D /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/confounds/sub-s1562/sub-s1562_task-seat_allruns_fd.1D s1562.results.AggPM053122/stimuli
3dcopy /data/projects/STUDIES/SEAT/fMRI/derivatives/fmriprep/sub-s1562/anat/sub-s1562_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz s1562.results.AggPM053122/sub-s1562_space-MNI152NLin2009cAsym_desc-preproc_T1w
++ 3dcopy: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
cp /data/projects/STUDIES/SEAT/fMRI/derivatives/afni/confounds/sub-s1562/sub-s1562_task-seat_allruns_motion.1D s1562.results.AggPM053122
3dTcat -prefix s1562.results.AggPM053122/pb00.s1562.r01.tcat /data/projects/STUDIES/SEAT/fMRI/derivatives/fmriprep/sub-s1562/func/sub-s1562_task-seat_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz[0..$]
++ 3dTcat: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ elapsed time = 1.9 s
3dTcat -prefix s1562.results.AggPM053122/pb00.s1562.r02.tcat /data/projects/STUDIES/SEAT/fMRI/derivatives/fmriprep/sub-s1562/func/sub-s1562_task-seat_run-2_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz[0..$]
++ 3dTcat: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ elapsed time = 1.9 s
3dTcat -prefix s1562.results.AggPM053122/pb00.s1562.r03.tcat /data/projects/STUDIES/SEAT/fMRI/derivatives/fmriprep/sub-s1562/func/sub-s1562_task-seat_run-3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz[0..$]
++ 3dTcat: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ elapsed time = 1.9 s
set tr_counts = ( 167 167 167 )
cd s1562.results.AggPM053122
touch out.pre_ss_warn.txt
foreach run ( 01 02 03 )
3dToutcount -automask -fraction -polort 2 -legendre pb00.s1562.r01.tcat+tlrc
++ 3dToutcount: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ 66269 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r01.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 2 -legendre pb00.s1562.r02.tcat+tlrc
++ 3dToutcount: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ 66300 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r02.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 2 -legendre pb00.s1562.r03.tcat+tlrc
++ 3dToutcount: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ 66240 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r03.1D{0} -expr step(a-0.4)
end
cat outcount.r01.1D outcount.r02.1D outcount.r03.1D
foreach run ( 01 02 03 )
3dmerge -1blur_fwhm 6 -doall -prefix pb01.s1562.r01.blur pb00.s1562.r01.tcat+tlrc
++ 3dmerge: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ default -1dindex = 0
++ default -1tindex = 1
-- Wrote edited dataset: ./pb01.s1562.r01.blur+tlrc.BRIK
end
3dmerge -1blur_fwhm 6 -doall -prefix pb01.s1562.r02.blur pb00.s1562.r02.tcat+tlrc
++ 3dmerge: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ default -1dindex = 0
++ default -1tindex = 1
-- Wrote edited dataset: ./pb01.s1562.r02.blur+tlrc.BRIK
end
3dmerge -1blur_fwhm 6 -doall -prefix pb01.s1562.r03.blur pb00.s1562.r03.tcat+tlrc
++ 3dmerge: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ default -1dindex = 0
++ default -1tindex = 1
-- Wrote edited dataset: ./pb01.s1562.r03.blur+tlrc.BRIK
end
foreach run ( 01 02 03 )
3dAutomask -prefix rm.mask_r01 pb01.s1562.r01.blur+tlrc
++ 3dAutomask: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset pb01.s1562.r01.blur+tlrc
++ Forming automask
+ Fixed clip level = 6708.465820
+ Used gradual clip level = 6566.184570 .. 6937.206543
+ Number voxels above clip level = 67566
+ Clustering voxels ...
+ Largest cluster has 67290 voxels
+ Clustering voxels ...
+ Largest cluster has 67260 voxels
+ Filled 85 voxels in small holes; now have 67345 voxels
+ Filled 1 voxels in large holes; now have 67346 voxels
+ Clustering voxels ...
+ Largest cluster has 67346 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 257979 voxels
+ Mask now has 67346 voxels
++ 67346 voxels in the mask [out of 325325: 20.70%]
++ first 9 x-planes are zero [from L]
++ last 8 x-planes are zero [from R]
++ first 8 y-planes are zero [from P]
++ last 7 y-planes are zero [from A]
++ first 0 z-planes are zero [from I]
++ last 11 z-planes are zero [from S]
++ CPU time = 0.000000 sec
end
3dAutomask -prefix rm.mask_r02 pb01.s1562.r02.blur+tlrc
++ 3dAutomask: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset pb01.s1562.r02.blur+tlrc
++ Forming automask
+ Fixed clip level = 6706.098633
+ Used gradual clip level = 6561.835938 .. 6931.929688
+ Number voxels above clip level = 67581
+ Clustering voxels ...
+ Largest cluster has 67288 voxels
+ Clustering voxels ...
+ Largest cluster has 67249 voxels
+ Filled 82 voxels in small holes; now have 67331 voxels
+ Filled 1 voxels in large holes; now have 67332 voxels
+ Clustering voxels ...
+ Largest cluster has 67332 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 257993 voxels
+ Mask now has 67332 voxels
++ 67332 voxels in the mask [out of 325325: 20.70%]
++ first 9 x-planes are zero [from L]
++ last 8 x-planes are zero [from R]
++ first 9 y-planes are zero [from P]
++ last 7 y-planes are zero [from A]
++ first 0 z-planes are zero [from I]
++ last 11 z-planes are zero [from S]
++ CPU time = 0.000000 sec
end
3dAutomask -prefix rm.mask_r03 pb01.s1562.r03.blur+tlrc
++ 3dAutomask: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset pb01.s1562.r03.blur+tlrc
++ Forming automask
+ Fixed clip level = 6715.770508
+ Used gradual clip level = 6567.285156 .. 6944.270020
+ Number voxels above clip level = 67567
+ Clustering voxels ...
+ Largest cluster has 67265 voxels
+ Clustering voxels ...
+ Largest cluster has 67232 voxels
+ Filled 92 voxels in small holes; now have 67324 voxels
+ Filled 1 voxels in large holes; now have 67325 voxels
+ Clustering voxels ...
+ Largest cluster has 67325 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 258000 voxels
+ Mask now has 67325 voxels
++ 67325 voxels in the mask [out of 325325: 20.69%]
++ first 9 x-planes are zero [from L]
++ last 8 x-planes are zero [from R]
++ first 9 y-planes are zero [from P]
++ last 7 y-planes are zero [from A]
++ first 0 z-planes are zero [from I]
++ last 11 z-planes are zero [from S]
++ CPU time = 0.000000 sec
end
3dmask_tool -inputs rm.mask_r01+tlrc.HEAD rm.mask_r02+tlrc.HEAD rm.mask_r03+tlrc.HEAD -union -prefix full_mask.s1562
++ processing 3 input dataset(s), NN=2...
++ padding all datasets by 0 (for dilations)
++ frac 0 over 3 volumes gives min count 0
++ voxel limits: 0 clipped, 67713 survived, 257612 were zero
++ writing result full_mask.s1562...
foreach run ( 01 02 03 )
3dTstat -prefix rm.mean_r01 pb01.s1562.r01.blur+tlrc
++ 3dTstat: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.mean_r01+tlrc.BRIK
3dcalc -a pb01.s1562.r01.blur+tlrc -b rm.mean_r01+tlrc -expr min(200, a/b*100)*step(a)*step(b) -prefix pb02.s1562.r01.scale
++ 3dcalc: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.s1562.r01.scale+tlrc.BRIK
end
3dTstat -prefix rm.mean_r02 pb01.s1562.r02.blur+tlrc
++ 3dTstat: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.mean_r02+tlrc.BRIK
3dcalc -a pb01.s1562.r02.blur+tlrc -b rm.mean_r02+tlrc -expr min(200, a/b*100)*step(a)*step(b) -prefix pb02.s1562.r02.scale
++ 3dcalc: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.s1562.r02.scale+tlrc.BRIK
end
3dTstat -prefix rm.mean_r03 pb01.s1562.r03.blur+tlrc
++ 3dTstat: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.mean_r03+tlrc.BRIK
3dcalc -a pb01.s1562.r03.blur+tlrc -b rm.mean_r03+tlrc -expr min(200, a/b*100)*step(a)*step(b) -prefix pb02.s1562.r03.scale
++ 3dcalc: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.s1562.r03.scale+tlrc.BRIK
end
1d_tool.py -infile sub-s1562_task-seat_allruns_motion.1D -set_nruns 3 -demean -write motion_demean.1D
1d_tool.py -infile sub-s1562_task-seat_allruns_motion.1D -set_nruns 3 -derivative -demean -write motion_deriv.1D
1d_tool.py -infile motion_demean.1D -set_nruns 3 -split_into_pad_runs mot_demean
3dDeconvolve -input pb02.s1562.r01.scale+tlrc.HEAD pb02.s1562.r02.scale+tlrc.HEAD pb02.s1562.r03.scale+tlrc.HEAD -ortvec stimuli/sub-s1562_task-seat_allruns_aCompCor6.1D aCompcor6 -ortvec stimuli/sub-s1562_task-seat_allruns_cosine.1D cosine -ortvec stimuli/sub-s1562_task-seat_allruns_fd.1D fd -ortvec mot_demean.r01.1D mot_demean_r01 -ortvec mot_demean.r02.1D mot_demean_r02 -ortvec mot_demean.r03.1D mot_demean_r03 -polort 2 -float -num_stimts 14 -stim_times_AM1 1 stimuli/offset_class_agg.1D dmBLOCK(1) -stim_label 1 Class -stim_times_AM1 2 stimuli/offset_Mean_anticipation_agg.1D dmBLOCK(1) -stim_label 2 Ant.Mean -stim_times_AM1 3 stimuli/offset_Mean_feedback_agg.1D dmBLOCK(1) -stim_label 3 FB.Mean -stim_times_AM1 4 stimuli/offset_Mean_response_agg.1D dmBLOCK(1) -stim_label 4 Resp.Mean -stim_times_AM1 5 stimuli/offset_Nice_anticipation_agg.1D dmBLOCK(1) -stim_label 5 Ant.Nice -stim_times_AM1 6 stimuli/offset_Nice_feedback_agg.1D dmBLOCK(1) -stim_label 6 FB.Nice -stim_times_AM1 7 stimuli/offset_Nice_response_agg.1D dmBLOCK(1) -stim_label 7 Resp.Nice -stim_times_AM1 8 stimuli/offset_UnpMean_anticipation_agg.1D dmBLOCK(1) -stim_label 8 Ant.UnpMean -stim_times_AM1 9 stimuli/offset_UnpMean_feedback_agg.1D dmBLOCK(1) -stim_label 9 FB.UnpMean -stim_times_AM1 10 stimuli/offset_UnpMean_response_agg.1D dmBLOCK(1) -stim_label 10 Resp.UnpMean -stim_times_AM1 11 stimuli/offset_UnpNice_anticipation_agg.1D dmBLOCK(1) -stim_label 11 Ant.UnpNice -stim_times_AM1 12 stimuli/offset_UnpNice_feedback_agg.1D dmBLOCK(1) -stim_label 12 FB.UnpNice -stim_times_AM1 13 stimuli/offset_UnpNice_response_agg.1D dmBLOCK(1) -stim_label 13 Resp.UnpNice -stim_times_AM1 14 stimuli/offset_missing_agg.1D dmBLOCK(1) -stim_label 14 Missing -num_glt 14 -gltsym SYM: +Ant.Mean[1] +FB.Mean[1] +Resp.Mean[1] +Ant.Nice[1]
+FB.Nice[1] +Resp.Nice[1] +Ant.UnpMean[1] +FB.UnpMean[1] +Resp.UnpMean[1]
+Ant.UnpNice[1] +FB.UnpNice[1] +Resp.Nice[1] -glt_label 1 Task.V.BL -gltsym SYM: +Ant.Mean[1] +Ant.Nice[1] +Ant.UnpMean[1] +Ant.UnpNice[1] -glt_label 2 Ant.V.BL -gltsym SYM: +Ant.Mean[1] -Ant.Nice[1] -glt_label 3 Ant.Mean.V.Nice -gltsym SYM: +Ant.Mean[1] +Ant.Nice[1] -Ant.UnpMean[1] -Ant.UnpNice[1] -glt_label 4 Ant.Pred.V.Unp -gltsym SYM: +FB.Mean[1] +FB.Nice[1] +FB.UnpMean[1] +FB.UnpNice[1] -glt_label 5 FB.V.BL -gltsym SYM: +FB.Mean[1] +FB.UnpMean[1] -FB.Nice[1] -FB.UnpNice[1] -glt_label 6 FB.Mean.V.Nice -gltsym SYM: +FB.Mean[1] -FB.UnpMean[1] -glt_label 7 FB.Mean.V.UnpMean -gltsym SYM: +FB.Nice[1] -FB.UnpNice[1] -glt_label 8 FB.Nice.V.UnpNice -gltsym SYM: +FB.Mean[1] +FB.Nice[1] -FB.UnpMean[1] -FB.UnpNice[1] -glt_label 9 FB.Pred.V.Unp -gltsym SYM: +Resp.Mean[1] +Resp.Nice[1] +Resp.UnpMean[1]
+Resp.UnpNice[1] -glt_label 10 Resp.V.BL -gltsym SYM: +Resp.Mean[1] -Resp.Nice[1] -glt_label 11 Resp.Mean.V.Nice -gltsym SYM: +Resp.Mean[1] -Resp.UnpMean[1] -glt_label 12 Resp.Mean.V.UnpMean -gltsym SYM: +Resp.Nice[1] -Resp.UnpNice[1] -glt_label 13 Resp.Nice.V.UnpNice -gltsym SYM: +Resp.Mean[1] +Resp.Nice[1] -Resp.UnpMean[1]
-Resp.UnpNice[1] -glt_label 14 Resp.Pred.V.Unp -cbucket cbucket.stats.s1562 -jobs 30 -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -fitts fitts.s1562 -errts errts.s1562 -bucket stats.s1562
*+ WARNING: '-stim_times_AM1 1' didn't read any good times from file 'stimuli/offset_class_agg.1D'
++ '-stim_times_AM1 1 stimuli/offset_class_agg.1D' has 1 auxiliary values per time point
++ '-stim_times_AM1 1': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 1 found in timing file 'stimuli/offset_class_agg.1D'
++ '-stim_times_AM1 2 stimuli/offset_Mean_anticipation_agg.1D' has 2 auxiliary values per time point
++ '-stim_times_AM1 2': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 2 found in timing file 'stimuli/offset_Mean_anticipation_agg.1D'
++ '-stim_times_AM1 3 stimuli/offset_Mean_feedback_agg.1D' has 2 auxiliary values per time point
++ '-stim_times_AM1 3': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 2 found in timing file 'stimuli/offset_Mean_feedback_agg.1D'
++ '-stim_times_AM1 4 stimuli/offset_Mean_response_agg.1D' has 2 auxiliary values per time point
++ '-stim_times_AM1 4': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 2 found in timing file 'stimuli/offset_Mean_response_agg.1D'
++ '-stim_times_AM1 5 stimuli/offset_Nice_anticipation_agg.1D' has 2 auxiliary values per time point
++ '-stim_times_AM1 5': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 2 found in timing file 'stimuli/offset_Nice_anticipation_agg.1D'
++ '-stim_times_AM1 6 stimuli/offset_Nice_feedback_agg.1D' has 2 auxiliary values per time point
++ '-stim_times_AM1 6': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 2 found in timing file 'stimuli/offset_Nice_feedback_agg.1D'
++ '-stim_times_AM1 7 stimuli/offset_Nice_response_agg.1D' has 2 auxiliary values per time point
++ '-stim_times_AM1 7': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 2 found in timing file 'stimuli/offset_Nice_response_agg.1D'
++ '-stim_times_AM1 8 stimuli/offset_UnpMean_anticipation_agg.1D' has 2 auxiliary values per time point
++ '-stim_times_AM1 8': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 2 found in timing file 'stimuli/offset_UnpMean_anticipation_agg.1D'
++ '-stim_times_AM1 9 stimuli/offset_UnpMean_feedback_agg.1D' has 2 auxiliary values per time point
++ '-stim_times_AM1 9': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 2 found in timing file 'stimuli/offset_UnpMean_feedback_agg.1D'
++ '-stim_times_AM1 10 stimuli/offset_UnpMean_response_agg.1D' has 2 auxiliary values per time point
++ '-stim_times_AM1 10': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 2 found in timing file 'stimuli/offset_UnpMean_response_agg.1D'
++ '-stim_times_AM1 11 stimuli/offset_UnpNice_anticipation_agg.1D' has 2 auxiliary values per time point
++ '-stim_times_AM1 11': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 2 found in timing file 'stimuli/offset_UnpNice_anticipation_agg.1D'
++ '-stim_times_AM1 12 stimuli/offset_UnpNice_feedback_agg.1D' has 2 auxiliary values per time point
++ '-stim_times_AM1 12': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 2 found in timing file 'stimuli/offset_UnpNice_feedback_agg.1D'
++ '-stim_times_AM1 13 stimuli/offset_UnpNice_response_agg.1D' has 2 auxiliary values per time point
++ '-stim_times_AM1 13': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 2 found in timing file 'stimuli/offset_UnpNice_response_agg.1D'
++ '-stim_times_AM1 14 stimuli/offset_missing_agg.1D' has 1 auxiliary values per time point
++ '-stim_times_AM1 14': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 1 found in timing file 'stimuli/offset_missing_agg.1D'
++ 3dDeconvolve extending num_stimts from 14 to 42 due to -ortvec
++ 3dDeconvolve: AFNI version=AFNI_22.1.10 (May 20 2022) [64-bit]
++ Authored by: B. Douglas Ward, et al.
++ loading dataset pb02.s1562.r01.scale+tlrc.HEAD pb02.s1562.r02.scale+tlrc.HEAD pb02.s1562.r03.scale+tlrc.HEAD
++ Auto-catenated input datasets treated as multiple imaging runs
++ Auto-catenated datasets start at: 0 167 334
++ STAT automask has 312819 voxels (out of 325325 = 96.2%)
++ Skipping check for initial transients
++ Input polort=2; Longest run=292.2 s; Recommended minimum polort=2 ++ OK ++
++ -stim_times using TR=1.75 s for stimulus timing conversion
++ -stim_times using TR=1.75 s for any -iresp output datasets
++ [you can alter the -iresp TR via the -TR_times option]
++ ** -stim_times NOTE ** guessing GLOBAL times if 1 time per line; LOCAL otherwise
++ ** GUESSED ** -stim_times_AM1 1 using GLOBAL times
*+ WARNING: '-stim_times_AM1 1' (GLOBAL) has 3 times outside range 0 .. 875 [PSFB syndrome]
+ dataset TR being used is 1.75 s -- unusable times follow
-0.82 -0.82 -0.815
*+ WARNING: '-stim_times_AM1 1' (GLOBAL) has 3 runs and 3 early events; do you want LOCAL times?
*+ WARNING: !! '-stim_times_AM1 1' file 'stimuli/offset_class_agg.1D' has no good stimulus time values
++ ** GUESSED ** -stim_times_AM1 2 using LOCAL times
++ '-stim_times_AM1 2' average amplitude#1=4.83333
++ ** GUESSED ** -stim_times_AM1 3 using LOCAL times
++ '-stim_times_AM1 3' average amplitude#1=4.83333
++ ** GUESSED ** -stim_times_AM1 4 using LOCAL times
++ '-stim_times_AM1 4' average amplitude#1=4.83333
++ ** GUESSED ** -stim_times_AM1 5 using LOCAL times
++ '-stim_times_AM1 5' average amplitude#1=1.17391
++ ** GUESSED ** -stim_times_AM1 6 using LOCAL times
++ '-stim_times_AM1 6' average amplitude#1=1.17391
++ ** GUESSED ** -stim_times_AM1 7 using LOCAL times
++ '-stim_times_AM1 7' average amplitude#1=1.17391
++ ** GUESSED ** -stim_times_AM1 8 using LOCAL times
++ '-stim_times_AM1 8' average amplitude#1=4.7
++ ** GUESSED ** -stim_times_AM1 9 using LOCAL times
++ '-stim_times_AM1 9' average amplitude#1=4.7
++ ** GUESSED ** -stim_times_AM1 10 using LOCAL times
++ '-stim_times_AM1 10' average amplitude#1=4.7
++ ** GUESSED ** -stim_times_AM1 11 using LOCAL times
++ '-stim_times_AM1 11' average amplitude#1=1.33333
++ ** GUESSED ** -stim_times_AM1 12 using LOCAL times
++ '-stim_times_AM1 12' average amplitude#1=1.33333
++ ** GUESSED ** -stim_times_AM1 13 using LOCAL times
++ '-stim_times_AM1 13' average amplitude#1=1.33333
++ ** GUESSED ** -stim_times_AM1 14 using LOCAL times
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
** ERROR: selector index 1 is out of range 0..0
++ Number of time points: 501 (no censoring)
+ Number of parameters: 51 [37 baseline ; 14 signal]
++ total shared memory needed = 1,510,809,300 bytes (about 1.5 billion)
++ mmap() memory allocated: 1,510,809,300 bytes (about 1.5 billion)
++ Memory required for output bricks = 1,510,809,300 bytes (about 1.5 billion)
++ Wrote matrix image to file X.jpg
++ Wrote matrix values to file X.xmat.1D
++ ========= Things you can do with the matrix file =========
++ (a) Linear regression with ARMA(1,1) modeling of serial correlation:

3dREMLfit -matrix X.xmat.1D \
-input "pb02.s1562.r01.scale+tlrc.HEAD pb02.s1562.r02.scale+tlrc.HEAD pb02.s1562.r03.scale+tlrc.HEAD" \
-Rbeta cbucket.stats.s1562_REML -fout -tout \
-Rbuck stats.s1562_REML -Rvar stats.s1562_REMLvar \
-Rfitts fitts.s1562_REML -Rerrts errts.s1562_REML -verb

++ N.B.: 3dREMLfit command above written to file stats.REML_cmd
++ (b) Visualization/analysis of the matrix via ExamineXmat.R
++ (c) Synthesis of sub-model datasets using 3dSynthesize
++ ==========================================================
*+ WARNING: -------------------------------------------------
*+ WARNING: Problems with the X matrix columns, listed below:
*+ WARNING: !! * Column 9 [Class#0] is all zeros
*+ WARNING: -------------------------------------------------
++ ----- Signal+Baseline matrix condition [X] (501x51): 9.92415 ++ VERY GOOD ++
*+ WARNING: !! in Signal+Baseline matrix:
* Largest singular value=2.50049
* 1 singular value is less than cutoff=2.50049e-07
* Implies strong collinearity in the matrix columns!
++ Signal+Baseline matrix singular values:
0 0.0253885 0.128598 0.151882 0.211466
0.22749 0.234306 0.261982 0.285499 0.310245
0.335758 0.350405 0.360276 0.366475 0.374521
0.390237 0.433172 0.47747 0.497689 0.555097
0.599489 0.637913 0.669912 0.704474 0.746848
0.783447 0.801076 0.820244 0.840997 0.847241
0.877699 0.949127 0.97059 0.999486 1.00646
1.02078 1.06083 1.08016 1.09913 1.15742
1.23871 1.28252 1.3154 1.44887 1.5474
1.58601 1.61843 1.74696 1.85904 2.09059
2.50049
++ ----- Signal-only matrix condition [X] (501x14): 2.01313 ++ VERY GOOD ++
*+ WARNING: !! in Signal-only matrix:
* Largest singular value=1.50129
* 1 singular value is less than cutoff=1.50129e-07
* Implies strong collinearity in the matrix columns!
++ Signal-only matrix singular values:
0 0.370443 0.371494 0.380213 0.402958
0.779105 0.835917 0.846634 0.854421 1.00465
1.45674 1.45911 1.46661 1.50129
++ ----- Baseline-only matrix condition [X] (501x37): 9.38201 ++ VERY GOOD ++
++ ----- stim_base-only matrix condition [X] (501x28): 4.02162 ++ VERY GOOD ++
++ ----- polort-only matrix condition [X] (501x9): 1 ++ VERY GOOD ++
++ +++++ Matrix inverse average error = 0.000384468 ++ OK ++
++ Matrix setup time = 1.55 s
** ERROR: !! 3dDeconvolve: Can't run past 4 matrix warnings without '-GOFORIT 4'
** ERROR: !! Currently at -GOFORIT 0
** ERROR: !! See file 3dDeconvolve.err for all WARNING and ERROR messages !!
** ERROR: !! Be sure you understand what you are doing before using -GOFORIT !!
** ERROR: !! If in doubt, consult with someone or with the AFNI message board !!
** FATAL ERROR: !! 3dDeconvolve (regretfully) shuts itself down !!
** Program compile date = May 20 2022
cla19097:/data/projects/STUDIES/SEAT/fMRI/code/afni/Aim1>
Subject Author Posted

regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 09:55AM

Re: regress_stim_times_offset after fmriPREP

Peter Molfese June 14, 2022 10:50AM

Re: regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 11:01AM

Re: regress_stim_times_offset after fmriPREP

rick reynolds June 14, 2022 11:05AM

Re: regress_stim_times_offset after fmriPREP

rick reynolds June 14, 2022 11:06AM

Re: regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 12:14PM

Re: regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 12:23PM

Re: regress_stim_times_offset after fmriPREP

rick reynolds June 14, 2022 02:11PM

Re: regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 02:14PM

Re: regress_stim_times_offset after fmriPREP

rick reynolds June 14, 2022 03:11PM

Re: regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 03:18PM

Re: regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 03:20PM

Re: regress_stim_times_offset after fmriPREP

rick reynolds June 14, 2022 04:05PM

Re: regress_stim_times_offset after fmriPREP

MeganQ June 14, 2022 04:11PM



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