afni.nimh.nih.gov
| October 24, 2019 01:34PM | |
Registered: 5 years ago Posts: 16 |
Hello Rick,
I am sorry that I already deleted the results folder because the folder size is very big (over 150GB), and I had to free up the disc space for other operation. Now that I have ran the script again, the process was killed during warping this time. I copy the output file below. Could this be a hardware problem as I also notice that this Linux machine was getting noticeably slow when I opened a new script or web browser?
Sungjin
echo auto-generated by afni_proc.py, Tue Oct 15 15:34:29 2019
auto-generated by afni_proc.py, Tue Oct 15 15:34:29 2019
echo (version 6.32, February 22, 2019)
(version 6.32, February 22, 2019)
echo execution started: `date`
date
execution started: Thu Oct 24 12:06:21 EDT 2019
afni -ver
Precompiled binary linux_ubuntu_16_64: Mar 20 2019 (Version AFNI_19.0.26 'Tiberius')
afni_history -check_date 17 Jan 2019
-- is current: afni_history as new as: 17 Jan 2019
most recent entry is: 20 Mar 2019
if ( 0 ) then
if ( 0 > 0 ) then
set subj = 265001
endif
set sNUM = 1
set output_dir = 265001.s1.results
if ( -d 265001.s1.results ) then
set runs = ( `count -digits 2 1 6` )
count -digits 2 1 6
mkdir 265001.s1.results
mkdir 265001.s1.results/stimuli
cp /home/sungjin/fMRI/CGE/CGE_Raw_Data/Timing_CGE.txt 265001.s1.results/stimuli
3dcopy CGE_Raw_Data/Session1/265001_S1/subject_raw/anatSS.SSW.nii 265001.s1.results/anatSS.SSW
++ 3dcopy: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
3dcopy CGE_Raw_Data/Session1/265001_S1/subject_raw/anatQQ.SSW.nii 265001.s1.results/anatQQ.SSW
++ 3dcopy: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
3dcopy CGE_Raw_Data/Session1/265001_S1/subject_raw/anatQQ.SSW.aff12.1D 265001.s1.results/anatQQ.SSW.aff12.1D
++ 3dcopy: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
3dcopy CGE_Raw_Data/Session1/265001_S1/subject_raw/anatQQ.SSW_WARP.nii 265001.s1.results/anatQQ.SSW_WARP.nii
++ 3dcopy: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
3dTcat -prefix 265001.s1.results/pb00.265001.r01.tcat CGE_Raw_Data/Session1/265001_S1/subject_raw/raw.rest1.s1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ elapsed time = 0.8 s
3dTcat -prefix 265001.s1.results/pb00.265001.r02.tcat CGE_Raw_Data/Session1/265001_S1/subject_raw/raw.pv.s1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ elapsed time = 0.6 s
3dTcat -prefix 265001.s1.results/pb00.265001.r03.tcat CGE_Raw_Data/Session1/265001_S1/subject_raw/raw.14p.s1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ elapsed time = 0.6 s
3dTcat -prefix 265001.s1.results/pb00.265001.r04.tcat CGE_Raw_Data/Session1/265001_S1/subject_raw/raw.6p.s1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ elapsed time = 0.6 s
3dTcat -prefix 265001.s1.results/pb00.265001.r05.tcat CGE_Raw_Data/Session1/265001_S1/subject_raw/raw.flk.s1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ elapsed time = 0.6 s
3dTcat -prefix 265001.s1.results/pb00.265001.r06.tcat CGE_Raw_Data/Session1/265001_S1/subject_raw/raw.rest2.s1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ elapsed time = 0.7 s
set tr_counts = ( 180 150 150 150 150 180 )
cd 265001.s1.results
touch out.pre_ss_warn.txt
foreach run ( 01 02 03 04 05 06 )
3dToutcount -automask -fraction -polort 3 -legendre pb00.265001.r01.tcat+orig
++ 3dToutcount: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r01.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r01.tcat+orig.BRIK is 0.799908 degrees from plumb.
++ 33485 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r01.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.265001.r02.tcat+orig
++ 3dToutcount: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r02.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r02.tcat+orig.BRIK is 0.799908 degrees from plumb.
++ 33500 voxels passed mask/clip
if ( `1deval -a outcount.r$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 3 -legendre pb00.265001.r03.tcat+orig
++ 3dToutcount: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r03.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r03.tcat+orig.BRIK is 0.799908 degrees from plumb.
++ 33501 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r03.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.265001.r04.tcat+orig
++ 3dToutcount: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r04.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r04.tcat+orig.BRIK is 0.799908 degrees from plumb.
++ 33658 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r04.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.265001.r05.tcat+orig
++ 3dToutcount: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r05.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r05.tcat+orig.BRIK is 0.799908 degrees from plumb.
++ 33509 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r05.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.265001.r06.tcat+orig
++ 3dToutcount: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r06.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r06.tcat+orig.BRIK is 0.799908 degrees from plumb.
++ 33587 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r06.1D{0} -expr step(a-0.4)
end
cat outcount.r01.1D outcount.r02.1D outcount.r03.1D outcount.r04.1D outcount.r05.1D outcount.r06.1D
set minindex = `3dTstat -argmin -prefix - outcount_rall.1D\'`
3dTstat -argmin -prefix - outcount_rall.1D'
++ 3dTstat: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: KR Hammett & RW Cox
[7m*+ WARNING:[0m Input dataset is not 3D+time; assuming TR=1.0
set ovals = ( `1d_tool.py -set_run_lengths $tr_counts
-index_to_run_tr $minindex` )
1d_tool.py -set_run_lengths 180 150 150 150 150 180 -index_to_run_tr 15
set minoutrun = 01
set minouttr = 15
echo min outlier: run 01, TR 15
tee out.min_outlier.txt
min outlier: run 01, TR 15
foreach run ( 01 02 03 04 05 06 )
3dTshift -tzero 0 -quintic -prefix pb01.265001.r01.tshift pb00.265001.r01.tcat+orig
++ 3dTshift: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r01.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r01.tcat+orig.BRIK is 0.799908 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.265001.r02.tshift pb00.265001.r02.tcat+orig
++ 3dTshift: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r02.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r02.tcat+orig.BRIK is 0.799908 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.265001.r03.tshift pb00.265001.r03.tcat+orig
++ 3dTshift: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r03.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r03.tcat+orig.BRIK is 0.799908 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.265001.r04.tshift pb00.265001.r04.tcat+orig
++ 3dTshift: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r04.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r04.tcat+orig.BRIK is 0.799908 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.265001.r05.tshift pb00.265001.r05.tcat+orig
++ 3dTshift: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r05.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r05.tcat+orig.BRIK is 0.799908 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.265001.r06.tshift pb00.265001.r06.tcat+orig
++ 3dTshift: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r06.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r06.tcat+orig.BRIK is 0.799908 degrees from plumb.
end
foreach run ( 01 02 03 04 05 06 )
3dDespike -NEW -nomask -prefix pb02.265001.r01.despike pb01.265001.r01.tshift+orig
++ 3dDespike: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb01.265001.r01.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.265001.r01.tshift+orig.BRIK is 0.799908 degrees from plumb.
++ Input dataset is in short format, but output will be in float format
++ ignoring first 0 time points, using last 180
++ using 180 time points => -corder 6
++ Loading dataset pb01.265001.r01.tshift+orig
++ processing all 143360 voxels in dataset
++ Procesing time series with NEW model fit algorithm
++ smash edit thresholds: 3.1 .. 5.0 MADs
+ [ 3.457% .. 0.072% of normal distribution]
+ [ 8.839% .. 3.125% of Laplace distribution]
++ start OpenMP thread #0
++ start OpenMP thread #1
++ start OpenMP thread #2
++ start OpenMP thread #3
.............................................................
++ Elapsed despike time = 905ms
++ FINAL: 25004700 data points, 1285900 edits [5.143%], 233777 big edits [0.935%]
++ Output dataset ./pb02.265001.r01.despike+orig.BRIK
end
3dDespike -NEW -nomask -prefix pb02.265001.r02.despike pb01.265001.r02.tshift+orig
++ 3dDespike: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb01.265001.r02.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.265001.r02.tshift+orig.BRIK is 0.799908 degrees from plumb.
++ Input dataset is in short format, but output will be in float format
++ ignoring first 0 time points, using last 150
++ using 150 time points => -corder 5
++ Loading dataset pb01.265001.r02.tshift+orig
++ processing all 143360 voxels in dataset
++ Procesing time series with NEW model fit algorithm
++ smash edit thresholds: 3.1 .. 5.0 MADs
+ [ 3.457% .. 0.072% of normal distribution]
+ [ 8.839% .. 3.125% of Laplace distribution]
++ start OpenMP thread #0
++ start OpenMP thread #3
++ start OpenMP thread #2
++ start OpenMP thread #1
.............................................................
++ Elapsed despike time = 691ms
++ FINAL: 20837250 data points, 979211 edits [4.699%], 149477 big edits [0.717%]
++ Output dataset ./pb02.265001.r02.despike+orig.BRIK
end
3dDespike -NEW -nomask -prefix pb02.265001.r03.despike pb01.265001.r03.tshift+orig
++ 3dDespike: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb01.265001.r03.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.265001.r03.tshift+orig.BRIK is 0.799908 degrees from plumb.
++ Input dataset is in short format, but output will be in float format
++ ignoring first 0 time points, using last 150
++ using 150 time points => -corder 5
++ Loading dataset pb01.265001.r03.tshift+orig
++ processing all 143360 voxels in dataset
++ Procesing time series with NEW model fit algorithm
++ smash edit thresholds: 3.1 .. 5.0 MADs
+ [ 3.457% .. 0.072% of normal distribution]
+ [ 8.839% .. 3.125% of Laplace distribution]
++ start OpenMP thread #1
++ start OpenMP thread #0
++ start OpenMP thread #2
++ start OpenMP thread #3
.............................................................
++ Elapsed despike time = 671ms
++ FINAL: 20837250 data points, 932750 edits [4.476%], 100598 big edits [0.483%]
++ Output dataset ./pb02.265001.r03.despike+orig.BRIK
end
3dDespike -NEW -nomask -prefix pb02.265001.r04.despike pb01.265001.r04.tshift+orig
++ 3dDespike: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb01.265001.r04.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.265001.r04.tshift+orig.BRIK is 0.799908 degrees from plumb.
++ Input dataset is in short format, but output will be in float format
++ ignoring first 0 time points, using last 150
++ using 150 time points => -corder 5
++ Loading dataset pb01.265001.r04.tshift+orig
++ processing all 143360 voxels in dataset
++ Procesing time series with NEW model fit algorithm
++ smash edit thresholds: 3.1 .. 5.0 MADs
+ [ 3.457% .. 0.072% of normal distribution]
+ [ 8.839% .. 3.125% of Laplace distribution]
++ start OpenMP thread #1
++ start OpenMP thread #3
++ start OpenMP thread #0
++ start OpenMP thread #2
.............................................................
++ Elapsed despike time = 667ms
++ FINAL: 20837250 data points, 806934 edits [3.873%], 62777 big edits [0.301%]
++ Output dataset ./pb02.265001.r04.despike+orig.BRIK
end
3dDespike -NEW -nomask -prefix pb02.265001.r05.despike pb01.265001.r05.tshift+orig
++ 3dDespike: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb01.265001.r05.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.265001.r05.tshift+orig.BRIK is 0.799908 degrees from plumb.
++ Input dataset is in short format, but output will be in float format
++ ignoring first 0 time points, using last 150
++ using 150 time points => -corder 5
++ Loading dataset pb01.265001.r05.tshift+orig
++ processing all 143360 voxels in dataset
++ Procesing time series with NEW model fit algorithm
++ smash edit thresholds: 3.1 .. 5.0 MADs
+ [ 3.457% .. 0.072% of normal distribution]
+ [ 8.839% .. 3.125% of Laplace distribution]
++ start OpenMP thread #0
++ start OpenMP thread #2
++ start OpenMP thread #1
++ start OpenMP thread #3
.............................................................
++ Elapsed despike time = 719ms
++ FINAL: 20837250 data points, 1004426 edits [4.820%], 214664 big edits [1.030%]
++ Output dataset ./pb02.265001.r05.despike+orig.BRIK
end
3dDespike -NEW -nomask -prefix pb02.265001.r06.despike pb01.265001.r06.tshift+orig
++ 3dDespike: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb01.265001.r06.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.265001.r06.tshift+orig.BRIK is 0.799908 degrees from plumb.
++ Input dataset is in short format, but output will be in float format
++ ignoring first 0 time points, using last 180
++ using 180 time points => -corder 6
++ Loading dataset pb01.265001.r06.tshift+orig
++ processing all 143360 voxels in dataset
++ Procesing time series with NEW model fit algorithm
++ smash edit thresholds: 3.1 .. 5.0 MADs
+ [ 3.457% .. 0.072% of normal distribution]
+ [ 8.839% .. 3.125% of Laplace distribution]
++ start OpenMP thread #2
++ start OpenMP thread #0
++ start OpenMP thread #3
++ start OpenMP thread #1
.............................................................
++ Elapsed despike time = 826ms
++ FINAL: 25004700 data points, 1076068 edits [4.303%], 128650 big edits [0.515%]
++ Output dataset ./pb02.265001.r06.despike+orig.BRIK
end
3dbucket -prefix vr_base_min_outlier pb02.265001.r01.despike+orig[15]
++ 3dbucket: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
align_epi_anat.py -anat2epi -anat anatSS.SSW+orig -suffix _al_junk -epi vr_base_min_outlier+orig -epi_base 0 -epi_strip 3dAutomask -anat_has_skull no -cost lpc+ZZ -volreg off -tshift off
#++ align_epi_anat version: 1.58
#++ turning off volume registration
#Script is running (command trimmed):
3dAttribute DELTA ./vr_base_min_outlier+orig
#Script is running (command trimmed):
3dAttribute DELTA ./vr_base_min_outlier+orig
#Script is running:
3dAttribute DELTA /home/sungjin/fMRI/CGE/265001.s1.results/anatSS.SSW+orig
#++ Multi-cost is lpc+ZZ
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_vr_base_min_outlier*
#Script is running:
\rm -f ./__tt_anatSS.SSW*
#Script is running (command trimmed):
3dcopy ./anatSS.SSW+orig ./__tt_anatSS.SSW+orig
++ 3dcopy: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
#Script is running (command trimmed):
3dinfo ./__tt_anatSS.SSW+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /home/sungjin/fMRI/CGE/265001.s1.results/__tt_anatSS.SSW+orig is not oblique
#Script is running (command trimmed):
3dinfo ./vr_base_min_outlier+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /home/sungjin/fMRI/CGE/265001.s1.results/vr_base_min_outlier+orig is ***oblique****
#Script is running:
3dAttribute DELTA /home/sungjin/fMRI/CGE/265001.s1.results/__tt_anatSS.SSW+orig
#++ Spacing for anat to oblique epi alignment is 1.000000
#++ Matching obliquity of anat to epi
#Script is running (command trimmed):
3dWarp -verb -card2oblique ./vr_base_min_outlier+orig -prefix ./__tt_anatSS.SSW_ob -newgrid 1.000000 ./__tt_anatSS.SSW+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./__tt_anatSS.SSW_obla2e_mat.1D
++ 3dWarp: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
#++ using 0th sub-brick because only one found
#Script is running (command trimmed):
3dbucket -prefix ./__tt_vr_base_min_outlier_ts ./vr_base_min_outlier+orig'[0]'
++ 3dbucket: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
#++ resampling epi to match anat data
#Script is running (command trimmed):
3dresample -master ./__tt_anatSS.SSW_ob+orig -prefix ./__tt_vr_base_min_outlier_ts_rs -inset ./__tt_vr_base_min_outlier_ts+orig'' -rmode Cu
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./__tt_vr_base_min_outlier_ts+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./__tt_vr_base_min_outlier_ts+orig.BRIK is 0.799908 degrees from plumb.
#++ removing skull or area outside brain
#Script is running (command trimmed):
3dAutomask -apply_prefix ./__tt_vr_base_min_outlier_ts_rs_ns ./__tt_vr_base_min_outlier_ts_rs+orig
++ 3dAutomask: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset ./__tt_vr_base_min_outlier_ts_rs+orig
++ Forming automask
+ Fixed clip level = 417.475769
+ Used gradual clip level = 139.019440 .. 478.463043
+ Number voxels above clip level = 98910
+ Clustering voxels ...
+ Largest cluster has 86317 voxels
+ Clustering voxels ...
+ Largest cluster has 85339 voxels
+ Filled 142 voxels in small holes; now have 85481 voxels
+ Filled 16044 voxels in large holes; now have 101525 voxels
+ Clustering voxels ...
+ Largest cluster has 101460 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 11879879 voxels
+ Mask now has 101461 voxels
++ 101461 voxels in the mask [out of 11981340: 0.85%]
++ first 156 x-planes are zero [from R]
++ last 0 x-planes are zero [from L]
++ first 61 y-planes are zero [from A]
++ last 68 y-planes are zero [from P]
++ first 84 z-planes are zero [from I]
++ last 79 z-planes are zero [from S]
++ applying mask to original data
++ Writing masked data
++ CPU time = 0.000000 sec
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_min_outlier_ts_rs_ns+orig
#++ Applying threshold of 1024.127319 on /home/sungjin/fMRI/CGE/265001.s1.results/__tt_vr_base_min_outlier_ts_rs_ns+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix ./__tt_vr_base_min_outlier_ts_rs_ns_wt -a ./__tt_vr_base_min_outlier_ts_rs_ns+orig -expr 'min(1,(a/1024.127319))'
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
#++ Aligning anat data to epi data
#Script is running (command trimmed):
3dAllineate -lpc+ZZ -wtprefix ./__tt_anatSS.SSW_ob_al_junk_wtal -weight ./__tt_vr_base_min_outlier_ts_rs_ns_wt+orig -source ./__tt_anatSS.SSW_ob+orig -prefix ./__tt_anatSS.SSW_ob_temp_al_junk -base ./__tt_vr_base_min_outlier_ts_rs_ns+orig -nocmass -1Dmatrix_save ./anatSS.SSW_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
++ 3dAllineate: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: Zhark the Registrator
++ lpc+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration]
++ Source dataset: ./__tt_anatSS.SSW_ob+orig.HEAD
++ Base dataset: ./__tt_vr_base_min_outlier_ts_rs_ns+orig.HEAD
++ Loading datasets
++ 1481954 voxels in -source_automask+4
++ Zero-pad: xbot=0 xtop=4
++ 101398 voxels [0.8%] in weight mask
++ Number of points for matching = 101398
++ Local correlation: blok type = 'RHDD(6.54321)'
++ lpc+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration]
++ shift param auto-range: -58.7..58.7 -82.2..82.2 -82.8..82.8
+ Range param#4 [z-angle] = -6.000000 .. 6.000000
+ Range param#5 [x-angle] = -6.000000 .. 6.000000
+ Range param#6 [y-angle] = -6.000000 .. 6.000000
+ Range param#1 [x-shift] = -10.000000 .. 10.000000
+ Range param#2 [y-shift] = -10.000000 .. 10.000000
+ Range param#3 [z-shift] = -10.000000 .. 10.000000
+ 12 free parameters
++ Normalized convergence radius = 0.001000
++ OpenMP thread count = 4
++ ======= Allineation of 1 sub-bricks using Local Pearson Signed + Others =======
++ ========== sub-brick #0 ========== [total CPU to here=0.0 s]
++ *** Fine pass begins ***
+ * Enter alignment setup routine
+ - copying base image
+ - copying source image
+ - copying weight image
+ - using 101398 points from base image [use_all=0]
+ * Exit alignment setup routine
+ - histogram: source clip 0 .. 0; base clip 0 .. 0
+ - versus source range 0 .. 964.198; base range -43.9971 .. 1367.43
+ 83524 total points stored in 177 'RHDD(6.54321)' bloks
+ - Initial cost = 40.199402
+ - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
**********************************
+ - Finalish cost = 39.493938 ; 186 funcs
+ - Set lpc+ parameters back to purity before Final iterations
+ - histogram: source clip 0 .. 0; base clip 0 .. 0
+ - versus source range 0 .. 964.198; base range -43.9971 .. 1367.43
***************
+ - Final cost = -0.543333 ; 179 funcs
+ Final fine fit Parameters:
x-shift= 5.7113 y-shift= 0.0663 z-shift= -0.2459 ... enorm= 5.7170 mm
z-angle= 0.6580 x-angle= 0.1489 y-angle= -0.2553 ... total= 0.7212 deg
x-scale= 0.9087 y-scale= 0.9985 z-scale= 1.0007 ... vol3D= 0.9079
y/x-shear= 0.0031 z/x-shear= -0.0096 z/y-shear= -0.0009
+ - Fine net CPU time = 0.0 s
++ Computing output image
++ image warp: parameters = 5.7113 0.0663 -0.2459 0.6580 0.1489 -0.2553 0.9087 0.9985 1.0007 0.0031 -0.0096 -0.0009
++ Wrote -1Dmatrix_save ./anatSS.SSW_al_junk_e2a_only_mat.aff12.1D
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 13.1
++ ###########################################################
++ # Please check results visually for alignment quality #
++ ###########################################################
++ # '-autoweight' is recommended when using -lpc or -lpa #
++ # If your results are not good, please try again. #
++ ###########################################################
#Script is running (command trimmed):
cat_matvec -ONELINE ./anatSS.SSW_al_junk_e2a_only_mat.aff12.1D ./__tt_anatSS.SSW_obla2e_mat.1D -I > ./anatSS.SSW_al_junk_mat.aff12.1D
#++ Combining anat to epi and oblique transformations
#Script is running (command trimmed):
3dAllineate -base ./__tt_vr_base_min_outlier_ts_rs_ns+orig -1Dmatrix_apply ./anatSS.SSW_al_junk_mat.aff12.1D -prefix ./anatSS.SSW_al_junk -input ./__tt_anatSS.SSW+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
++ 3dAllineate: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./__tt_anatSS.SSW+orig.HEAD
++ Base dataset: ./__tt_vr_base_min_outlier_ts_rs_ns+orig.HEAD
++ Loading datasets
+ Range param#4 [z-angle] = -6.000000 .. 6.000000
+ Range param#5 [x-angle] = -6.000000 .. 6.000000
+ Range param#6 [y-angle] = -6.000000 .. 6.000000
+ Range param#1 [x-shift] = -10.000000 .. 10.000000
+ Range param#2 [y-shift] = -10.000000 .. 10.000000
+ Range param#3 [z-shift] = -10.000000 .. 10.000000
++ OpenMP thread count = 4
++ ========== Applying transformation to 1 sub-bricks ==========
++ ========== sub-brick #0 ========== [total CPU to here=0.0 s]
+ * Enter alignment setup routine
+ - copying base image
+ - copying source image
+ - no weight image
+ - using 11 points from base image [use_all=0]
+ * Exit alignment setup routine
++ using -1Dmatrix_apply
++ Computing output image
++ image warp: parameters = -0.9084 -0.0088 -0.0179 29.2348 -0.0072 0.9984 0.0026 0.6169 -0.0257 -0.0038 1.0006 1.3968
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 1.0
++ ###########################################################
#++ Creating final output: anat data aligned to epi
# copy is not necessary
#++ Saving history
#Script is running (command trimmed):
3dNotes -h "align_epi_anat.py -anat2epi -anat anatSS.SSW+orig -suffix \
_al_junk -epi vr_base_min_outlier+orig -epi_base 0 -epi_strip 3dAutomask \
-anat_has_skull no -cost lpc+ZZ -volreg off -tshift off" \
./anatSS.SSW_al_junk+orig
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_vr_base_min_outlier*
#Script is running:
\rm -f ./__tt_anatSS.SSW*
# Finished alignment successfully
if ( ! -f anatQQ.SSW+tlrc.HEAD ) then
foreach run ( 01 02 03 04 05 06 )
3dvolreg -verbose -zpad 1 -base vr_base_min_outlier+orig -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb02.265001.r01.despike+orig
++ 3dvolreg: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./vr_base_min_outlier+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./vr_base_min_outlier+orig.BRIK is 0.799908 degrees from plumb.
++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK
++ Oblique dataset:./pb02.265001.r01.despike+orig.BRIK is 0.799908 degrees from plumb.
++ Reading input dataset ./pb02.265001.r01.despike+orig.BRIK
++ Edging: x=3 y=3 z=2
++ Creating mask for -maxdisp
+ Automask has 42045 voxels
+ 8524 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 180 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..
++ CPU time for realignment=0 s [=0 s/sub-brick]
++ Min : roll=-1.408 pitch=-0.099 yaw=-1.571 dS=-0.090 dL=-0.354 dP=-0.187
++ Mean: roll=-0.359 pitch=+0.627 yaw=-0.027 dS=+0.342 dL=+0.016 dP=+0.004
++ Max : roll=+0.026 pitch=+1.639 yaw=+0.459 dS=+1.065 dL=+0.413 dP=+0.161
++ Max displacements (mm) for each sub-brick:
0.52(0.00) 0.30(0.34) 0.19(0.17) 0.29(0.18) 0.34(0.12) 0.19(0.25) 0.24(0.15) 0.33(0.14) 0.17(0.21) 0.19(0.12) 0.33(0.20) 0.17(0.19) 0.11(0.12) 0.27(0.21) 0.15(0.15) 0.00(0.15) 0.18(0.18) 0.25(0.15) 0.11(0.17) 0.20(0.15) 0.26(0.12) 0.20(0.18) 0.29(0.13) 0.33(0.15) 0.28(0.22) 0.44(0.19) 0.40(0.18) 0.30(0.12) 0.39(0.23) 0.43(0.13) 0.33(0.19) 0.40(0.17) 0.54(0.16) 0.55(0.19) 0.50(0.19) 0.43(0.12) 0.35(0.19) 0.49(0.29) 0.43(0.19) 0.39(0.13) 0.53(0.20) 0.47(0.17) 0.45(0.11) 0.58(0.16) 0.48(0.26) 0.58(0.11) 0.76(0.56) 0.78(0.23) 0.56(0.37) 0.57(0.14) 0.64(0.20) 0.60(0.24) 0.76(0.31) 0.94(0.33) 0.78(0.35) 2.30(1.79) 2.62(0.35) 1.88(0.83) 2.01(0.17) 1.95(0.16) 1.87(0.27) 1.84(0.18) 1.77(0.10) 1.76(0.23) 1.78(0.16) 1.71(0.13) 1.74(0.28) 1.74(0.19) 1.69(0.10) 1.72(0.23) 1.78(0.19) 1.74(0.09) 1.77(0.20) 1.77(0.20) 1.69(0.18) 1.68(0.12) 1.75(0.14) 1.69(0.16) 1.74(0.16) 1.74(0.19) 1.69(0.11) 1.67(0.14) 1.56(0.35) 1.55(0.25) 1.64(0.19) 1.61(0.20) 1.57(0.27) 1.66(0.17) 1.62(0.16) 1.64(0.30) 1.72(0.31) 1.66(0.18) 1.69(0.15) 1.72(0.16) 1.63(0.20) 1.70(0.10) 1.77(0.26) 1.75(0.25) 1.78(0.19) 1.75(0.20) 1.68(0.25) 1.74(0.10) 1.75(0.17) 1.67(0.15) 1.77(0.45) 1.86(0.54) 1.68(0.48) 1.61(0.48) 1.52(0.26) 1.51(0.24) 1.54(0.20) 1.57(0.27) 1.59(0.13) 1.58(0.21) 1.57(0.25) 1.56(0.11) 1.68(0.18) 1.65(0.21) 1.60(0.24) 1.69(0.14) 1.70(0.23) 1.65(0.22) 1.80(0.33) 1.63(0.45) 1.58(0.38) 1.57(0.37) 1.45(0.28) 1.48(0.18) 1.46(0.23) 1.55(0.13) 1.58(0.17) 1.60(0.14) 1.68(0.20) 1.66(0.23) 1.80(0.63) 1.80(0.19) 1.65(0.25) 1.80(0.21) 4.22(2.97) 5.80(1.66) 5.61(0.21) 5.46(0.15) 5.43(0.12) 5.45(0.60) 4.58(0.99) 4.72(0.39) 5.09(0.61) 4.71(0.64) 4.99(0.28) 4.96(0.27) 3.07(2.37) 2.83(0.32) 2.51(0.36) 2.31(0.42) 2.40(0.16) 2.35(0.21) 2.47(0.21) 2.45(0.10) 2.41(0.19) 2.29(0.26) 2.92(0.71) 3.35(0.47) 2.68(0.72) 2.80(0.19) 2.64(0.23) 2.64(0.16) 2.53(0.23) 2.09(0.46) 2.34(0.28) 2.49(0.24) 2.26(0.29) 2.59(0.54) 2.31(0.39) 2.42(0.17) 2.46(0.16) 2.21(0.30) 2.47(0.28) 2.36(0.19) 2.63(0.51) 2.59(0.23)
++ Max displacement in automask = 5.80 (mm) at sub-brick 139
++ Max delta displ in automask = 2.97 (mm) at sub-brick 138
++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK
3dcalc -overwrite -a pb02.265001.r01.despike+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
[7m*+ WARNING:[0m input 'a' is not used in the expression
cat_matvec -ONELINE anatQQ.SSW.aff12.1D anatSS.SSW_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D
3dNwarpApply -master anatQQ.SSW+tlrc -dxyz 1 -source pb02.265001.r01.despike+orig -nwarp anatQQ.SSW_WARP.nii mat.r01.warp.aff12.1D -prefix rm.epi.nomask.r01
++ 3dNwarpApply: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is 'anatQQ.SSW+tlrc'
++ output grid size = 1 mm
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb02.265001.r01.despike+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb02.265001.r01.despike+orig.BRIK is 0.799908 degrees from plumb.
++ opened source dataset 'pb02.265001.r01.despike+orig'
++ Processing -nwarp
++ Warping:.........................................Killed
I am sorry that I already deleted the results folder because the folder size is very big (over 150GB), and I had to free up the disc space for other operation. Now that I have ran the script again, the process was killed during warping this time. I copy the output file below. Could this be a hardware problem as I also notice that this Linux machine was getting noticeably slow when I opened a new script or web browser?
Sungjin
echo auto-generated by afni_proc.py, Tue Oct 15 15:34:29 2019
auto-generated by afni_proc.py, Tue Oct 15 15:34:29 2019
echo (version 6.32, February 22, 2019)
(version 6.32, February 22, 2019)
echo execution started: `date`
date
execution started: Thu Oct 24 12:06:21 EDT 2019
afni -ver
Precompiled binary linux_ubuntu_16_64: Mar 20 2019 (Version AFNI_19.0.26 'Tiberius')
afni_history -check_date 17 Jan 2019
-- is current: afni_history as new as: 17 Jan 2019
most recent entry is: 20 Mar 2019
if ( 0 ) then
if ( 0 > 0 ) then
set subj = 265001
endif
set sNUM = 1
set output_dir = 265001.s1.results
if ( -d 265001.s1.results ) then
set runs = ( `count -digits 2 1 6` )
count -digits 2 1 6
mkdir 265001.s1.results
mkdir 265001.s1.results/stimuli
cp /home/sungjin/fMRI/CGE/CGE_Raw_Data/Timing_CGE.txt 265001.s1.results/stimuli
3dcopy CGE_Raw_Data/Session1/265001_S1/subject_raw/anatSS.SSW.nii 265001.s1.results/anatSS.SSW
++ 3dcopy: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
3dcopy CGE_Raw_Data/Session1/265001_S1/subject_raw/anatQQ.SSW.nii 265001.s1.results/anatQQ.SSW
++ 3dcopy: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
3dcopy CGE_Raw_Data/Session1/265001_S1/subject_raw/anatQQ.SSW.aff12.1D 265001.s1.results/anatQQ.SSW.aff12.1D
++ 3dcopy: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
3dcopy CGE_Raw_Data/Session1/265001_S1/subject_raw/anatQQ.SSW_WARP.nii 265001.s1.results/anatQQ.SSW_WARP.nii
++ 3dcopy: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
3dTcat -prefix 265001.s1.results/pb00.265001.r01.tcat CGE_Raw_Data/Session1/265001_S1/subject_raw/raw.rest1.s1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ elapsed time = 0.8 s
3dTcat -prefix 265001.s1.results/pb00.265001.r02.tcat CGE_Raw_Data/Session1/265001_S1/subject_raw/raw.pv.s1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ elapsed time = 0.6 s
3dTcat -prefix 265001.s1.results/pb00.265001.r03.tcat CGE_Raw_Data/Session1/265001_S1/subject_raw/raw.14p.s1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ elapsed time = 0.6 s
3dTcat -prefix 265001.s1.results/pb00.265001.r04.tcat CGE_Raw_Data/Session1/265001_S1/subject_raw/raw.6p.s1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ elapsed time = 0.6 s
3dTcat -prefix 265001.s1.results/pb00.265001.r05.tcat CGE_Raw_Data/Session1/265001_S1/subject_raw/raw.flk.s1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ elapsed time = 0.6 s
3dTcat -prefix 265001.s1.results/pb00.265001.r06.tcat CGE_Raw_Data/Session1/265001_S1/subject_raw/raw.rest2.s1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ elapsed time = 0.7 s
set tr_counts = ( 180 150 150 150 150 180 )
cd 265001.s1.results
touch out.pre_ss_warn.txt
foreach run ( 01 02 03 04 05 06 )
3dToutcount -automask -fraction -polort 3 -legendre pb00.265001.r01.tcat+orig
++ 3dToutcount: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r01.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r01.tcat+orig.BRIK is 0.799908 degrees from plumb.
++ 33485 voxels passed mask/clip
if ( `1deval -a outcount.r$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 3 -legendre pb00.265001.r02.tcat+orig
++ 3dToutcount: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r02.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r02.tcat+orig.BRIK is 0.799908 degrees from plumb.
++ 33500 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r02.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.265001.r03.tcat+orig
++ 3dToutcount: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r03.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r03.tcat+orig.BRIK is 0.799908 degrees from plumb.
++ 33501 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r03.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.265001.r04.tcat+orig
++ 3dToutcount: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r04.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r04.tcat+orig.BRIK is 0.799908 degrees from plumb.
++ 33658 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r04.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.265001.r05.tcat+orig
++ 3dToutcount: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r05.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r05.tcat+orig.BRIK is 0.799908 degrees from plumb.
++ 33509 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r05.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.265001.r06.tcat+orig
++ 3dToutcount: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r06.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r06.tcat+orig.BRIK is 0.799908 degrees from plumb.
++ 33587 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r06.1D{0} -expr step(a-0.4)
end
cat outcount.r01.1D outcount.r02.1D outcount.r03.1D outcount.r04.1D outcount.r05.1D outcount.r06.1D
set minindex = `3dTstat -argmin -prefix - outcount_rall.1D\'`
3dTstat -argmin -prefix - outcount_rall.1D'
++ 3dTstat: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: KR Hammett & RW Cox
[7m*+ WARNING:[0m Input dataset is not 3D+time; assuming TR=1.0
set ovals = ( `1d_tool.py -set_run_lengths $tr_counts
-index_to_run_tr $minindex` )
1d_tool.py -set_run_lengths 180 150 150 150 150 180 -index_to_run_tr 15
set minoutrun = 01
set minouttr = 15
echo min outlier: run 01, TR 15
tee out.min_outlier.txt
min outlier: run 01, TR 15
foreach run ( 01 02 03 04 05 06 )
3dTshift -tzero 0 -quintic -prefix pb01.265001.r01.tshift pb00.265001.r01.tcat+orig
++ 3dTshift: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r01.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r01.tcat+orig.BRIK is 0.799908 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.265001.r02.tshift pb00.265001.r02.tcat+orig
++ 3dTshift: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r02.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r02.tcat+orig.BRIK is 0.799908 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.265001.r03.tshift pb00.265001.r03.tcat+orig
++ 3dTshift: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r03.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r03.tcat+orig.BRIK is 0.799908 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.265001.r04.tshift pb00.265001.r04.tcat+orig
++ 3dTshift: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r04.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r04.tcat+orig.BRIK is 0.799908 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.265001.r05.tshift pb00.265001.r05.tcat+orig
++ 3dTshift: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r05.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r05.tcat+orig.BRIK is 0.799908 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.265001.r06.tshift pb00.265001.r06.tcat+orig
++ 3dTshift: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb00.265001.r06.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.265001.r06.tcat+orig.BRIK is 0.799908 degrees from plumb.
end
foreach run ( 01 02 03 04 05 06 )
3dDespike -NEW -nomask -prefix pb02.265001.r01.despike pb01.265001.r01.tshift+orig
++ 3dDespike: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb01.265001.r01.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.265001.r01.tshift+orig.BRIK is 0.799908 degrees from plumb.
++ Input dataset is in short format, but output will be in float format
++ ignoring first 0 time points, using last 180
++ using 180 time points => -corder 6
++ Loading dataset pb01.265001.r01.tshift+orig
++ processing all 143360 voxels in dataset
++ Procesing time series with NEW model fit algorithm
++ smash edit thresholds: 3.1 .. 5.0 MADs
+ [ 3.457% .. 0.072% of normal distribution]
+ [ 8.839% .. 3.125% of Laplace distribution]
++ start OpenMP thread #0
++ start OpenMP thread #1
++ start OpenMP thread #2
++ start OpenMP thread #3
.............................................................
++ Elapsed despike time = 905ms
++ FINAL: 25004700 data points, 1285900 edits [5.143%], 233777 big edits [0.935%]
++ Output dataset ./pb02.265001.r01.despike+orig.BRIK
end
3dDespike -NEW -nomask -prefix pb02.265001.r02.despike pb01.265001.r02.tshift+orig
++ 3dDespike: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb01.265001.r02.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.265001.r02.tshift+orig.BRIK is 0.799908 degrees from plumb.
++ Input dataset is in short format, but output will be in float format
++ ignoring first 0 time points, using last 150
++ using 150 time points => -corder 5
++ Loading dataset pb01.265001.r02.tshift+orig
++ processing all 143360 voxels in dataset
++ Procesing time series with NEW model fit algorithm
++ smash edit thresholds: 3.1 .. 5.0 MADs
+ [ 3.457% .. 0.072% of normal distribution]
+ [ 8.839% .. 3.125% of Laplace distribution]
++ start OpenMP thread #0
++ start OpenMP thread #3
++ start OpenMP thread #2
++ start OpenMP thread #1
.............................................................
++ Elapsed despike time = 691ms
++ FINAL: 20837250 data points, 979211 edits [4.699%], 149477 big edits [0.717%]
++ Output dataset ./pb02.265001.r02.despike+orig.BRIK
end
3dDespike -NEW -nomask -prefix pb02.265001.r03.despike pb01.265001.r03.tshift+orig
++ 3dDespike: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb01.265001.r03.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.265001.r03.tshift+orig.BRIK is 0.799908 degrees from plumb.
++ Input dataset is in short format, but output will be in float format
++ ignoring first 0 time points, using last 150
++ using 150 time points => -corder 5
++ Loading dataset pb01.265001.r03.tshift+orig
++ processing all 143360 voxels in dataset
++ Procesing time series with NEW model fit algorithm
++ smash edit thresholds: 3.1 .. 5.0 MADs
+ [ 3.457% .. 0.072% of normal distribution]
+ [ 8.839% .. 3.125% of Laplace distribution]
++ start OpenMP thread #1
++ start OpenMP thread #0
++ start OpenMP thread #2
++ start OpenMP thread #3
.............................................................
++ Elapsed despike time = 671ms
++ FINAL: 20837250 data points, 932750 edits [4.476%], 100598 big edits [0.483%]
++ Output dataset ./pb02.265001.r03.despike+orig.BRIK
end
3dDespike -NEW -nomask -prefix pb02.265001.r04.despike pb01.265001.r04.tshift+orig
++ 3dDespike: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb01.265001.r04.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.265001.r04.tshift+orig.BRIK is 0.799908 degrees from plumb.
++ Input dataset is in short format, but output will be in float format
++ ignoring first 0 time points, using last 150
++ using 150 time points => -corder 5
++ Loading dataset pb01.265001.r04.tshift+orig
++ processing all 143360 voxels in dataset
++ Procesing time series with NEW model fit algorithm
++ smash edit thresholds: 3.1 .. 5.0 MADs
+ [ 3.457% .. 0.072% of normal distribution]
+ [ 8.839% .. 3.125% of Laplace distribution]
++ start OpenMP thread #1
++ start OpenMP thread #3
++ start OpenMP thread #0
++ start OpenMP thread #2
.............................................................
++ Elapsed despike time = 667ms
++ FINAL: 20837250 data points, 806934 edits [3.873%], 62777 big edits [0.301%]
++ Output dataset ./pb02.265001.r04.despike+orig.BRIK
end
3dDespike -NEW -nomask -prefix pb02.265001.r05.despike pb01.265001.r05.tshift+orig
++ 3dDespike: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb01.265001.r05.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.265001.r05.tshift+orig.BRIK is 0.799908 degrees from plumb.
++ Input dataset is in short format, but output will be in float format
++ ignoring first 0 time points, using last 150
++ using 150 time points => -corder 5
++ Loading dataset pb01.265001.r05.tshift+orig
++ processing all 143360 voxels in dataset
++ Procesing time series with NEW model fit algorithm
++ smash edit thresholds: 3.1 .. 5.0 MADs
+ [ 3.457% .. 0.072% of normal distribution]
+ [ 8.839% .. 3.125% of Laplace distribution]
++ start OpenMP thread #0
++ start OpenMP thread #2
++ start OpenMP thread #1
++ start OpenMP thread #3
.............................................................
++ Elapsed despike time = 719ms
++ FINAL: 20837250 data points, 1004426 edits [4.820%], 214664 big edits [1.030%]
++ Output dataset ./pb02.265001.r05.despike+orig.BRIK
end
3dDespike -NEW -nomask -prefix pb02.265001.r06.despike pb01.265001.r06.tshift+orig
++ 3dDespike: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb01.265001.r06.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.265001.r06.tshift+orig.BRIK is 0.799908 degrees from plumb.
++ Input dataset is in short format, but output will be in float format
++ ignoring first 0 time points, using last 180
++ using 180 time points => -corder 6
++ Loading dataset pb01.265001.r06.tshift+orig
++ processing all 143360 voxels in dataset
++ Procesing time series with NEW model fit algorithm
++ smash edit thresholds: 3.1 .. 5.0 MADs
+ [ 3.457% .. 0.072% of normal distribution]
+ [ 8.839% .. 3.125% of Laplace distribution]
++ start OpenMP thread #2
++ start OpenMP thread #0
++ start OpenMP thread #3
++ start OpenMP thread #1
.............................................................
++ Elapsed despike time = 826ms
++ FINAL: 25004700 data points, 1076068 edits [4.303%], 128650 big edits [0.515%]
++ Output dataset ./pb02.265001.r06.despike+orig.BRIK
end
3dbucket -prefix vr_base_min_outlier pb02.265001.r01.despike+orig[15]
++ 3dbucket: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
align_epi_anat.py -anat2epi -anat anatSS.SSW+orig -suffix _al_junk -epi vr_base_min_outlier+orig -epi_base 0 -epi_strip 3dAutomask -anat_has_skull no -cost lpc+ZZ -volreg off -tshift off
#++ align_epi_anat version: 1.58
#++ turning off volume registration
#Script is running (command trimmed):
3dAttribute DELTA ./vr_base_min_outlier+orig
#Script is running (command trimmed):
3dAttribute DELTA ./vr_base_min_outlier+orig
#Script is running:
3dAttribute DELTA /home/sungjin/fMRI/CGE/265001.s1.results/anatSS.SSW+orig
#++ Multi-cost is lpc+ZZ
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_vr_base_min_outlier*
#Script is running:
\rm -f ./__tt_anatSS.SSW*
#Script is running (command trimmed):
3dcopy ./anatSS.SSW+orig ./__tt_anatSS.SSW+orig
++ 3dcopy: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
#Script is running (command trimmed):
3dinfo ./__tt_anatSS.SSW+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /home/sungjin/fMRI/CGE/265001.s1.results/__tt_anatSS.SSW+orig is not oblique
#Script is running (command trimmed):
3dinfo ./vr_base_min_outlier+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /home/sungjin/fMRI/CGE/265001.s1.results/vr_base_min_outlier+orig is ***oblique****
#Script is running:
3dAttribute DELTA /home/sungjin/fMRI/CGE/265001.s1.results/__tt_anatSS.SSW+orig
#++ Spacing for anat to oblique epi alignment is 1.000000
#++ Matching obliquity of anat to epi
#Script is running (command trimmed):
3dWarp -verb -card2oblique ./vr_base_min_outlier+orig -prefix ./__tt_anatSS.SSW_ob -newgrid 1.000000 ./__tt_anatSS.SSW+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./__tt_anatSS.SSW_obla2e_mat.1D
++ 3dWarp: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
#++ using 0th sub-brick because only one found
#Script is running (command trimmed):
3dbucket -prefix ./__tt_vr_base_min_outlier_ts ./vr_base_min_outlier+orig'[0]'
++ 3dbucket: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
#++ resampling epi to match anat data
#Script is running (command trimmed):
3dresample -master ./__tt_anatSS.SSW_ob+orig -prefix ./__tt_vr_base_min_outlier_ts_rs -inset ./__tt_vr_base_min_outlier_ts+orig'' -rmode Cu
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./__tt_vr_base_min_outlier_ts+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./__tt_vr_base_min_outlier_ts+orig.BRIK is 0.799908 degrees from plumb.
#++ removing skull or area outside brain
#Script is running (command trimmed):
3dAutomask -apply_prefix ./__tt_vr_base_min_outlier_ts_rs_ns ./__tt_vr_base_min_outlier_ts_rs+orig
++ 3dAutomask: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset ./__tt_vr_base_min_outlier_ts_rs+orig
++ Forming automask
+ Fixed clip level = 417.475769
+ Used gradual clip level = 139.019440 .. 478.463043
+ Number voxels above clip level = 98910
+ Clustering voxels ...
+ Largest cluster has 86317 voxels
+ Clustering voxels ...
+ Largest cluster has 85339 voxels
+ Filled 142 voxels in small holes; now have 85481 voxels
+ Filled 16044 voxels in large holes; now have 101525 voxels
+ Clustering voxels ...
+ Largest cluster has 101460 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 11879879 voxels
+ Mask now has 101461 voxels
++ 101461 voxels in the mask [out of 11981340: 0.85%]
++ first 156 x-planes are zero [from R]
++ last 0 x-planes are zero [from L]
++ first 61 y-planes are zero [from A]
++ last 68 y-planes are zero [from P]
++ first 84 z-planes are zero [from I]
++ last 79 z-planes are zero [from S]
++ applying mask to original data
++ Writing masked data
++ CPU time = 0.000000 sec
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_min_outlier_ts_rs_ns+orig
#++ Applying threshold of 1024.127319 on /home/sungjin/fMRI/CGE/265001.s1.results/__tt_vr_base_min_outlier_ts_rs_ns+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix ./__tt_vr_base_min_outlier_ts_rs_ns_wt -a ./__tt_vr_base_min_outlier_ts_rs_ns+orig -expr 'min(1,(a/1024.127319))'
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
#++ Aligning anat data to epi data
#Script is running (command trimmed):
3dAllineate -lpc+ZZ -wtprefix ./__tt_anatSS.SSW_ob_al_junk_wtal -weight ./__tt_vr_base_min_outlier_ts_rs_ns_wt+orig -source ./__tt_anatSS.SSW_ob+orig -prefix ./__tt_anatSS.SSW_ob_temp_al_junk -base ./__tt_vr_base_min_outlier_ts_rs_ns+orig -nocmass -1Dmatrix_save ./anatSS.SSW_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
++ 3dAllineate: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: Zhark the Registrator
++ lpc+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration]
++ Source dataset: ./__tt_anatSS.SSW_ob+orig.HEAD
++ Base dataset: ./__tt_vr_base_min_outlier_ts_rs_ns+orig.HEAD
++ Loading datasets
++ 1481954 voxels in -source_automask+4
++ Zero-pad: xbot=0 xtop=4
++ 101398 voxels [0.8%] in weight mask
++ Number of points for matching = 101398
++ Local correlation: blok type = 'RHDD(6.54321)'
++ lpc+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration]
++ shift param auto-range: -58.7..58.7 -82.2..82.2 -82.8..82.8
+ Range param#4 [z-angle] = -6.000000 .. 6.000000
+ Range param#5 [x-angle] = -6.000000 .. 6.000000
+ Range param#6 [y-angle] = -6.000000 .. 6.000000
+ Range param#1 [x-shift] = -10.000000 .. 10.000000
+ Range param#2 [y-shift] = -10.000000 .. 10.000000
+ Range param#3 [z-shift] = -10.000000 .. 10.000000
+ 12 free parameters
++ Normalized convergence radius = 0.001000
++ OpenMP thread count = 4
++ ======= Allineation of 1 sub-bricks using Local Pearson Signed + Others =======
++ ========== sub-brick #0 ========== [total CPU to here=0.0 s]
++ *** Fine pass begins ***
+ * Enter alignment setup routine
+ - copying base image
+ - copying source image
+ - copying weight image
+ - using 101398 points from base image [use_all=0]
+ * Exit alignment setup routine
+ - histogram: source clip 0 .. 0; base clip 0 .. 0
+ - versus source range 0 .. 964.198; base range -43.9971 .. 1367.43
+ 83524 total points stored in 177 'RHDD(6.54321)' bloks
+ - Initial cost = 40.199402
+ - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
**********************************
+ - Finalish cost = 39.493938 ; 186 funcs
+ - Set lpc+ parameters back to purity before Final iterations
+ - histogram: source clip 0 .. 0; base clip 0 .. 0
+ - versus source range 0 .. 964.198; base range -43.9971 .. 1367.43
***************
+ - Final cost = -0.543333 ; 179 funcs
+ Final fine fit Parameters:
x-shift= 5.7113 y-shift= 0.0663 z-shift= -0.2459 ... enorm= 5.7170 mm
z-angle= 0.6580 x-angle= 0.1489 y-angle= -0.2553 ... total= 0.7212 deg
x-scale= 0.9087 y-scale= 0.9985 z-scale= 1.0007 ... vol3D= 0.9079
y/x-shear= 0.0031 z/x-shear= -0.0096 z/y-shear= -0.0009
+ - Fine net CPU time = 0.0 s
++ Computing output image
++ image warp: parameters = 5.7113 0.0663 -0.2459 0.6580 0.1489 -0.2553 0.9087 0.9985 1.0007 0.0031 -0.0096 -0.0009
++ Wrote -1Dmatrix_save ./anatSS.SSW_al_junk_e2a_only_mat.aff12.1D
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 13.1
++ ###########################################################
++ # Please check results visually for alignment quality #
++ ###########################################################
++ # '-autoweight' is recommended when using -lpc or -lpa #
++ # If your results are not good, please try again. #
++ ###########################################################
#Script is running (command trimmed):
cat_matvec -ONELINE ./anatSS.SSW_al_junk_e2a_only_mat.aff12.1D ./__tt_anatSS.SSW_obla2e_mat.1D -I > ./anatSS.SSW_al_junk_mat.aff12.1D
#++ Combining anat to epi and oblique transformations
#Script is running (command trimmed):
3dAllineate -base ./__tt_vr_base_min_outlier_ts_rs_ns+orig -1Dmatrix_apply ./anatSS.SSW_al_junk_mat.aff12.1D -prefix ./anatSS.SSW_al_junk -input ./__tt_anatSS.SSW+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
++ 3dAllineate: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./__tt_anatSS.SSW+orig.HEAD
++ Base dataset: ./__tt_vr_base_min_outlier_ts_rs_ns+orig.HEAD
++ Loading datasets
+ Range param#4 [z-angle] = -6.000000 .. 6.000000
+ Range param#5 [x-angle] = -6.000000 .. 6.000000
+ Range param#6 [y-angle] = -6.000000 .. 6.000000
+ Range param#1 [x-shift] = -10.000000 .. 10.000000
+ Range param#2 [y-shift] = -10.000000 .. 10.000000
+ Range param#3 [z-shift] = -10.000000 .. 10.000000
++ OpenMP thread count = 4
++ ========== Applying transformation to 1 sub-bricks ==========
++ ========== sub-brick #0 ========== [total CPU to here=0.0 s]
+ * Enter alignment setup routine
+ - copying base image
+ - copying source image
+ - no weight image
+ - using 11 points from base image [use_all=0]
+ * Exit alignment setup routine
++ using -1Dmatrix_apply
++ Computing output image
++ image warp: parameters = -0.9084 -0.0088 -0.0179 29.2348 -0.0072 0.9984 0.0026 0.6169 -0.0257 -0.0038 1.0006 1.3968
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 1.0
++ ###########################################################
#++ Creating final output: anat data aligned to epi
# copy is not necessary
#++ Saving history
#Script is running (command trimmed):
3dNotes -h "align_epi_anat.py -anat2epi -anat anatSS.SSW+orig -suffix \
_al_junk -epi vr_base_min_outlier+orig -epi_base 0 -epi_strip 3dAutomask \
-anat_has_skull no -cost lpc+ZZ -volreg off -tshift off" \
./anatSS.SSW_al_junk+orig
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_vr_base_min_outlier*
#Script is running:
\rm -f ./__tt_anatSS.SSW*
# Finished alignment successfully
if ( ! -f anatQQ.SSW+tlrc.HEAD ) then
foreach run ( 01 02 03 04 05 06 )
3dvolreg -verbose -zpad 1 -base vr_base_min_outlier+orig -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb02.265001.r01.despike+orig
++ 3dvolreg: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./vr_base_min_outlier+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./vr_base_min_outlier+orig.BRIK is 0.799908 degrees from plumb.
++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK
++ Oblique dataset:./pb02.265001.r01.despike+orig.BRIK is 0.799908 degrees from plumb.
++ Reading input dataset ./pb02.265001.r01.despike+orig.BRIK
++ Edging: x=3 y=3 z=2
++ Creating mask for -maxdisp
+ Automask has 42045 voxels
+ 8524 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 180 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..
++ CPU time for realignment=0 s [=0 s/sub-brick]
++ Min : roll=-1.408 pitch=-0.099 yaw=-1.571 dS=-0.090 dL=-0.354 dP=-0.187
++ Mean: roll=-0.359 pitch=+0.627 yaw=-0.027 dS=+0.342 dL=+0.016 dP=+0.004
++ Max : roll=+0.026 pitch=+1.639 yaw=+0.459 dS=+1.065 dL=+0.413 dP=+0.161
++ Max displacements (mm) for each sub-brick:
0.52(0.00) 0.30(0.34) 0.19(0.17) 0.29(0.18) 0.34(0.12) 0.19(0.25) 0.24(0.15) 0.33(0.14) 0.17(0.21) 0.19(0.12) 0.33(0.20) 0.17(0.19) 0.11(0.12) 0.27(0.21) 0.15(0.15) 0.00(0.15) 0.18(0.18) 0.25(0.15) 0.11(0.17) 0.20(0.15) 0.26(0.12) 0.20(0.18) 0.29(0.13) 0.33(0.15) 0.28(0.22) 0.44(0.19) 0.40(0.18) 0.30(0.12) 0.39(0.23) 0.43(0.13) 0.33(0.19) 0.40(0.17) 0.54(0.16) 0.55(0.19) 0.50(0.19) 0.43(0.12) 0.35(0.19) 0.49(0.29) 0.43(0.19) 0.39(0.13) 0.53(0.20) 0.47(0.17) 0.45(0.11) 0.58(0.16) 0.48(0.26) 0.58(0.11) 0.76(0.56) 0.78(0.23) 0.56(0.37) 0.57(0.14) 0.64(0.20) 0.60(0.24) 0.76(0.31) 0.94(0.33) 0.78(0.35) 2.30(1.79) 2.62(0.35) 1.88(0.83) 2.01(0.17) 1.95(0.16) 1.87(0.27) 1.84(0.18) 1.77(0.10) 1.76(0.23) 1.78(0.16) 1.71(0.13) 1.74(0.28) 1.74(0.19) 1.69(0.10) 1.72(0.23) 1.78(0.19) 1.74(0.09) 1.77(0.20) 1.77(0.20) 1.69(0.18) 1.68(0.12) 1.75(0.14) 1.69(0.16) 1.74(0.16) 1.74(0.19) 1.69(0.11) 1.67(0.14) 1.56(0.35) 1.55(0.25) 1.64(0.19) 1.61(0.20) 1.57(0.27) 1.66(0.17) 1.62(0.16) 1.64(0.30) 1.72(0.31) 1.66(0.18) 1.69(0.15) 1.72(0.16) 1.63(0.20) 1.70(0.10) 1.77(0.26) 1.75(0.25) 1.78(0.19) 1.75(0.20) 1.68(0.25) 1.74(0.10) 1.75(0.17) 1.67(0.15) 1.77(0.45) 1.86(0.54) 1.68(0.48) 1.61(0.48) 1.52(0.26) 1.51(0.24) 1.54(0.20) 1.57(0.27) 1.59(0.13) 1.58(0.21) 1.57(0.25) 1.56(0.11) 1.68(0.18) 1.65(0.21) 1.60(0.24) 1.69(0.14) 1.70(0.23) 1.65(0.22) 1.80(0.33) 1.63(0.45) 1.58(0.38) 1.57(0.37) 1.45(0.28) 1.48(0.18) 1.46(0.23) 1.55(0.13) 1.58(0.17) 1.60(0.14) 1.68(0.20) 1.66(0.23) 1.80(0.63) 1.80(0.19) 1.65(0.25) 1.80(0.21) 4.22(2.97) 5.80(1.66) 5.61(0.21) 5.46(0.15) 5.43(0.12) 5.45(0.60) 4.58(0.99) 4.72(0.39) 5.09(0.61) 4.71(0.64) 4.99(0.28) 4.96(0.27) 3.07(2.37) 2.83(0.32) 2.51(0.36) 2.31(0.42) 2.40(0.16) 2.35(0.21) 2.47(0.21) 2.45(0.10) 2.41(0.19) 2.29(0.26) 2.92(0.71) 3.35(0.47) 2.68(0.72) 2.80(0.19) 2.64(0.23) 2.64(0.16) 2.53(0.23) 2.09(0.46) 2.34(0.28) 2.49(0.24) 2.26(0.29) 2.59(0.54) 2.31(0.39) 2.42(0.17) 2.46(0.16) 2.21(0.30) 2.47(0.28) 2.36(0.19) 2.63(0.51) 2.59(0.23)
++ Max displacement in automask = 5.80 (mm) at sub-brick 139
++ Max delta displ in automask = 2.97 (mm) at sub-brick 138
++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK
3dcalc -overwrite -a pb02.265001.r01.despike+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: A cast of thousands
[7m*+ WARNING:[0m input 'a' is not used in the expression
cat_matvec -ONELINE anatQQ.SSW.aff12.1D anatSS.SSW_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D
3dNwarpApply -master anatQQ.SSW+tlrc -dxyz 1 -source pb02.265001.r01.despike+orig -nwarp anatQQ.SSW_WARP.nii mat.r01.warp.aff12.1D -prefix rm.epi.nomask.r01
++ 3dNwarpApply: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is 'anatQQ.SSW+tlrc'
++ output grid size = 1 mm
[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
such as ./pb02.265001.r01.despike+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb02.265001.r01.despike+orig.BRIK is 0.799908 degrees from plumb.
++ opened source dataset 'pb02.265001.r01.despike+orig'
++ Processing -nwarp
++ Warping:.........................................Killed
