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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| 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
