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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
| June 28, 2018 04:15PM | |
Hello,
I manually tlrc my anatomical images and ran the uber_subject.py to pre-process the data. In the GUI I checked off "include copy of anat+tlrc" in the "anatomical dataset" section, so the +tlrc version can be included. When I ran my script, there was an error message regarding finding a specific file: "** FATAL ERROR: can't open -base dataset 'final_epi_vr_base_min_outlier+tlrc'
". It seems like I have the final_epi_vr_base_min_outlier+orig file but not the final_epi_vr_base_min_outlier+tlrc file in the results folder. Did I include the manual tlrc anat file into the uber_subject.py script incorrectly?
Thank you,
Tamara
My script is pasted below:
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /home/bmiadmin/subjects
MNI_DIR /usr/local/freesurfer/mni
SUBJECTS_DIR= /home/bmiadmin/subjects
mitchelllab-linux:~/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306> tcsh -xef proc.s_10306 |& tee output.proc.s_10306
echo auto-generated by afni_proc.py, Thu Jun 28 14:43:09 2018
auto-generated by afni_proc.py, Thu Jun 28 14:43:09 2018
echo (version 6.10, Apr 26, 2018)
(version 6.10, Apr 26, 2018)
echo execution started: `date`
date
execution started: Thu Jun 28 14:51:40 EDT 2018
afni -ver
Precompiled binary linux_ubuntu_16_64: Apr 30 2018 (Version AFNI_18.1.09)
afni_history -check_date 23 Mar 2018
-- is current: afni_history as new as: 23 Mar 2018
most recent entry is: 29 Apr 2018
if ( 0 ) then
if ( 0 > 0 ) then
set subj = s_10306
endif
set output_dir = s_10306.results
if ( -d s_10306.results ) then
set runs = ( `count -digits 2 1 4` )
count -digits 2 1 4
mkdir s_10306.results
mkdir s_10306.results/stimuli
cp /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_learn_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_learn_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_learn_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_learn_incor.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_perf_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_perf_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_perf_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_perf_incor.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_acq_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_acq_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_acq_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_acq_incor.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_rev_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_rev_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_rev_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_rev_incor.txt s_10306.results/stimuli
3dcopy /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/10306.anat s_10306.results/10306.anat
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
3dTcat -prefix s_10306.results/pb00.s_10306.r01.tcat /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/10306.1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 0.4 s
3dTcat -prefix s_10306.results/pb00.s_10306.r02.tcat /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/10306.2+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 1.7 s
3dTcat -prefix s_10306.results/pb00.s_10306.r03.tcat /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/10306.3+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 1.9 s
3dTcat -prefix s_10306.results/pb00.s_10306.r04.tcat /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/10306.4+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 1.6 s
set tr_counts = ( 153 153 153 153 )
cd s_10306.results
touch out.pre_ss_warn.txt
foreach run ( 01 02 03 04 )
3dToutcount -automask -fraction -polort 3 -legendre pb00.s_10306.r01.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.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.s_10306.r01.tcat+orig.BRIK is 9.240993 degrees from plumb.
++ 123854 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r01.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.s_10306.r02.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.r02.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.s_10306.r02.tcat+orig.BRIK is 9.240993 degrees from plumb.
++ 123963 voxels passed mask/clip
if ( `1deval -a outcount.r$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.s_10306.r03.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.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.s_10306.r03.tcat+orig.BRIK is 9.240993 degrees from plumb.
++ 123950 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r03.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.s_10306.r04.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.r04.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.s_10306.r04.tcat+orig.BRIK is 9.240993 degrees from plumb.
++ 124094 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r04.1D{0} -expr step(a-0.4)
end
cat outcount.r01.1D outcount.r02.1D outcount.r03.1D outcount.r04.1D
set minindex = `3dTstat -argmin -prefix - outcount_rall.1D\'`
3dTstat -argmin -prefix - outcount_rall.1D'
++ 3dTstat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: 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 153 153 153 153 -index_to_run_tr 47
set minoutrun = 01
set minouttr = 47
echo min outlier: run 01, TR 47
tee out.min_outlier.txt
min outlier: run 01, TR 47
foreach run ( 01 02 03 04 )
3dTshift -tzero 0 -quintic -prefix pb01.s_10306.r01.tshift pb00.s_10306.r01.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.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.s_10306.r01.tcat+orig.BRIK is 9.240993 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.s_10306.r02.tshift pb00.s_10306.r02.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.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.s_10306.r02.tcat+orig.BRIK is 9.240993 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.s_10306.r03.tshift pb00.s_10306.r03.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.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.s_10306.r03.tcat+orig.BRIK is 9.240993 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.s_10306.r04.tshift pb00.s_10306.r04.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.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.s_10306.r04.tcat+orig.BRIK is 9.240993 degrees from plumb.
end
3dbucket -prefix vr_base_min_outlier pb01.s_10306.r01.tshift+orig[47]
++ 3dbucket: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
align_epi_anat.py -anat2epi -anat 10306.anat+orig -save_skullstrip -suffix _al_junk -epi vr_base_min_outlier+orig -epi_base 0 -epi_strip 3dAutomask -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 (command trimmed):
3dAttribute DELTA ./10306.anat+orig
#++ Multi-cost is lpc
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_vr_base_min_outlier*
#Script is running:
\rm -f ./__tt_10306.anat*
#Script is running (command trimmed):
3dcopy ./10306.anat+orig ./__tt_10306.anat+orig
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
#++ Removing skull from anat data
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_10306.anat+orig -prefix ./__tt_10306.anat_ns
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./__tt_10306.anat+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_10306.anat+orig.BRIK is 9.286984 degrees from plumb.
#Script is running (command trimmed):
3dinfo ./__tt_10306.anat_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/s_10306.results/__tt_10306.anat_ns+orig is ***oblique****
#Script is running (command trimmed):
3dAttribute DELTA ./__tt_10306.anat_ns+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_10306.anat_ns_ob -newgrid 1.000000 ./__tt_10306.anat_ns+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./__tt_10306.anat_ns_obla2e_mat.1D
++ 3dWarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
++ Deobliquing original dataset before obliquing
++ Combining oblique transformations
#++ 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_18.1.09 (Apr 30 2018) [64-bit]
#++ resampling epi to match anat data
#Script is running (command trimmed):
3dresample -master ./__tt_10306.anat_ns_ob+orig -prefix ./__tt_vr_base_min_outlier_ts_rs -inset ./__tt_vr_base_min_outlier_ts+orig'' -rmode Cu
*+ WARNING: 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 9.240993 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_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset ./__tt_vr_base_min_outlier_ts_rs+orig
++ Forming automask
+ Fixed clip level = 347.489990
+ Used gradual clip level = 325.106812 .. 375.963989
+ Number voxels above clip level = 1511331
+ Clustering voxels ...
+ Largest cluster has 1475917 voxels
+ Clustering voxels ...
+ Largest cluster has 1472906 voxels
+ Filled 2190 voxels in small holes; now have 1475096 voxels
+ Filled 30893 voxels in large holes; now have 1505989 voxels
+ Clustering voxels ...
+ Largest cluster has 1505961 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 10447880 voxels
+ Mask now has 1505961 voxels
++ 1505961 voxels in the mask [out of 11953841: 12.60%]
++ first 56 x-planes are zero [from R]
++ last 59 x-planes are zero [from L]
++ first 40 y-planes are zero [from A]
++ last 21 y-planes are zero [from P]
++ first 45 z-planes are zero [from I]
++ last 37 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 896.000000 on /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/s_10306.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/896.000000))'
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
#++ Aligning anat data to epi data
#Script is running (command trimmed):
3dAllineate -lpc -wtprefix ./__tt_10306.anat_ns_ob_al_junk_wtal -weight ./__tt_vr_base_min_outlier_ts_rs_ns_wt+orig -source ./__tt_10306.anat_ns_ob+orig -prefix ./__tt_10306.anat_ns_ob_temp_al_junk -base ./__tt_vr_base_min_outlier_ts_rs_ns+orig -nocmass -1Dmatrix_save ./10306.anat_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_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./__tt_10306.anat_ns_ob+orig.HEAD
++ Base dataset: ./__tt_vr_base_min_outlier_ts_rs_ns+orig.HEAD
++ Loading datasets
++ 1781474 voxels in -source_automask+4
++ Zero-pad: not needed
++ 1505957 voxels [12.6%] in weight mask
++ Number of points for matching = 1505957
++ Local correlation: blok type = 'RHDD(6.54321)'
++ shift param auto-range: -82.2..82.2 -77.0..77.0 -61.6..61.6
+ 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 = 8
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed =======
++ ========== 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 1505957 points from base image [use_all=0]
+ * Exit alignment setup routine
+ 1433110 total points stored in 2694 'RHDD(6.54321)' bloks
+ - Initial cost = -0.561667
+ - 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 = -0.792899 ; 255 funcs
****
+ - Final cost = -0.792915 ; 109 funcs
+ Final fine fit Parameters:
x-shift=-0.3118 y-shift= 1.0663 z-shift= 1.5575
z-angle= 0.0541 x-angle=-0.1426 y-angle=-0.1662
x-scale= 0.9993 y-scale= 0.9915 z-scale= 0.9869
y/x-shear=-0.0000 z/x-shear=-0.0026 z/y-shear=-0.0133
+ - Fine net CPU time = 0.0 s
++ Computing output image
++ image warp: parameters = -0.3118 1.0663 1.5575 0.0541 -0.1426 -0.1662 0.9993 0.9915 0.9869 -0.0000 -0.0026 -0.0133
++ Wrote -1Dmatrix_save ./10306.anat_al_junk_e2a_only_mat.aff12.1D
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 72.3
++ ###########################################################
++ # 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 ./10306.anat_al_junk_e2a_only_mat.aff12.1D ./__tt_10306.anat_ns_obla2e_mat.1D -I > ./10306.anat_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 ./10306.anat_al_junk_mat.aff12.1D -prefix ./10306.anat_al_junk -input ./__tt_10306.anat_ns+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./__tt_10306.anat_ns+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_10306.anat_ns+orig.BRIK is 9.286984 degrees from plumb.
++ Source dataset: ./__tt_10306.anat_ns+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 = 8
++ ========== 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 = 0.9993 0.0010 -0.0009 -2.6814 -0.0010 0.9915 -0.0024 -17.3116 -0.0017 -0.0108 0.9869 29.4628
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 2.4
++ ###########################################################
#++ Creating final output: skullstripped anat data
copying from dataset /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/s_10306.results/__tt_10306.anat_ns+orig to /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/s_10306.results/10306.anat_ns+orig
#Script is running (command trimmed):
3dcopy ./__tt_10306.anat_ns+orig 10306.anat_ns
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
#++ 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 10306.anat+orig \
-save_skullstrip -suffix _al_junk -epi vr_base_min_outlier+orig -epi_base \
0 -epi_strip 3dAutomask -volreg off -tshift off" \
./10306.anat_al_junk+orig
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_vr_base_min_outlier*
#Script is running:
\rm -f ./__tt_10306.anat*
# Finished alignment successfully
if ( ! -f 10306.anat+tlrc.HEAD ) then
foreach run ( 01 02 03 04 )
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 pb01.s_10306.r01.tshift+orig
++ 3dvolreg: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
*+ WARNING: 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 9.240993 degrees from plumb.
++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK
++ Oblique dataset:./pb01.s_10306.r01.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Reading input dataset ./pb01.s_10306.r01.tshift+orig.BRIK
++ Edging: x=6 y=6 z=2
++ Creating mask for -maxdisp
+ Automask has 127575 voxels
+ 13040 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 153 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..
++ CPU time for realignment=0 s [=0 s/sub-brick]
++ Min : roll=-0.151 pitch=-0.339 yaw=-0.135 dS=-0.287 dL=-0.042 dP=-0.109
++ Mean: roll=-0.003 pitch=-0.055 yaw=-0.021 dS=+0.046 dL=+0.010 dP=-0.011
++ Max : roll=+0.261 pitch=+0.431 yaw=+0.177 dS=+0.201 dL=+0.104 dP=+0.168
++ Max displacements (mm) for each sub-brick:
0.78(0.00) 0.93(0.21) 0.93(0.04) 0.94(0.03) 0.91(0.05) 0.89(0.05) 0.91(0.06) 0.86(0.08) 0.85(0.06) 0.72(0.14) 0.69(0.05) 0.67(0.04) 0.69(0.06) 0.72(0.05) 0.65(0.08) 0.61(0.07) 0.63(0.04) 0.53(0.14) 0.51(0.05) 0.49(0.06) 0.49(0.02) 0.41(0.08) 0.44(0.12) 0.41(0.04) 0.27(0.25) 0.33(0.15) 0.65(0.39) 0.47(0.24) 0.37(0.15) 0.35(0.13) 0.21(0.31) 0.26(0.16) 0.20(0.12) 0.19(0.21) 0.18(0.04) 0.20(0.04) 0.19(0.09) 0.18(0.02) 0.14(0.06) 0.08(0.06) 0.09(0.06) 0.09(0.05) 0.07(0.05) 0.08(0.05) 0.05(0.08) 0.06(0.02) 0.05(0.05) 0.00(0.05) 0.06(0.06) 0.11(0.07) 0.09(0.03) 0.11(0.04) 0.15(0.18) 0.03(0.12) 0.10(0.12) 0.07(0.09) 0.08(0.08) 0.09(0.05) 0.11(0.04) 0.09(0.05) 0.13(0.06) 0.15(0.04) 0.20(0.06) 0.18(0.04) 0.18(0.06) 0.23(0.07) 0.22(0.05) 0.22(0.03) 0.21(0.02) 0.21(0.03) 0.23(0.04) 0.25(0.04) 0.23(0.08) 0.23(0.04) 0.19(0.07) 0.24(0.07) 0.23(0.04) 0.22(0.08) 0.25(0.06) 0.28(0.08) 0.24(0.07) 0.25(0.06) 0.25(0.06) 0.29(0.05) 0.29(0.02) 0.29(0.03) 0.33(0.05) 0.41(0.08) 0.37(0.07) 0.30(0.07) 0.39(0.09) 0.34(0.08) 0.29(0.10) 0.31(0.08) 0.31(0.07) 0.30(0.07) 0.35(0.08) 0.43(0.10) 0.35(0.08) 0.38(0.03) 0.28(0.11) 0.28(0.07) 0.32(0.06) 0.30(0.04) 0.24(0.08) 0.37(0.15) 0.38(0.06) 0.36(0.05) 0.32(0.07) 0.41(0.11) 0.46(0.10) 0.30(0.20) 0.43(0.23) 0.38(0.07) 0.43(0.08) 0.51(0.10) 0.48(0.04) 0.59(0.11) 0.53(0.06) 0.66(0.13) 0.69(0.06) 0.52(0.22) 0.59(0.13) 0.53(0.08) 0.50(0.10) 0.51(0.09) 0.60(0.09) 0.59(0.06) 0.62(0.05) 0.64(0.03) 0.65(0.02) 0.66(0.03) 0.59(0.07) 0.59(0.02) 0.51(0.09) 0.53(0.08) 0.55(0.06) 0.52(0.04) 0.52(0.05) 0.59(0.09) 0.59(0.04) 0.62(0.03) 0.71(0.11) 0.68(0.07) 0.64(0.07) 0.63(0.04) 0.69(0.07) 0.68(0.03) 0.65(0.06) 0.56(0.11) 0.55(0.03) 0.64(0.11) 0.64(0.07)
++ Max displacement in automask = 0.94 (mm) at sub-brick 3
++ Max delta displ in automask = 0.39 (mm) at sub-brick 26
++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK
3dcalc -overwrite -a pb01.s_10306.r01.tshift+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: input 'a' is not used in the expression
cat_matvec -ONELINE 10306.anat_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D
3dAllineate -base 10306.anat+orig -input pb01.s_10306.r01.tshift+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 2 -prefix rm.epi.nomask.r01
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./pb01.s_10306.r01.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Source dataset: ./pb01.s_10306.r01.tshift+orig.HEAD
++ Base dataset: ./10306.anat+orig.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 2.0000 mm
++ OpenMP thread count = 8
++ ========== Applying transformation to 153 sub-bricks ==========
volume 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
++ Output dataset ./rm.epi.nomask.r01+orig.BRIK
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 49.1
++ ###########################################################
3dAllineate -base 10306.anat+orig -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 2 -final NN -quiet -prefix rm.epi.1.r01
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./rm.epi.all1+orig.BRIK is 9.240993 degrees from plumb.
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 44.7
3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+orig
++ 3dTstat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
end
3dvolreg -verbose -zpad 1 -base vr_base_min_outlier+orig -1Dfile dfile.r02.1D -prefix rm.epi.volreg.r02 -cubic -1Dmatrix_save mat.r02.vr.aff12.1D pb01.s_10306.r02.tshift+orig
++ 3dvolreg: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
*+ WARNING: 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 9.240993 degrees from plumb.
++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK
++ Oblique dataset:./pb01.s_10306.r02.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Reading input dataset ./pb01.s_10306.r02.tshift+orig.BRIK
++ Edging: x=6 y=6 z=2
++ Creating mask for -maxdisp
+ Automask has 127614 voxels
+ 13110 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 153 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..
++ CPU time for realignment=0 s [=0 s/sub-brick]
++ Min : roll=-0.321 pitch=-0.360 yaw=-0.187 dS=-0.296 dL=-0.050 dP=+0.051
++ Mean: roll=-0.165 pitch=-0.094 yaw=-0.111 dS=-0.071 dL=-0.016 dP=+0.224
++ Max : roll=-0.102 pitch=+0.050 yaw=-0.033 dS=+0.109 dL=+0.028 dP=+0.511
++ Max displacements (mm) for each sub-brick:
0.43(0.00) 0.42(0.06) 0.41(0.06) 0.43(0.04) 0.45(0.02) 0.45(0.03) 0.47(0.09) 0.51(0.14) 0.40(0.26) 0.36(0.07) 0.41(0.16) 0.42(0.06) 0.41(0.06) 0.40(0.09) 0.44(0.06) 0.42(0.09) 0.41(0.03) 0.40(0.08) 0.41(0.06) 0.45(0.07) 0.45(0.10) 0.44(0.08) 0.41(0.08) 0.43(0.08) 0.44(0.02) 0.41(0.09) 0.41(0.04) 0.43(0.06) 0.40(0.07) 0.38(0.07) 0.41(0.03) 0.43(0.09) 0.41(0.08) 0.39(0.07) 0.43(0.08) 0.45(0.03) 0.43(0.12) 0.44(0.12) 0.47(0.05) 0.47(0.08) 0.44(0.05) 0.42(0.05) 0.44(0.08) 0.46(0.04) 0.43(0.03) 0.39(0.05) 0.41(0.03) 0.44(0.04) 0.44(0.04) 0.43(0.02) 0.46(0.07) 0.46(0.02) 0.45(0.16) 0.47(0.06) 0.47(0.04) 0.49(0.04) 0.47(0.03) 0.43(0.06) 0.43(0.11) 0.44(0.05) 0.42(0.04) 0.43(0.10) 0.43(0.06) 0.45(0.03) 0.44(0.05) 0.41(0.07) 0.42(0.03) 0.45(0.09) 0.43(0.11) 0.42(0.07) 0.38(0.06) 0.42(0.08) 0.42(0.06) 0.54(0.25) 0.55(0.06) 0.45(0.16) 0.49(0.07) 0.52(0.04) 0.51(0.03) 0.51(0.07) 0.47(0.06) 0.49(0.05) 0.51(0.04) 0.49(0.04) 0.49(0.02) 0.51(0.05) 0.50(0.05) 0.75(0.48) 0.90(0.37) 1.05(0.47) 0.77(0.28) 0.70(0.09) 0.70(0.04) 0.65(0.07) 0.65(0.04) 0.63(0.03) 0.64(0.04) 0.71(0.09) 0.66(0.11) 0.67(0.05) 0.79(0.20) 0.71(0.11) 0.67(0.08) 0.67(0.07) 0.66(0.02) 0.68(0.03) 0.65(0.09) 0.67(0.07) 0.66(0.04) 0.66(0.03) 0.64(0.03) 0.62(0.10) 0.61(0.05) 0.59(0.04) 0.60(0.05) 0.62(0.04) 0.64(0.10) 0.63(0.05) 0.60(0.05) 0.60(0.02) 0.64(0.13) 0.65(0.17) 0.67(0.16) 0.65(0.14) 0.61(0.09) 0.64(0.04) 0.65(0.07) 0.61(0.15) 0.58(0.18) 0.66(0.10) 0.54(0.15) 0.51(0.11) 0.55(0.05) 0.50(0.08) 0.54(0.13) 0.57(0.06) 0.62(0.10) 0.62(0.05) 0.59(0.07) 0.53(0.09) 0.54(0.04) 0.56(0.11) 0.56(0.09) 0.54(0.08) 0.55(0.03) 0.56(0.05) 0.83(0.46) 0.84(0.06) 0.68(0.25) 0.67(0.05) 0.70(0.04) 0.67(0.04) 0.64(0.03)
++ Max displacement in automask = 1.05 (mm) at sub-brick 89
++ Max delta displ in automask = 0.48 (mm) at sub-brick 87
++ Wrote dataset to disk in ./rm.epi.volreg.r02+orig.BRIK
3dcalc -overwrite -a pb01.s_10306.r02.tshift+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: input 'a' is not used in the expression
cat_matvec -ONELINE 10306.anat_al_junk_mat.aff12.1D -I mat.r02.vr.aff12.1D
3dAllineate -base 10306.anat+orig -input pb01.s_10306.r02.tshift+orig -1Dmatrix_apply mat.r02.warp.aff12.1D -mast_dxyz 2 -prefix rm.epi.nomask.r02
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./pb01.s_10306.r02.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Source dataset: ./pb01.s_10306.r02.tshift+orig.HEAD
++ Base dataset: ./10306.anat+orig.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 2.0000 mm
++ OpenMP thread count = 8
++ ========== Applying transformation to 153 sub-bricks ==========
volume 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
++ Output dataset ./rm.epi.nomask.r02+orig.BRIK
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 49.3
++ ###########################################################
3dAllineate -base 10306.anat+orig -input rm.epi.all1+orig -1Dmatrix_apply mat.r02.warp.aff12.1D -mast_dxyz 2 -final NN -quiet -prefix rm.epi.1.r02
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./rm.epi.all1+orig.BRIK is 9.240993 degrees from plumb.
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 39.2
3dTstat -min -prefix rm.epi.min.r02 rm.epi.1.r02+orig
++ 3dTstat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
end
3dvolreg -verbose -zpad 1 -base vr_base_min_outlier+orig -1Dfile dfile.r03.1D -prefix rm.epi.volreg.r03 -cubic -1Dmatrix_save mat.r03.vr.aff12.1D pb01.s_10306.r03.tshift+orig
++ 3dvolreg: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
*+ WARNING: 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 9.240993 degrees from plumb.
++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK
++ Oblique dataset:./pb01.s_10306.r03.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Reading input dataset ./pb01.s_10306.r03.tshift+orig.BRIK
++ Edging: x=6 y=6 z=2
++ Creating mask for -maxdisp
+ Automask has 127577 voxels
+ 13108 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 153 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..
++ CPU time for realignment=0 s [=0 s/sub-brick]
++ Min : roll=-0.201 pitch=+0.026 yaw=-0.263 dS=-0.205 dL=-0.071 dP=-0.137
++ Mean: roll=-0.159 pitch=+0.103 yaw=-0.202 dS=-0.084 dL=-0.047 dP=-0.041
++ Max : roll=-0.106 pitch=+0.191 yaw=-0.139 dS=+0.016 dL=-0.022 dP=+0.083
++ Max displacements (mm) for each sub-brick:
0.48(0.00) 0.48(0.07) 0.45(0.05) 0.46(0.05) 0.49(0.05) 0.52(0.04) 0.47(0.08) 0.48(0.10) 0.47(0.05) 0.47(0.04) 0.54(0.14) 0.49(0.08) 0.54(0.05) 0.57(0.06) 0.51(0.07) 0.52(0.02) 0.54(0.04) 0.47(0.13) 0.45(0.04) 0.47(0.04) 0.52(0.09) 0.52(0.04) 0.48(0.08) 0.46(0.03) 0.43(0.04) 0.43(0.03) 0.45(0.03) 0.43(0.06) 0.40(0.04) 0.39(0.02) 0.43(0.04) 0.47(0.05) 0.45(0.05) 0.45(0.07) 0.46(0.05) 0.49(0.06) 0.47(0.07) 0.49(0.07) 0.47(0.03) 0.46(0.04) 0.46(0.04) 0.46(0.01) 0.45(0.04) 0.43(0.06) 0.48(0.09) 0.52(0.10) 0.50(0.04) 0.48(0.06) 0.50(0.03) 0.48(0.05) 0.46(0.03) 0.44(0.04) 0.51(0.12) 0.56(0.07) 0.49(0.10) 0.50(0.03) 0.46(0.04) 0.46(0.04) 0.49(0.05) 0.47(0.06) 0.44(0.07) 0.44(0.03) 0.49(0.11) 0.56(0.15) 0.49(0.11) 0.50(0.04) 0.53(0.05) 0.53(0.10) 0.55(0.03) 0.50(0.06) 0.53(0.04) 0.55(0.03) 0.53(0.05) 0.54(0.02) 0.51(0.05) 0.50(0.03) 0.49(0.06) 0.48(0.02) 0.51(0.06) 0.54(0.06) 0.49(0.09) 0.48(0.01) 0.48(0.06) 0.51(0.06) 0.45(0.11) 0.43(0.07) 0.42(0.03) 0.42(0.04) 0.42(0.04) 0.43(0.03) 0.50(0.15) 0.49(0.04) 0.44(0.12) 0.50(0.13) 0.48(0.05) 0.47(0.05) 0.47(0.03) 0.47(0.07) 0.47(0.07) 0.45(0.09) 0.45(0.08) 0.50(0.10) 0.51(0.05) 0.50(0.03) 0.51(0.06) 0.50(0.03) 0.47(0.04) 0.47(0.03) 0.46(0.02) 0.50(0.07) 0.48(0.06) 0.46(0.10) 0.44(0.04) 0.44(0.07) 0.43(0.06) 0.43(0.03) 0.44(0.13) 0.44(0.05) 0.43(0.07) 0.45(0.09) 0.41(0.06) 0.41(0.02) 0.43(0.05) 0.43(0.04) 0.41(0.05) 0.42(0.02) 0.42(0.05) 0.40(0.07) 0.45(0.06) 0.44(0.03) 0.43(0.01) 0.44(0.10) 0.43(0.05) 0.41(0.10) 0.40(0.02) 0.40(0.03) 0.41(0.04) 0.43(0.05) 0.46(0.06) 0.44(0.06) 0.44(0.07) 0.45(0.04) 0.44(0.12) 0.48(0.10) 0.45(0.09) 0.48(0.06) 0.47(0.07) 0.48(0.02) 0.48(0.03) 0.50(0.03) 0.50(0.05) 0.50(0.05) 0.52(0.04)
++ Max displacement in automask = 0.57 (mm) at sub-brick 13
++ Max delta displ in automask = 0.15 (mm) at sub-brick 90
++ Wrote dataset to disk in ./rm.epi.volreg.r03+orig.BRIK
3dcalc -overwrite -a pb01.s_10306.r03.tshift+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: input 'a' is not used in the expression
cat_matvec -ONELINE 10306.anat_al_junk_mat.aff12.1D -I mat.r03.vr.aff12.1D
3dAllineate -base 10306.anat+orig -input pb01.s_10306.r03.tshift+orig -1Dmatrix_apply mat.r03.warp.aff12.1D -mast_dxyz 2 -prefix rm.epi.nomask.r03
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./pb01.s_10306.r03.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Source dataset: ./pb01.s_10306.r03.tshift+orig.HEAD
++ Base dataset: ./10306.anat+orig.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 2.0000 mm
++ OpenMP thread count = 8
++ ========== Applying transformation to 153 sub-bricks ==========
volume 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
++ Output dataset ./rm.epi.nomask.r03+orig.BRIK
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 44.8
++ ###########################################################
3dAllineate -base 10306.anat+orig -input rm.epi.all1+orig -1Dmatrix_apply mat.r03.warp.aff12.1D -mast_dxyz 2 -final NN -quiet -prefix rm.epi.1.r03
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./rm.epi.all1+orig.BRIK is 9.240993 degrees from plumb.
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 41.8
3dTstat -min -prefix rm.epi.min.r03 rm.epi.1.r03+orig
++ 3dTstat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
end
3dvolreg -verbose -zpad 1 -base vr_base_min_outlier+orig -1Dfile dfile.r04.1D -prefix rm.epi.volreg.r04 -cubic -1Dmatrix_save mat.r04.vr.aff12.1D pb01.s_10306.r04.tshift+orig
++ 3dvolreg: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
*+ WARNING: 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 9.240993 degrees from plumb.
++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK
++ Oblique dataset:./pb01.s_10306.r04.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Reading input dataset ./pb01.s_10306.r04.tshift+orig.BRIK
++ Edging: x=6 y=6 z=2
++ Creating mask for -maxdisp
+ Automask has 127740 voxels
+ 13106 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 153 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..
++ CPU time for realignment=0 s [=0 s/sub-brick]
++ Min : roll=-0.174 pitch=-0.135 yaw=-0.316 dS=-0.712 dL=-0.095 dP=-0.259
++ Mean: roll=-0.073 pitch=+0.151 yaw=-0.262 dS=-0.150 dL=-0.018 dP=-0.021
++ Max : roll=+0.033 pitch=+0.309 yaw=-0.123 dS=+0.138 dL=+0.096 dP=+0.172
++ Max displacements (mm) for each sub-brick:
0.44(0.00) 0.50(0.17) 0.49(0.05) 0.48(0.05) 0.48(0.03) 0.52(0.08) 0.40(0.21) 0.46(0.24) 0.40(0.20) 0.40(0.11) 0.42(0.04) 0.45(0.04) 0.45(0.04) 0.50(0.10) 0.48(0.05) 0.54(0.11) 0.80(0.48) 0.56(0.28) 0.52(0.15) 0.55(0.06) 0.51(0.09) 0.53(0.08) 0.49(0.05) 0.50(0.06) 0.52(0.06) 0.50(0.04) 0.52(0.07) 0.49(0.07) 0.48(0.05) 0.52(0.05) 0.51(0.04) 0.50(0.06) 0.51(0.05) 0.54(0.04) 0.49(0.12) 0.46(0.09) 0.46(0.05) 0.49(0.05) 0.46(0.05) 0.45(0.06) 0.45(0.05) 0.46(0.02) 0.44(0.05) 0.46(0.05) 0.47(0.05) 0.48(0.03) 0.43(0.15) 0.53(0.17) 0.51(0.12) 0.52(0.12) 0.49(0.06) 0.49(0.04) 0.52(0.07) 0.47(0.06) 0.44(0.06) 0.50(0.06) 0.50(0.01) 0.50(0.03) 0.49(0.06) 0.53(0.05) 0.58(0.10) 0.57(0.04) 0.54(0.06) 0.59(0.09) 0.58(0.02) 0.55(0.05) 0.59(0.04) 0.59(0.03) 0.52(0.07) 0.52(0.04) 0.60(0.11) 0.61(0.07) 0.56(0.10) 0.55(0.08) 0.58(0.07) 0.50(0.11) 0.55(0.06) 0.58(0.04) 0.59(0.04) 0.66(0.07) 0.62(0.06) 0.59(0.05) 0.59(0.04) 0.59(0.04) 0.57(0.04) 0.64(0.77) 0.48(0.32) 0.47(0.13) 0.49(0.06) 0.45(0.06) 0.46(0.05) 0.48(0.08) 0.49(0.04) 0.49(0.04) 0.48(0.07) 0.52(0.07) 0.53(0.04) 0.53(0.03) 0.52(0.06) 0.51(0.03) 0.50(0.06) 0.51(0.03) 0.52(0.04) 0.52(0.02) 0.55(0.09) 0.56(0.07) 0.60(0.07) 0.62(0.05) 0.58(0.04) 0.61(0.04) 0.59(0.05) 0.65(0.08) 0.65(0.05) 0.57(0.12) 0.59(0.08) 0.60(0.05) 0.59(0.08) 0.65(0.07) 0.57(0.10) 0.60(0.08) 0.69(0.10) 0.68(0.05) 0.55(0.47) 0.82(0.63) 0.89(0.26) 0.80(0.28) 0.80(0.05) 0.80(0.03) 0.80(0.03) 0.85(0.07) 0.77(0.10) 0.78(0.04) 0.81(0.03) 0.87(0.08) 0.89(0.06) 0.85(0.04) 0.87(0.03) 0.83(0.05) 0.77(0.08) 0.71(0.11) 0.72(0.03) 0.74(0.05) 0.79(0.06) 0.81(0.07) 0.93(0.66) 0.90(0.32) 0.73(0.35) 0.84(0.19) 0.84(0.06) 0.86(0.13) 0.93(0.12) 0.96(0.07) 0.93(0.06)
++ Max displacement in automask = 0.96 (mm) at sub-brick 151
++ Max delta displ in automask = 0.77 (mm) at sub-brick 85
++ Wrote dataset to disk in ./rm.epi.volreg.r04+orig.BRIK
3dcalc -overwrite -a pb01.s_10306.r04.tshift+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: input 'a' is not used in the expression
cat_matvec -ONELINE 10306.anat_al_junk_mat.aff12.1D -I mat.r04.vr.aff12.1D
3dAllineate -base 10306.anat+orig -input pb01.s_10306.r04.tshift+orig -1Dmatrix_apply mat.r04.warp.aff12.1D -mast_dxyz 2 -prefix rm.epi.nomask.r04
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./pb01.s_10306.r04.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Source dataset: ./pb01.s_10306.r04.tshift+orig.HEAD
++ Base dataset: ./10306.anat+orig.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 2.0000 mm
++ OpenMP thread count = 8
++ ========== Applying transformation to 153 sub-bricks ==========
volume 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
++ Output dataset ./rm.epi.nomask.r04+orig.BRIK
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 44.7
++ ###########################################################
3dAllineate -base 10306.anat+orig -input rm.epi.all1+orig -1Dmatrix_apply mat.r04.warp.aff12.1D -mast_dxyz 2 -final NN -quiet -prefix rm.epi.1.r04
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./rm.epi.all1+orig.BRIK is 9.240993 degrees from plumb.
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 42.2
3dTstat -min -prefix rm.epi.min.r04 rm.epi.1.r04+orig
++ 3dTstat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
end
cat dfile.r01.1D dfile.r02.1D dfile.r03.1D dfile.r04.1D
3dMean -datum short -prefix rm.epi.mean rm.epi.min.r01+orig.HEAD rm.epi.min.r02+orig.HEAD rm.epi.min.r03+orig.HEAD rm.epi.min.r04+orig.HEAD
++ 3dMean: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
3dcalc -a rm.epi.mean+orig -expr step(a-0.999) -prefix mask_epi_extents
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
foreach run ( 01 02 03 04 )
3dcalc -a rm.epi.nomask.r01+orig -b mask_epi_extents+orig -expr a*b -prefix pb02.s_10306.r01.volreg
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.s_10306.r01.volreg+orig.BRIK
end
3dcalc -a rm.epi.nomask.r02+orig -b mask_epi_extents+orig -expr a*b -prefix pb02.s_10306.r02.volreg
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.s_10306.r02.volreg+orig.BRIK
end
3dcalc -a rm.epi.nomask.r03+orig -b mask_epi_extents+orig -expr a*b -prefix pb02.s_10306.r03.volreg
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.s_10306.r03.volreg+orig.BRIK
end
3dcalc -a rm.epi.nomask.r04+orig -b mask_epi_extents+orig -expr a*b -prefix pb02.s_10306.r04.volreg
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.s_10306.r04.volreg+orig.BRIK
end
foreach run ( 01 02 03 04 )
adwarp -apar 10306.anat+tlrc -dpar pb02.s_10306.r01.volreg+orig -dxyz 2 -resam Cu
++ adwarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: R. W. Cox and B. D. Ward
*+ WARNING: Over-writing dataset ./pb02.s_10306.r01.volreg+tlrc.HEAD
end
adwarp -apar 10306.anat+tlrc -dpar pb02.s_10306.r02.volreg+orig -dxyz 2 -resam Cu
++ adwarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: R. W. Cox and B. D. Ward
*+ WARNING: Over-writing dataset ./pb02.s_10306.r02.volreg+tlrc.HEAD
end
adwarp -apar 10306.anat+tlrc -dpar pb02.s_10306.r03.volreg+orig -dxyz 2 -resam Cu
++ adwarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: R. W. Cox and B. D. Ward
*+ WARNING: Over-writing dataset ./pb02.s_10306.r03.volreg+tlrc.HEAD
end
adwarp -apar 10306.anat+tlrc -dpar pb02.s_10306.r04.volreg+orig -dxyz 2 -resam Cu
++ adwarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: R. W. Cox and B. D. Ward
*+ WARNING: Over-writing dataset ./pb02.s_10306.r04.volreg+tlrc.HEAD
end
adwarp -apar 10306.anat+tlrc -dpar mask_epi_extents+orig -dxyz 2 -resam NN
++ adwarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: R. W. Cox and B. D. Ward
*+ WARNING: Over-writing dataset ./mask_epi_extents+tlrc.HEAD
cat_matvec -ONELINE 10306.anat_al_junk_mat.aff12.1D -I
3dAllineate -base 10306.anat+orig -input vr_base_min_outlier+orig -1Dmatrix_apply mat.basewarp.aff12.1D -mast_dxyz 2 -prefix final_epi_vr_base_min_outlier
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./vr_base_min_outlier+orig.BRIK is 9.240993 degrees from plumb.
++ Source dataset: ./vr_base_min_outlier+orig.HEAD
++ Base dataset: ./10306.anat+orig.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 2.0000 mm
++ OpenMP thread count = 8
++ ========== Applying transformation to 1 sub-bricks ==========
++ Output dataset ./final_epi_vr_base_min_outlier+orig.BRIK
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.5
++ ###########################################################
3dcopy 10306.anat+tlrc anat_final.s_10306
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
3dAllineate -base final_epi_vr_base_min_outlier+tlrc -allcostX -input anat_final.s_10306+tlrc
tee out.allcostX.txt
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
** FATAL ERROR: can't open -base dataset 'final_epi_vr_base_min_outlier+tlrc'
** Program compile date = Apr 30 2018
mitchelllab-linux:~/Tamara/PRR_Analysis/Manual_tlrc/Manual/1030
I manually tlrc my anatomical images and ran the uber_subject.py to pre-process the data. In the GUI I checked off "include copy of anat+tlrc" in the "anatomical dataset" section, so the +tlrc version can be included. When I ran my script, there was an error message regarding finding a specific file: "** FATAL ERROR: can't open -base dataset 'final_epi_vr_base_min_outlier+tlrc'
". It seems like I have the final_epi_vr_base_min_outlier+orig file but not the final_epi_vr_base_min_outlier+tlrc file in the results folder. Did I include the manual tlrc anat file into the uber_subject.py script incorrectly?
Thank you,
Tamara
My script is pasted below:
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /home/bmiadmin/subjects
MNI_DIR /usr/local/freesurfer/mni
SUBJECTS_DIR= /home/bmiadmin/subjects
mitchelllab-linux:~/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306> tcsh -xef proc.s_10306 |& tee output.proc.s_10306
echo auto-generated by afni_proc.py, Thu Jun 28 14:43:09 2018
auto-generated by afni_proc.py, Thu Jun 28 14:43:09 2018
echo (version 6.10, Apr 26, 2018)
(version 6.10, Apr 26, 2018)
echo execution started: `date`
date
execution started: Thu Jun 28 14:51:40 EDT 2018
afni -ver
Precompiled binary linux_ubuntu_16_64: Apr 30 2018 (Version AFNI_18.1.09)
afni_history -check_date 23 Mar 2018
-- is current: afni_history as new as: 23 Mar 2018
most recent entry is: 29 Apr 2018
if ( 0 ) then
if ( 0 > 0 ) then
set subj = s_10306
endif
set output_dir = s_10306.results
if ( -d s_10306.results ) then
set runs = ( `count -digits 2 1 4` )
count -digits 2 1 4
mkdir s_10306.results
mkdir s_10306.results/stimuli
cp /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_learn_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_learn_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_learn_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_learn_incor.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_perf_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_perf_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_perf_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/NonRevP_perf_incor.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_acq_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_acq_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_acq_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_acq_incor.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_rev_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_rev_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_rev_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/RevP_rev_incor.txt s_10306.results/stimuli
3dcopy /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/10306.anat s_10306.results/10306.anat
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
3dTcat -prefix s_10306.results/pb00.s_10306.r01.tcat /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/10306.1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 0.4 s
3dTcat -prefix s_10306.results/pb00.s_10306.r02.tcat /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/10306.2+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 1.7 s
3dTcat -prefix s_10306.results/pb00.s_10306.r03.tcat /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/10306.3+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 1.9 s
3dTcat -prefix s_10306.results/pb00.s_10306.r04.tcat /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/10306.4+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 1.6 s
set tr_counts = ( 153 153 153 153 )
cd s_10306.results
touch out.pre_ss_warn.txt
foreach run ( 01 02 03 04 )
3dToutcount -automask -fraction -polort 3 -legendre pb00.s_10306.r01.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.r01.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.s_10306.r01.tcat+orig.BRIK is 9.240993 degrees from plumb.
++ 123854 voxels passed mask/clip
if ( `1deval -a outcount.r$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.s_10306.r02.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.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.s_10306.r02.tcat+orig.BRIK is 9.240993 degrees from plumb.
++ 123963 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r02.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.s_10306.r03.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.r03.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.s_10306.r03.tcat+orig.BRIK is 9.240993 degrees from plumb.
++ 123950 voxels passed mask/clip
if ( `1deval -a outcount.r$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.s_10306.r04.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.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.s_10306.r04.tcat+orig.BRIK is 9.240993 degrees from plumb.
++ 124094 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
cat outcount.r01.1D outcount.r02.1D outcount.r03.1D outcount.r04.1D
set minindex = `3dTstat -argmin -prefix - outcount_rall.1D\'`
3dTstat -argmin -prefix - outcount_rall.1D'
++ 3dTstat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: 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 153 153 153 153 -index_to_run_tr 47
set minoutrun = 01
set minouttr = 47
echo min outlier: run 01, TR 47
tee out.min_outlier.txt
min outlier: run 01, TR 47
foreach run ( 01 02 03 04 )
3dTshift -tzero 0 -quintic -prefix pb01.s_10306.r01.tshift pb00.s_10306.r01.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.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.s_10306.r01.tcat+orig.BRIK is 9.240993 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.s_10306.r02.tshift pb00.s_10306.r02.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.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.s_10306.r02.tcat+orig.BRIK is 9.240993 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.s_10306.r03.tshift pb00.s_10306.r03.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.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.s_10306.r03.tcat+orig.BRIK is 9.240993 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.s_10306.r04.tshift pb00.s_10306.r04.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.s_10306.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.s_10306.r04.tcat+orig.BRIK is 9.240993 degrees from plumb.
end
3dbucket -prefix vr_base_min_outlier pb01.s_10306.r01.tshift+orig[47]
++ 3dbucket: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
align_epi_anat.py -anat2epi -anat 10306.anat+orig -save_skullstrip -suffix _al_junk -epi vr_base_min_outlier+orig -epi_base 0 -epi_strip 3dAutomask -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 (command trimmed):
3dAttribute DELTA ./10306.anat+orig
#++ Multi-cost is lpc
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_vr_base_min_outlier*
#Script is running:
\rm -f ./__tt_10306.anat*
#Script is running (command trimmed):
3dcopy ./10306.anat+orig ./__tt_10306.anat+orig
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
#++ Removing skull from anat data
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_10306.anat+orig -prefix ./__tt_10306.anat_ns
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./__tt_10306.anat+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_10306.anat+orig.BRIK is 9.286984 degrees from plumb.
#Script is running (command trimmed):
3dinfo ./__tt_10306.anat_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/s_10306.results/__tt_10306.anat_ns+orig is ***oblique****
#Script is running (command trimmed):
3dAttribute DELTA ./__tt_10306.anat_ns+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_10306.anat_ns_ob -newgrid 1.000000 ./__tt_10306.anat_ns+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./__tt_10306.anat_ns_obla2e_mat.1D
++ 3dWarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
++ Deobliquing original dataset before obliquing
++ Combining oblique transformations
#++ 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_18.1.09 (Apr 30 2018) [64-bit]
#++ resampling epi to match anat data
#Script is running (command trimmed):
3dresample -master ./__tt_10306.anat_ns_ob+orig -prefix ./__tt_vr_base_min_outlier_ts_rs -inset ./__tt_vr_base_min_outlier_ts+orig'' -rmode Cu
*+ WARNING: 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 9.240993 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_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset ./__tt_vr_base_min_outlier_ts_rs+orig
++ Forming automask
+ Fixed clip level = 347.489990
+ Used gradual clip level = 325.106812 .. 375.963989
+ Number voxels above clip level = 1511331
+ Clustering voxels ...
+ Largest cluster has 1475917 voxels
+ Clustering voxels ...
+ Largest cluster has 1472906 voxels
+ Filled 2190 voxels in small holes; now have 1475096 voxels
+ Filled 30893 voxels in large holes; now have 1505989 voxels
+ Clustering voxels ...
+ Largest cluster has 1505961 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 10447880 voxels
+ Mask now has 1505961 voxels
++ 1505961 voxels in the mask [out of 11953841: 12.60%]
++ first 56 x-planes are zero [from R]
++ last 59 x-planes are zero [from L]
++ first 40 y-planes are zero [from A]
++ last 21 y-planes are zero [from P]
++ first 45 z-planes are zero [from I]
++ last 37 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 896.000000 on /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/s_10306.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/896.000000))'
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
#++ Aligning anat data to epi data
#Script is running (command trimmed):
3dAllineate -lpc -wtprefix ./__tt_10306.anat_ns_ob_al_junk_wtal -weight ./__tt_vr_base_min_outlier_ts_rs_ns_wt+orig -source ./__tt_10306.anat_ns_ob+orig -prefix ./__tt_10306.anat_ns_ob_temp_al_junk -base ./__tt_vr_base_min_outlier_ts_rs_ns+orig -nocmass -1Dmatrix_save ./10306.anat_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_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./__tt_10306.anat_ns_ob+orig.HEAD
++ Base dataset: ./__tt_vr_base_min_outlier_ts_rs_ns+orig.HEAD
++ Loading datasets
++ 1781474 voxels in -source_automask+4
++ Zero-pad: not needed
++ 1505957 voxels [12.6%] in weight mask
++ Number of points for matching = 1505957
++ Local correlation: blok type = 'RHDD(6.54321)'
++ shift param auto-range: -82.2..82.2 -77.0..77.0 -61.6..61.6
+ 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 = 8
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed =======
++ ========== 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 1505957 points from base image [use_all=0]
+ * Exit alignment setup routine
+ 1433110 total points stored in 2694 'RHDD(6.54321)' bloks
+ - Initial cost = -0.561667
+ - 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 = -0.792899 ; 255 funcs
****
+ - Final cost = -0.792915 ; 109 funcs
+ Final fine fit Parameters:
x-shift=-0.3118 y-shift= 1.0663 z-shift= 1.5575
z-angle= 0.0541 x-angle=-0.1426 y-angle=-0.1662
x-scale= 0.9993 y-scale= 0.9915 z-scale= 0.9869
y/x-shear=-0.0000 z/x-shear=-0.0026 z/y-shear=-0.0133
+ - Fine net CPU time = 0.0 s
++ Computing output image
++ image warp: parameters = -0.3118 1.0663 1.5575 0.0541 -0.1426 -0.1662 0.9993 0.9915 0.9869 -0.0000 -0.0026 -0.0133
++ Wrote -1Dmatrix_save ./10306.anat_al_junk_e2a_only_mat.aff12.1D
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 72.3
++ ###########################################################
++ # 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 ./10306.anat_al_junk_e2a_only_mat.aff12.1D ./__tt_10306.anat_ns_obla2e_mat.1D -I > ./10306.anat_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 ./10306.anat_al_junk_mat.aff12.1D -prefix ./10306.anat_al_junk -input ./__tt_10306.anat_ns+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./__tt_10306.anat_ns+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_10306.anat_ns+orig.BRIK is 9.286984 degrees from plumb.
++ Source dataset: ./__tt_10306.anat_ns+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 = 8
++ ========== 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 = 0.9993 0.0010 -0.0009 -2.6814 -0.0010 0.9915 -0.0024 -17.3116 -0.0017 -0.0108 0.9869 29.4628
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 2.4
++ ###########################################################
#++ Creating final output: skullstripped anat data
copying from dataset /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/s_10306.results/__tt_10306.anat_ns+orig to /home/bmiadmin/Tamara/PRR_Analysis/Manual_tlrc/Manual/10306/s_10306.results/10306.anat_ns+orig
#Script is running (command trimmed):
3dcopy ./__tt_10306.anat_ns+orig 10306.anat_ns
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
#++ 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 10306.anat+orig \
-save_skullstrip -suffix _al_junk -epi vr_base_min_outlier+orig -epi_base \
0 -epi_strip 3dAutomask -volreg off -tshift off" \
./10306.anat_al_junk+orig
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_vr_base_min_outlier*
#Script is running:
\rm -f ./__tt_10306.anat*
# Finished alignment successfully
if ( ! -f 10306.anat+tlrc.HEAD ) then
foreach run ( 01 02 03 04 )
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 pb01.s_10306.r01.tshift+orig
++ 3dvolreg: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
*+ WARNING: 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 9.240993 degrees from plumb.
++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK
++ Oblique dataset:./pb01.s_10306.r01.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Reading input dataset ./pb01.s_10306.r01.tshift+orig.BRIK
++ Edging: x=6 y=6 z=2
++ Creating mask for -maxdisp
+ Automask has 127575 voxels
+ 13040 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 153 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..
++ CPU time for realignment=0 s [=0 s/sub-brick]
++ Min : roll=-0.151 pitch=-0.339 yaw=-0.135 dS=-0.287 dL=-0.042 dP=-0.109
++ Mean: roll=-0.003 pitch=-0.055 yaw=-0.021 dS=+0.046 dL=+0.010 dP=-0.011
++ Max : roll=+0.261 pitch=+0.431 yaw=+0.177 dS=+0.201 dL=+0.104 dP=+0.168
++ Max displacements (mm) for each sub-brick:
0.78(0.00) 0.93(0.21) 0.93(0.04) 0.94(0.03) 0.91(0.05) 0.89(0.05) 0.91(0.06) 0.86(0.08) 0.85(0.06) 0.72(0.14) 0.69(0.05) 0.67(0.04) 0.69(0.06) 0.72(0.05) 0.65(0.08) 0.61(0.07) 0.63(0.04) 0.53(0.14) 0.51(0.05) 0.49(0.06) 0.49(0.02) 0.41(0.08) 0.44(0.12) 0.41(0.04) 0.27(0.25) 0.33(0.15) 0.65(0.39) 0.47(0.24) 0.37(0.15) 0.35(0.13) 0.21(0.31) 0.26(0.16) 0.20(0.12) 0.19(0.21) 0.18(0.04) 0.20(0.04) 0.19(0.09) 0.18(0.02) 0.14(0.06) 0.08(0.06) 0.09(0.06) 0.09(0.05) 0.07(0.05) 0.08(0.05) 0.05(0.08) 0.06(0.02) 0.05(0.05) 0.00(0.05) 0.06(0.06) 0.11(0.07) 0.09(0.03) 0.11(0.04) 0.15(0.18) 0.03(0.12) 0.10(0.12) 0.07(0.09) 0.08(0.08) 0.09(0.05) 0.11(0.04) 0.09(0.05) 0.13(0.06) 0.15(0.04) 0.20(0.06) 0.18(0.04) 0.18(0.06) 0.23(0.07) 0.22(0.05) 0.22(0.03) 0.21(0.02) 0.21(0.03) 0.23(0.04) 0.25(0.04) 0.23(0.08) 0.23(0.04) 0.19(0.07) 0.24(0.07) 0.23(0.04) 0.22(0.08) 0.25(0.06) 0.28(0.08) 0.24(0.07) 0.25(0.06) 0.25(0.06) 0.29(0.05) 0.29(0.02) 0.29(0.03) 0.33(0.05) 0.41(0.08) 0.37(0.07) 0.30(0.07) 0.39(0.09) 0.34(0.08) 0.29(0.10) 0.31(0.08) 0.31(0.07) 0.30(0.07) 0.35(0.08) 0.43(0.10) 0.35(0.08) 0.38(0.03) 0.28(0.11) 0.28(0.07) 0.32(0.06) 0.30(0.04) 0.24(0.08) 0.37(0.15) 0.38(0.06) 0.36(0.05) 0.32(0.07) 0.41(0.11) 0.46(0.10) 0.30(0.20) 0.43(0.23) 0.38(0.07) 0.43(0.08) 0.51(0.10) 0.48(0.04) 0.59(0.11) 0.53(0.06) 0.66(0.13) 0.69(0.06) 0.52(0.22) 0.59(0.13) 0.53(0.08) 0.50(0.10) 0.51(0.09) 0.60(0.09) 0.59(0.06) 0.62(0.05) 0.64(0.03) 0.65(0.02) 0.66(0.03) 0.59(0.07) 0.59(0.02) 0.51(0.09) 0.53(0.08) 0.55(0.06) 0.52(0.04) 0.52(0.05) 0.59(0.09) 0.59(0.04) 0.62(0.03) 0.71(0.11) 0.68(0.07) 0.64(0.07) 0.63(0.04) 0.69(0.07) 0.68(0.03) 0.65(0.06) 0.56(0.11) 0.55(0.03) 0.64(0.11) 0.64(0.07)
++ Max displacement in automask = 0.94 (mm) at sub-brick 3
++ Max delta displ in automask = 0.39 (mm) at sub-brick 26
++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK
3dcalc -overwrite -a pb01.s_10306.r01.tshift+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: input 'a' is not used in the expression
cat_matvec -ONELINE 10306.anat_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D
3dAllineate -base 10306.anat+orig -input pb01.s_10306.r01.tshift+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 2 -prefix rm.epi.nomask.r01
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./pb01.s_10306.r01.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Source dataset: ./pb01.s_10306.r01.tshift+orig.HEAD
++ Base dataset: ./10306.anat+orig.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 2.0000 mm
++ OpenMP thread count = 8
++ ========== Applying transformation to 153 sub-bricks ==========
volume 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
++ Output dataset ./rm.epi.nomask.r01+orig.BRIK
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 49.1
++ ###########################################################
3dAllineate -base 10306.anat+orig -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 2 -final NN -quiet -prefix rm.epi.1.r01
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./rm.epi.all1+orig.BRIK is 9.240993 degrees from plumb.
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 44.7
3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+orig
++ 3dTstat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
end
3dvolreg -verbose -zpad 1 -base vr_base_min_outlier+orig -1Dfile dfile.r02.1D -prefix rm.epi.volreg.r02 -cubic -1Dmatrix_save mat.r02.vr.aff12.1D pb01.s_10306.r02.tshift+orig
++ 3dvolreg: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
*+ WARNING: 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 9.240993 degrees from plumb.
++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK
++ Oblique dataset:./pb01.s_10306.r02.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Reading input dataset ./pb01.s_10306.r02.tshift+orig.BRIK
++ Edging: x=6 y=6 z=2
++ Creating mask for -maxdisp
+ Automask has 127614 voxels
+ 13110 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 153 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..
++ CPU time for realignment=0 s [=0 s/sub-brick]
++ Min : roll=-0.321 pitch=-0.360 yaw=-0.187 dS=-0.296 dL=-0.050 dP=+0.051
++ Mean: roll=-0.165 pitch=-0.094 yaw=-0.111 dS=-0.071 dL=-0.016 dP=+0.224
++ Max : roll=-0.102 pitch=+0.050 yaw=-0.033 dS=+0.109 dL=+0.028 dP=+0.511
++ Max displacements (mm) for each sub-brick:
0.43(0.00) 0.42(0.06) 0.41(0.06) 0.43(0.04) 0.45(0.02) 0.45(0.03) 0.47(0.09) 0.51(0.14) 0.40(0.26) 0.36(0.07) 0.41(0.16) 0.42(0.06) 0.41(0.06) 0.40(0.09) 0.44(0.06) 0.42(0.09) 0.41(0.03) 0.40(0.08) 0.41(0.06) 0.45(0.07) 0.45(0.10) 0.44(0.08) 0.41(0.08) 0.43(0.08) 0.44(0.02) 0.41(0.09) 0.41(0.04) 0.43(0.06) 0.40(0.07) 0.38(0.07) 0.41(0.03) 0.43(0.09) 0.41(0.08) 0.39(0.07) 0.43(0.08) 0.45(0.03) 0.43(0.12) 0.44(0.12) 0.47(0.05) 0.47(0.08) 0.44(0.05) 0.42(0.05) 0.44(0.08) 0.46(0.04) 0.43(0.03) 0.39(0.05) 0.41(0.03) 0.44(0.04) 0.44(0.04) 0.43(0.02) 0.46(0.07) 0.46(0.02) 0.45(0.16) 0.47(0.06) 0.47(0.04) 0.49(0.04) 0.47(0.03) 0.43(0.06) 0.43(0.11) 0.44(0.05) 0.42(0.04) 0.43(0.10) 0.43(0.06) 0.45(0.03) 0.44(0.05) 0.41(0.07) 0.42(0.03) 0.45(0.09) 0.43(0.11) 0.42(0.07) 0.38(0.06) 0.42(0.08) 0.42(0.06) 0.54(0.25) 0.55(0.06) 0.45(0.16) 0.49(0.07) 0.52(0.04) 0.51(0.03) 0.51(0.07) 0.47(0.06) 0.49(0.05) 0.51(0.04) 0.49(0.04) 0.49(0.02) 0.51(0.05) 0.50(0.05) 0.75(0.48) 0.90(0.37) 1.05(0.47) 0.77(0.28) 0.70(0.09) 0.70(0.04) 0.65(0.07) 0.65(0.04) 0.63(0.03) 0.64(0.04) 0.71(0.09) 0.66(0.11) 0.67(0.05) 0.79(0.20) 0.71(0.11) 0.67(0.08) 0.67(0.07) 0.66(0.02) 0.68(0.03) 0.65(0.09) 0.67(0.07) 0.66(0.04) 0.66(0.03) 0.64(0.03) 0.62(0.10) 0.61(0.05) 0.59(0.04) 0.60(0.05) 0.62(0.04) 0.64(0.10) 0.63(0.05) 0.60(0.05) 0.60(0.02) 0.64(0.13) 0.65(0.17) 0.67(0.16) 0.65(0.14) 0.61(0.09) 0.64(0.04) 0.65(0.07) 0.61(0.15) 0.58(0.18) 0.66(0.10) 0.54(0.15) 0.51(0.11) 0.55(0.05) 0.50(0.08) 0.54(0.13) 0.57(0.06) 0.62(0.10) 0.62(0.05) 0.59(0.07) 0.53(0.09) 0.54(0.04) 0.56(0.11) 0.56(0.09) 0.54(0.08) 0.55(0.03) 0.56(0.05) 0.83(0.46) 0.84(0.06) 0.68(0.25) 0.67(0.05) 0.70(0.04) 0.67(0.04) 0.64(0.03)
++ Max displacement in automask = 1.05 (mm) at sub-brick 89
++ Max delta displ in automask = 0.48 (mm) at sub-brick 87
++ Wrote dataset to disk in ./rm.epi.volreg.r02+orig.BRIK
3dcalc -overwrite -a pb01.s_10306.r02.tshift+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: input 'a' is not used in the expression
cat_matvec -ONELINE 10306.anat_al_junk_mat.aff12.1D -I mat.r02.vr.aff12.1D
3dAllineate -base 10306.anat+orig -input pb01.s_10306.r02.tshift+orig -1Dmatrix_apply mat.r02.warp.aff12.1D -mast_dxyz 2 -prefix rm.epi.nomask.r02
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./pb01.s_10306.r02.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Source dataset: ./pb01.s_10306.r02.tshift+orig.HEAD
++ Base dataset: ./10306.anat+orig.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 2.0000 mm
++ OpenMP thread count = 8
++ ========== Applying transformation to 153 sub-bricks ==========
volume 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
++ Output dataset ./rm.epi.nomask.r02+orig.BRIK
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 49.3
++ ###########################################################
3dAllineate -base 10306.anat+orig -input rm.epi.all1+orig -1Dmatrix_apply mat.r02.warp.aff12.1D -mast_dxyz 2 -final NN -quiet -prefix rm.epi.1.r02
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./rm.epi.all1+orig.BRIK is 9.240993 degrees from plumb.
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 39.2
3dTstat -min -prefix rm.epi.min.r02 rm.epi.1.r02+orig
++ 3dTstat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
end
3dvolreg -verbose -zpad 1 -base vr_base_min_outlier+orig -1Dfile dfile.r03.1D -prefix rm.epi.volreg.r03 -cubic -1Dmatrix_save mat.r03.vr.aff12.1D pb01.s_10306.r03.tshift+orig
++ 3dvolreg: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
*+ WARNING: 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 9.240993 degrees from plumb.
++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK
++ Oblique dataset:./pb01.s_10306.r03.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Reading input dataset ./pb01.s_10306.r03.tshift+orig.BRIK
++ Edging: x=6 y=6 z=2
++ Creating mask for -maxdisp
+ Automask has 127577 voxels
+ 13108 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 153 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..
++ CPU time for realignment=0 s [=0 s/sub-brick]
++ Min : roll=-0.201 pitch=+0.026 yaw=-0.263 dS=-0.205 dL=-0.071 dP=-0.137
++ Mean: roll=-0.159 pitch=+0.103 yaw=-0.202 dS=-0.084 dL=-0.047 dP=-0.041
++ Max : roll=-0.106 pitch=+0.191 yaw=-0.139 dS=+0.016 dL=-0.022 dP=+0.083
++ Max displacements (mm) for each sub-brick:
0.48(0.00) 0.48(0.07) 0.45(0.05) 0.46(0.05) 0.49(0.05) 0.52(0.04) 0.47(0.08) 0.48(0.10) 0.47(0.05) 0.47(0.04) 0.54(0.14) 0.49(0.08) 0.54(0.05) 0.57(0.06) 0.51(0.07) 0.52(0.02) 0.54(0.04) 0.47(0.13) 0.45(0.04) 0.47(0.04) 0.52(0.09) 0.52(0.04) 0.48(0.08) 0.46(0.03) 0.43(0.04) 0.43(0.03) 0.45(0.03) 0.43(0.06) 0.40(0.04) 0.39(0.02) 0.43(0.04) 0.47(0.05) 0.45(0.05) 0.45(0.07) 0.46(0.05) 0.49(0.06) 0.47(0.07) 0.49(0.07) 0.47(0.03) 0.46(0.04) 0.46(0.04) 0.46(0.01) 0.45(0.04) 0.43(0.06) 0.48(0.09) 0.52(0.10) 0.50(0.04) 0.48(0.06) 0.50(0.03) 0.48(0.05) 0.46(0.03) 0.44(0.04) 0.51(0.12) 0.56(0.07) 0.49(0.10) 0.50(0.03) 0.46(0.04) 0.46(0.04) 0.49(0.05) 0.47(0.06) 0.44(0.07) 0.44(0.03) 0.49(0.11) 0.56(0.15) 0.49(0.11) 0.50(0.04) 0.53(0.05) 0.53(0.10) 0.55(0.03) 0.50(0.06) 0.53(0.04) 0.55(0.03) 0.53(0.05) 0.54(0.02) 0.51(0.05) 0.50(0.03) 0.49(0.06) 0.48(0.02) 0.51(0.06) 0.54(0.06) 0.49(0.09) 0.48(0.01) 0.48(0.06) 0.51(0.06) 0.45(0.11) 0.43(0.07) 0.42(0.03) 0.42(0.04) 0.42(0.04) 0.43(0.03) 0.50(0.15) 0.49(0.04) 0.44(0.12) 0.50(0.13) 0.48(0.05) 0.47(0.05) 0.47(0.03) 0.47(0.07) 0.47(0.07) 0.45(0.09) 0.45(0.08) 0.50(0.10) 0.51(0.05) 0.50(0.03) 0.51(0.06) 0.50(0.03) 0.47(0.04) 0.47(0.03) 0.46(0.02) 0.50(0.07) 0.48(0.06) 0.46(0.10) 0.44(0.04) 0.44(0.07) 0.43(0.06) 0.43(0.03) 0.44(0.13) 0.44(0.05) 0.43(0.07) 0.45(0.09) 0.41(0.06) 0.41(0.02) 0.43(0.05) 0.43(0.04) 0.41(0.05) 0.42(0.02) 0.42(0.05) 0.40(0.07) 0.45(0.06) 0.44(0.03) 0.43(0.01) 0.44(0.10) 0.43(0.05) 0.41(0.10) 0.40(0.02) 0.40(0.03) 0.41(0.04) 0.43(0.05) 0.46(0.06) 0.44(0.06) 0.44(0.07) 0.45(0.04) 0.44(0.12) 0.48(0.10) 0.45(0.09) 0.48(0.06) 0.47(0.07) 0.48(0.02) 0.48(0.03) 0.50(0.03) 0.50(0.05) 0.50(0.05) 0.52(0.04)
++ Max displacement in automask = 0.57 (mm) at sub-brick 13
++ Max delta displ in automask = 0.15 (mm) at sub-brick 90
++ Wrote dataset to disk in ./rm.epi.volreg.r03+orig.BRIK
3dcalc -overwrite -a pb01.s_10306.r03.tshift+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: input 'a' is not used in the expression
cat_matvec -ONELINE 10306.anat_al_junk_mat.aff12.1D -I mat.r03.vr.aff12.1D
3dAllineate -base 10306.anat+orig -input pb01.s_10306.r03.tshift+orig -1Dmatrix_apply mat.r03.warp.aff12.1D -mast_dxyz 2 -prefix rm.epi.nomask.r03
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./pb01.s_10306.r03.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Source dataset: ./pb01.s_10306.r03.tshift+orig.HEAD
++ Base dataset: ./10306.anat+orig.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 2.0000 mm
++ OpenMP thread count = 8
++ ========== Applying transformation to 153 sub-bricks ==========
volume 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
++ Output dataset ./rm.epi.nomask.r03+orig.BRIK
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 44.8
++ ###########################################################
3dAllineate -base 10306.anat+orig -input rm.epi.all1+orig -1Dmatrix_apply mat.r03.warp.aff12.1D -mast_dxyz 2 -final NN -quiet -prefix rm.epi.1.r03
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./rm.epi.all1+orig.BRIK is 9.240993 degrees from plumb.
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 41.8
3dTstat -min -prefix rm.epi.min.r03 rm.epi.1.r03+orig
++ 3dTstat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
end
3dvolreg -verbose -zpad 1 -base vr_base_min_outlier+orig -1Dfile dfile.r04.1D -prefix rm.epi.volreg.r04 -cubic -1Dmatrix_save mat.r04.vr.aff12.1D pb01.s_10306.r04.tshift+orig
++ 3dvolreg: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
*+ WARNING: 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 9.240993 degrees from plumb.
++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK
++ Oblique dataset:./pb01.s_10306.r04.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Reading input dataset ./pb01.s_10306.r04.tshift+orig.BRIK
++ Edging: x=6 y=6 z=2
++ Creating mask for -maxdisp
+ Automask has 127740 voxels
+ 13106 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 153 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..
++ CPU time for realignment=0 s [=0 s/sub-brick]
++ Min : roll=-0.174 pitch=-0.135 yaw=-0.316 dS=-0.712 dL=-0.095 dP=-0.259
++ Mean: roll=-0.073 pitch=+0.151 yaw=-0.262 dS=-0.150 dL=-0.018 dP=-0.021
++ Max : roll=+0.033 pitch=+0.309 yaw=-0.123 dS=+0.138 dL=+0.096 dP=+0.172
++ Max displacements (mm) for each sub-brick:
0.44(0.00) 0.50(0.17) 0.49(0.05) 0.48(0.05) 0.48(0.03) 0.52(0.08) 0.40(0.21) 0.46(0.24) 0.40(0.20) 0.40(0.11) 0.42(0.04) 0.45(0.04) 0.45(0.04) 0.50(0.10) 0.48(0.05) 0.54(0.11) 0.80(0.48) 0.56(0.28) 0.52(0.15) 0.55(0.06) 0.51(0.09) 0.53(0.08) 0.49(0.05) 0.50(0.06) 0.52(0.06) 0.50(0.04) 0.52(0.07) 0.49(0.07) 0.48(0.05) 0.52(0.05) 0.51(0.04) 0.50(0.06) 0.51(0.05) 0.54(0.04) 0.49(0.12) 0.46(0.09) 0.46(0.05) 0.49(0.05) 0.46(0.05) 0.45(0.06) 0.45(0.05) 0.46(0.02) 0.44(0.05) 0.46(0.05) 0.47(0.05) 0.48(0.03) 0.43(0.15) 0.53(0.17) 0.51(0.12) 0.52(0.12) 0.49(0.06) 0.49(0.04) 0.52(0.07) 0.47(0.06) 0.44(0.06) 0.50(0.06) 0.50(0.01) 0.50(0.03) 0.49(0.06) 0.53(0.05) 0.58(0.10) 0.57(0.04) 0.54(0.06) 0.59(0.09) 0.58(0.02) 0.55(0.05) 0.59(0.04) 0.59(0.03) 0.52(0.07) 0.52(0.04) 0.60(0.11) 0.61(0.07) 0.56(0.10) 0.55(0.08) 0.58(0.07) 0.50(0.11) 0.55(0.06) 0.58(0.04) 0.59(0.04) 0.66(0.07) 0.62(0.06) 0.59(0.05) 0.59(0.04) 0.59(0.04) 0.57(0.04) 0.64(0.77) 0.48(0.32) 0.47(0.13) 0.49(0.06) 0.45(0.06) 0.46(0.05) 0.48(0.08) 0.49(0.04) 0.49(0.04) 0.48(0.07) 0.52(0.07) 0.53(0.04) 0.53(0.03) 0.52(0.06) 0.51(0.03) 0.50(0.06) 0.51(0.03) 0.52(0.04) 0.52(0.02) 0.55(0.09) 0.56(0.07) 0.60(0.07) 0.62(0.05) 0.58(0.04) 0.61(0.04) 0.59(0.05) 0.65(0.08) 0.65(0.05) 0.57(0.12) 0.59(0.08) 0.60(0.05) 0.59(0.08) 0.65(0.07) 0.57(0.10) 0.60(0.08) 0.69(0.10) 0.68(0.05) 0.55(0.47) 0.82(0.63) 0.89(0.26) 0.80(0.28) 0.80(0.05) 0.80(0.03) 0.80(0.03) 0.85(0.07) 0.77(0.10) 0.78(0.04) 0.81(0.03) 0.87(0.08) 0.89(0.06) 0.85(0.04) 0.87(0.03) 0.83(0.05) 0.77(0.08) 0.71(0.11) 0.72(0.03) 0.74(0.05) 0.79(0.06) 0.81(0.07) 0.93(0.66) 0.90(0.32) 0.73(0.35) 0.84(0.19) 0.84(0.06) 0.86(0.13) 0.93(0.12) 0.96(0.07) 0.93(0.06)
++ Max displacement in automask = 0.96 (mm) at sub-brick 151
++ Max delta displ in automask = 0.77 (mm) at sub-brick 85
++ Wrote dataset to disk in ./rm.epi.volreg.r04+orig.BRIK
3dcalc -overwrite -a pb01.s_10306.r04.tshift+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: input 'a' is not used in the expression
cat_matvec -ONELINE 10306.anat_al_junk_mat.aff12.1D -I mat.r04.vr.aff12.1D
3dAllineate -base 10306.anat+orig -input pb01.s_10306.r04.tshift+orig -1Dmatrix_apply mat.r04.warp.aff12.1D -mast_dxyz 2 -prefix rm.epi.nomask.r04
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./pb01.s_10306.r04.tshift+orig.BRIK is 9.240993 degrees from plumb.
++ Source dataset: ./pb01.s_10306.r04.tshift+orig.HEAD
++ Base dataset: ./10306.anat+orig.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 2.0000 mm
++ OpenMP thread count = 8
++ ========== Applying transformation to 153 sub-bricks ==========
volume 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
++ Output dataset ./rm.epi.nomask.r04+orig.BRIK
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 44.7
++ ###########################################################
3dAllineate -base 10306.anat+orig -input rm.epi.all1+orig -1Dmatrix_apply mat.r04.warp.aff12.1D -mast_dxyz 2 -final NN -quiet -prefix rm.epi.1.r04
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./rm.epi.all1+orig.BRIK is 9.240993 degrees from plumb.
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 42.2
3dTstat -min -prefix rm.epi.min.r04 rm.epi.1.r04+orig
++ 3dTstat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
end
cat dfile.r01.1D dfile.r02.1D dfile.r03.1D dfile.r04.1D
3dMean -datum short -prefix rm.epi.mean rm.epi.min.r01+orig.HEAD rm.epi.min.r02+orig.HEAD rm.epi.min.r03+orig.HEAD rm.epi.min.r04+orig.HEAD
++ 3dMean: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
3dcalc -a rm.epi.mean+orig -expr step(a-0.999) -prefix mask_epi_extents
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
foreach run ( 01 02 03 04 )
3dcalc -a rm.epi.nomask.r01+orig -b mask_epi_extents+orig -expr a*b -prefix pb02.s_10306.r01.volreg
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.s_10306.r01.volreg+orig.BRIK
end
3dcalc -a rm.epi.nomask.r02+orig -b mask_epi_extents+orig -expr a*b -prefix pb02.s_10306.r02.volreg
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.s_10306.r02.volreg+orig.BRIK
end
3dcalc -a rm.epi.nomask.r03+orig -b mask_epi_extents+orig -expr a*b -prefix pb02.s_10306.r03.volreg
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.s_10306.r03.volreg+orig.BRIK
end
3dcalc -a rm.epi.nomask.r04+orig -b mask_epi_extents+orig -expr a*b -prefix pb02.s_10306.r04.volreg
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.s_10306.r04.volreg+orig.BRIK
end
foreach run ( 01 02 03 04 )
adwarp -apar 10306.anat+tlrc -dpar pb02.s_10306.r01.volreg+orig -dxyz 2 -resam Cu
++ adwarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: R. W. Cox and B. D. Ward
*+ WARNING: Over-writing dataset ./pb02.s_10306.r01.volreg+tlrc.HEAD
end
adwarp -apar 10306.anat+tlrc -dpar pb02.s_10306.r02.volreg+orig -dxyz 2 -resam Cu
++ adwarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: R. W. Cox and B. D. Ward
*+ WARNING: Over-writing dataset ./pb02.s_10306.r02.volreg+tlrc.HEAD
end
adwarp -apar 10306.anat+tlrc -dpar pb02.s_10306.r03.volreg+orig -dxyz 2 -resam Cu
++ adwarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: R. W. Cox and B. D. Ward
*+ WARNING: Over-writing dataset ./pb02.s_10306.r03.volreg+tlrc.HEAD
end
adwarp -apar 10306.anat+tlrc -dpar pb02.s_10306.r04.volreg+orig -dxyz 2 -resam Cu
++ adwarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: R. W. Cox and B. D. Ward
*+ WARNING: Over-writing dataset ./pb02.s_10306.r04.volreg+tlrc.HEAD
end
adwarp -apar 10306.anat+tlrc -dpar mask_epi_extents+orig -dxyz 2 -resam NN
++ adwarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: R. W. Cox and B. D. Ward
*+ WARNING: Over-writing dataset ./mask_epi_extents+tlrc.HEAD
cat_matvec -ONELINE 10306.anat_al_junk_mat.aff12.1D -I
3dAllineate -base 10306.anat+orig -input vr_base_min_outlier+orig -1Dmatrix_apply mat.basewarp.aff12.1D -mast_dxyz 2 -prefix final_epi_vr_base_min_outlier
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./10306.anat+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:./10306.anat+orig.BRIK is 9.286984 degrees from plumb.
++ Oblique dataset:./vr_base_min_outlier+orig.BRIK is 9.240993 degrees from plumb.
++ Source dataset: ./vr_base_min_outlier+orig.HEAD
++ Base dataset: ./10306.anat+orig.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 2.0000 mm
++ OpenMP thread count = 8
++ ========== Applying transformation to 1 sub-bricks ==========
++ Output dataset ./final_epi_vr_base_min_outlier+orig.BRIK
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.5
++ ###########################################################
3dcopy 10306.anat+tlrc anat_final.s_10306
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
3dAllineate -base final_epi_vr_base_min_outlier+tlrc -allcostX -input anat_final.s_10306+tlrc
tee out.allcostX.txt
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
** FATAL ERROR: can't open -base dataset 'final_epi_vr_base_min_outlier+tlrc'
** Program compile date = Apr 30 2018
mitchelllab-linux:~/Tamara/PRR_Analysis/Manual_tlrc/Manual/1030
| Subject | Author | Posted |
|---|---|---|
|
tamtam | June 28, 2018 04:15PM |
