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’ sad smiley”. 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
- Fine net CPU time = 0.0 s
- 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
- Exit alignment setup routine
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 ab -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 ab -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 ab -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’ sad smiley
** Program compile date = Apr 30 2018
mitchelllab-linux:~/Tamara/PRR_Analysis/Manual_tlrc/Manual/1030