Hello,

I have a question regarding an error related to affine transformations (see error message below). Upon inspection I saw that this participant's anatomical scan has a lot of movement -it is very blurry and "grainy". I have attempted to rectify the error by following the suggestion in a related post by skipping the affine step using "-affine_input_xmat ID"; however I received an error message indicating that "awpy/anat.un.aff.Xat.1D" cannot be found. I was wondering whether there are any other steps I can do to solve this issue? I am speculating that the affine transformation errors may be due to the head motion in the anatomical scan?

Thank you so much for your assistance!
Tamara


Previous post:
[afni.nimh.nih.gov]

Error Message with affine step:

echo auto-generated by afni_proc.py, Wed Jul 18 09:58:21 2018
auto-generated by afni_proc.py, Wed Jul 18 09:58:21 2018
echo (version 6.10, Apr 26, 2018)
(version 6.10, Apr 26, 2018)
echo execution started: `date`
date
execution started: Fri Aug 3 08:54:05 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 = July19_Final_9409
endif
set output_dir = July19_Final_9409.results
if ( -d July19_Final_9409.results ) then
set runs = ( `count -digits 2 1 4` )
count -digits 2 1 4
mkdir July19_Final_9409.results
mkdir July19_Final_9409.results/stimuli
cp /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_learn_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_learn_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_learn_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_learn_incor.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_perf_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_perf_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_perf_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/NonRevP_perf_incor.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_acq_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_acq_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_acq_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_acq_incor.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_rev_corr_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_rev_corr.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_rev_incor_fed.txt /home/bmiadmin/Tamara/PRR_Analysis/9409/RevP_rev_incor.txt July19_Final_9409.results/stimuli
3dcopy 9409.anat+orig July19_Final_9409.results/9409.anat
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
3dTcat -prefix July19_Final_9409.results/pb00.July19_Final_9409.r01.tcat 9409.1+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 0.3 s
3dTcat -prefix July19_Final_9409.results/pb00.July19_Final_9409.r02.tcat 9409.2+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 0.4 s
3dTcat -prefix July19_Final_9409.results/pb00.July19_Final_9409.r03.tcat 9409.3+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 0.4 s
3dTcat -prefix July19_Final_9409.results/pb00.July19_Final_9409.r04.tcat 9409.4+orig[0..$]
++ 3dTcat: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ elapsed time = 0.3 s
set tr_counts = ( 153 153 153 153 )
cd July19_Final_9409.results
touch out.pre_ss_warn.txt
foreach run ( 01 02 03 04 )
3dToutcount -automask -fraction -polort 3 -legendre pb00.July19_Final_9409.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.July19_Final_9409.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.July19_Final_9409.r01.tcat+orig.BRIK is 3.359754 degrees from plumb.
++ 107968 voxels passed mask/clip
1deval -a outcount.r01.1D -expr 1-step(a-0.1)
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r01.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.July19_Final_9409.r02.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.July19_Final_9409.r02.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.July19_Final_9409.r02.tcat+orig.BRIK is 3.359754 degrees from plumb.
++ 108219 voxels passed mask/clip
1deval -a outcount.r02.1D -expr 1-step(a-0.1)
if ( `1deval -a outcount.r$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.July19_Final_9409.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.July19_Final_9409.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.July19_Final_9409.r03.tcat+orig.BRIK is 3.359754 degrees from plumb.
++ 108215 voxels passed mask/clip
1deval -a outcount.r03.1D -expr 1-step(a-0.1)
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r03.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.July19_Final_9409.r04.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb00.July19_Final_9409.r04.tcat+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb00.July19_Final_9409.r04.tcat+orig.BRIK is 3.359754 degrees from plumb.
++ 107669 voxels passed mask/clip
1deval -a outcount.r04.1D -expr 1-step(a-0.1)
if ( `1deval -a outcount.r$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
cat rm.out.cen.r01.1D rm.out.cen.r02.1D rm.out.cen.r03.1D rm.out.cen.r04.1D
foreach run ( 01 02 03 04 )
3dTshift -tzero 0 -quintic -prefix pb01.July19_Final_9409.r01.tshift pb00.July19_Final_9409.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.July19_Final_9409.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.July19_Final_9409.r01.tcat+orig.BRIK is 3.359754 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.July19_Final_9409.r02.tshift pb00.July19_Final_9409.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.July19_Final_9409.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.July19_Final_9409.r02.tcat+orig.BRIK is 3.359754 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.July19_Final_9409.r03.tshift pb00.July19_Final_9409.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.July19_Final_9409.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.July19_Final_9409.r03.tcat+orig.BRIK is 3.359754 degrees from plumb.
end
3dTshift -tzero 0 -quintic -prefix pb01.July19_Final_9409.r04.tshift pb00.July19_Final_9409.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.July19_Final_9409.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.July19_Final_9409.r04.tcat+orig.BRIK is 3.359754 degrees from plumb.
end
3dbucket -prefix vr_base pb01.July19_Final_9409.r04.tshift+orig[152]
++ 3dbucket: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
align_epi_anat.py -anat2epi -anat 9409.anat+orig -save_skullstrip -suffix _al_junk -epi vr_base+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+orig
#Script is running (command trimmed):
3dAttribute DELTA ./vr_base+orig
#Script is running (command trimmed):
3dAttribute DELTA ./9409.anat+orig
#++ Multi-cost is lpc
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_vr_base*
#Script is running:
\rm -f ./__tt_9409.anat*
#Script is running (command trimmed):
3dcopy ./9409.anat+orig ./__tt_9409.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_9409.anat+orig -prefix ./__tt_9409.anat_ns
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./__tt_9409.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_9409.anat+orig.BRIK is 3.359754 degrees from plumb.
#Script is running (command trimmed):
3dinfo ./__tt_9409.anat_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /home/bmiadmin/Tamara/PRR_Analysis/9409/July19_Final_9409.results/__tt_9409.anat_ns+orig is ***oblique****
#Script is running (command trimmed):
3dAttribute DELTA ./__tt_9409.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+orig -prefix ./__tt_9409.anat_ns_ob -newgrid 1.000000 ./__tt_9409.anat_ns+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./__tt_9409.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_ts ./vr_base+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_9409.anat_ns_ob+orig -prefix ./__tt_vr_base_ts_rs -inset ./__tt_vr_base_ts+orig'' -rmode Cu
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./__tt_vr_base_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_ts+orig.BRIK is 3.359754 degrees from plumb.
#++ removing skull or area outside brain
#Script is running (command trimmed):
3dAutomask -apply_prefix ./__tt_vr_base_ts_rs_ns ./__tt_vr_base_ts_rs+orig
++ 3dAutomask: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset ./__tt_vr_base_ts_rs+orig
++ Forming automask
+ Fixed clip level = 190.991699
+ Used gradual clip level = 166.982407 .. 202.581894
+ Number voxels above clip level = 1290370
+ Clustering voxels ...
+ Largest cluster has 1277036 voxels
+ Clustering voxels ...
+ Largest cluster has 1275274 voxels
+ Filled 2908 voxels in small holes; now have 1278182 voxels
+ Filled 31021 voxels in large holes; now have 1309203 voxels
+ Clustering voxels ...
+ Largest cluster has 1309187 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 10487293 voxels
+ Mask now has 1309187 voxels
++ 1309187 voxels in the mask [out of 11796480: 11.10%]
++ first 63 x-planes are zero [from R]
++ last 60 x-planes are zero [from L]
++ first 48 y-planes are zero [from A]
++ last 18 y-planes are zero [from P]
++ first 41 z-planes are zero [from I]
++ last 46 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_ts_rs_ns+orig
#++ Applying threshold of 491.000000 on /home/bmiadmin/Tamara/PRR_Analysis/9409/July19_Final_9409.results/__tt_vr_base_ts_rs_ns+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix ./__tt_vr_base_ts_rs_ns_wt -a ./__tt_vr_base_ts_rs_ns+orig -expr 'min(1,(a/491.000000))'
++ 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_9409.anat_ns_ob_al_junk_wtal -weight ./__tt_vr_base_ts_rs_ns_wt+orig -source ./__tt_9409.anat_ns_ob+orig -prefix ./__tt_9409.anat_ns_ob_temp_al_junk -base ./__tt_vr_base_ts_rs_ns+orig -nocmass -1Dmatrix_save ./9409.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_9409.anat_ns_ob+orig.HEAD
++ Base dataset: ./__tt_vr_base_ts_rs_ns+orig.HEAD
++ Loading datasets
++ 2154889 voxels in -source_automask+4
++ Zero-pad: not needed
++ 1309170 voxels [11.1%] in weight mask
++ Number of points for matching = 1309170
++ Local correlation: blok type = 'RHDD(6.54321)'
++ shift param auto-range: -81.9..81.9 -76.7..76.7 -61.3..61.3
+ 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 1309170 points from base image [use_all=0]
+ * Exit alignment setup routine
+ 1234541 total points stored in 2308 'RHDD(6.54321)' bloks
+ - Initial cost = -0.317216
+ - 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 = -0.517211 ; 303 funcs
*********
+ - Final cost = -0.517227 ; 136 funcs
+ Final fine fit Parameters:
x-shift=-0.0546 y-shift= 0.8048 z-shift=-0.3872
z-angle=-0.6566 x-angle= 0.1385 y-angle= 0.1496
x-scale= 1.0013 y-scale= 0.9705 z-scale= 0.9997
y/x-shear= 0.0022 z/x-shear=-0.0062 z/y-shear=-0.0267
+ - Fine net CPU time = 0.0 s
++ Computing output image
++ image warp: parameters = -0.0546 0.8048 -0.3872 -0.6566 0.1385 0.1496 1.0013 0.9705 0.9997 0.0022 -0.0062 -0.0267
++ Wrote -1Dmatrix_save ./9409.anat_al_junk_e2a_only_mat.aff12.1D
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 51.0
++ ###########################################################
++ # 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 ./9409.anat_al_junk_e2a_only_mat.aff12.1D ./__tt_9409.anat_ns_obla2e_mat.1D -I > ./9409.anat_al_junk_mat.aff12.1D
#++ Combining anat to epi and oblique transformations
#Script is running (command trimmed):
3dAllineate -base ./__tt_vr_base_ts_rs_ns+orig -1Dmatrix_apply ./9409.anat_al_junk_mat.aff12.1D -prefix ./9409.anat_al_junk -input ./__tt_9409.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_9409.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_9409.anat_ns+orig.BRIK is 3.359754 degrees from plumb.
++ Source dataset: ./__tt_9409.anat_ns+orig.HEAD
++ Base dataset: ./__tt_vr_base_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 = 1.0012 -0.0115 -0.0026 -0.1389 0.0133 0.9704 0.0023 -0.5475 -0.0039 -0.0283 0.9996 14.6615
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 1.9
++ ###########################################################
#++ Creating final output: skullstripped anat data
copying from dataset /home/bmiadmin/Tamara/PRR_Analysis/9409/July19_Final_9409.results/__tt_9409.anat_ns+orig to /home/bmiadmin/Tamara/PRR_Analysis/9409/July19_Final_9409.results/9409.anat_ns+orig
#Script is running (command trimmed):
3dcopy ./__tt_9409.anat_ns+orig 9409.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 9409.anat+orig -save_skullstrip \
-suffix _al_junk -epi vr_base+orig -epi_base 0 -epi_strip 3dAutomask \
-volreg off -tshift off" \
./9409.anat_al_junk+orig

#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_vr_base*
#Script is running:
\rm -f ./__tt_9409.anat*

# Finished alignment successfully

auto_warp.py -base MNI152_T1_2009c+tlrc -input 9409.anat_ns+orig -skull_strip_input no
#++ auto_warp.py version: 0.04
# Output directory /home/bmiadmin/Tamara/PRR_Analysis/9409/July19_Final_9409.results/awpy/
#Script is running:
mkdir /home/bmiadmin/Tamara/PRR_Analysis/9409/July19_Final_9409.results/awpy/
cd /home/bmiadmin/Tamara/PRR_Analysis/9409/July19_Final_9409.results/awpy/
#Script is running (command trimmed):
3dcopy /home/bmiadmin/Tamara/PRR_Analysis/9409/July19_Final_9409.results/9409.anat_ns+orig ./anat.nii
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
#Script is running (command trimmed):
3dUnifize -GM -input ./anat.nii -prefix ./anat.un.nii
++ 3dUnifize: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./anat.nii,
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:./anat.nii is 3.359754 degrees from plumb.
+ Pre-processing: ADV......UWG
++ Output dataset ./anat.un.nii
++ ===== Elapsed = 15.5 sec
#Script is running (command trimmed):
3dcopy /home/bmiadmin/abin/MNI152_T1_2009c+tlrc ./base.nii
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
#++ Aligning /home/bmiadmin/Tamara/PRR_Analysis/9409/July19_Final_9409.results/awpy/base.nii data to /home/bmiadmin/Tamara/PRR_Analysis/9409/July19_Final_9409.results/awpy/anat.un.nii data
#Script is running (command trimmed):
@auto_tlrc -base ./base.nii -input ./anat.un.nii -suffix .aff -no_ss -no_pre -init_xform CENTER
Copying NIFTI volume to ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+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:./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK is 3.359754 degrees from plumb.

Performing center alignment with @Align_Centers

*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+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:./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK is 3.359754 degrees from plumb.
++ 3dcopy: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ 3drefit: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig
+ deoblique
++ 3drefit processed 1 datasets
++ 3drename: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ THD_rename_dataset_files: rename anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.HEAD -> __ats_tmp__anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.HEAD
++ THD_rename_dataset_files: rename anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.BRIK -> __ats_tmp__anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+orig.BRIK
** THD_rename_dataset_files: old header anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+acpc.HEAD doesn't exist!
** THD_rename_dataset_files: old header anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA_shft+tlrc.HEAD doesn't exist!
++ 3dWarp: 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 ./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+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:./anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+orig.BRIK is 3.359754 degrees from plumb.
++ 3.359754 degrees from plumb.
*+ WARNING: Deoblique datasets with 3dWarp before proceeding with other transformations
Center distance of 0.000000 mm
Padding ...
++ 3dZeropad: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ output dataset: ./__ats_tmp__ref_base.nii_40pad+tlrc.BRIK
Resampling ...
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
Clipping -0.000100 3768.040100 ...
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
++ 3drefit: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___rs_pre.anat.un_AFN_OYmeqfZ3JqF7n9LNC7gDAA+tlrc.HEAD
+ changing dataset view code
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD
+ changing dataset view code
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD
+ changing dataset view code
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
Registration (linear final interpolation) ...
++ 3dWarpDrive: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
RMS[0] = 103.624 74.1942 ITER = 137/137
103.624

Warping used up maximum iterations of 137
Convergence might not have
been reached.
Doubling number of iterations

++ 3drename: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ THD_rename_dataset_files: rename __ats_tmp__reg_warpdriveout+orig.HEAD -> __ats_tmp__reg_warpdriveout_maxed_iters+orig.HEAD
++ THD_rename_dataset_files: rename __ats_tmp__reg_warpdriveout+orig.BRIK.gz -> __ats_tmp__reg_warpdriveout_maxed_iters+orig.BRIK.gz
++ 3dWarpDrive: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: RW Cox
RMS[0] = 103.624 74.1942 ITER = 274/274
103.624

Warping used up maximum iterations
even after doubling number of iterations to 274.
Convergence might not have been reached.

If you find the alignment poor, try
rerunning the script with a transform
type of fewer parameters (-xform) or by using
an even higher number of iterations (-maxite).
You can also choose to continue with the
current result (dset: __ats_tmp__reg_warpdriveout+orig
by using the option: -OK_maxite

Script will stop ...

#**ERROR Failed in affine step
** ERROR - script failed
3dbucket: No match.