Dear Btaylor,
Thank you for your kind response. And I am not using Freesurfer with AFNI. Here are my processing script file details.
echo auto-generated by afni_proc.py, Tue Nov 23 16:41:35 2021
auto-generated by afni_proc.py, Tue Nov 23 16:41:35 2021
echo (version 7.17, July 16, 2021)
(version 7.17, July 16, 2021)
echo execution started: `date`
date
execution started: Tue Nov 23 16:42:05 PKT 2021
afni -ver
Precompiled binary linux_ubuntu_16_64: Jul 28 2021 (Version AFNI_21.2.04 'Nerva')
afni_history -check_date 27 Jun 2019
-- is current: afni_history as new as: 27 Jun 2019
most recent entry is: 27 Jul 2021
if ( 0 ) then
if ( 0 > 0 ) then
set subj = sub_001
endif
set output_dir = sub_001.results
if ( -d sub_001.results ) then
set runs = ( `count -digits 2 1 1` )
count -digits 2 1 1
mkdir -p sub_001.results
mkdir sub_001.results/stimuli
3dcopy /mnt/d/Fizza/84/lmci/sub-01/anat/sub-01_T2.nii sub_001.results/sub-01_T2
++ 3dcopy: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
3dTcat -prefix sub_001.results/pb00.sub_001.r01.tcat /mnt/d/Fizza/84/lmci/sub-01/func/sub-01_rest-LMCI.nii[0..$]
++ 3dTcat: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ elapsed time = 2.9 s
set tr_counts = ( 197 )
cd sub_001.results
touch out.pre_ss_warn.txt
foreach run ( 01 )
3dToutcount -automask -fraction -polort 4 -legendre pb00.sub_001.r01.tcat+orig
++ 3dToutcount: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ 34362 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r01.1D{0} -expr step(a-0.4)
end
cat outcount.r01.1D
set minindex = `3dTstat -argmin -prefix - outcount_rall.1D\'`
3dTstat -argmin -prefix - outcount_rall.1D'
++ 3dTstat: AFNI version=AFNI_21.2.04 (Jul 28 2021) [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 197 -index_to_run_tr 70
set minoutrun = 01
set minouttr = 70
echo min outlier: run 01, TR 70
tee out.min_outlier.txt
min outlier: run 01, TR 70
foreach run ( 01 )
3dTshift -tzero 0 -quintic -prefix pb01.sub_001.r01.tshift pb00.sub_001.r01.tcat+orig
++ 3dTshift: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
*+ WARNING: dataset is already aligned in time!
*+ WARNING: ==>> output dataset is just a copy of input dataset
end
3dbucket -prefix vr_base_min_outlier pb01.sub_001.r01.tshift+orig[70]
++ 3dbucket: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
align_epi_anat.py -anat2epi -anat sub-01_T2+orig -save_skullstrip -suffix _al_junk -epi vr_base_min_outlier+orig -epi_base 0 -epi_strip 3dAutomask -giant_move -volreg off -tshift off
#++ align_epi_anat version: 1.62
#++ 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 ./sub-01_T2+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_sub-01_T2*
#Script is running (command trimmed):
3dcopy ./sub-01_T2+orig ./__tt_sub-01_T2+orig
++ 3dcopy: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
#++ Removing skull from anat data
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_sub-01_T2+orig -prefix ./__tt_sub-01_T2_ns
#Script is running (command trimmed):
3dinfo ./__tt_sub-01_T2_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /mnt/d/Fizza/84/lmci/sub-01/subject_results/group.lmci/subj.sub_001/sub_001.results/__tt_sub-01_T2_ns+orig is not oblique
#Script is running (command trimmed):
3dinfo ./vr_base_min_outlier+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /mnt/d/Fizza/84/lmci/sub-01/subject_results/group.lmci/subj.sub_001/sub_001.results/vr_base_min_outlier+orig is not oblique
#++ 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_21.2.04 (Jul 28 2021) [64-bit]
#++ removing skull or area outside brain
#Script is running (command trimmed):
3dAutomask -apply_prefix ./__tt_vr_base_min_outlier_ts_ns ./__tt_vr_base_min_outlier_ts+orig
++ 3dAutomask: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset ./__tt_vr_base_min_outlier_ts+orig
++ Forming automask
+ Fixed clip level = 173.982605
+ Used gradual clip level = 107.031197 .. 189.536606
+ Number voxels above clip level = 35389
+ Clustering voxels ...
+ Largest cluster has 34987 voxels
+ Clustering voxels ...
+ Largest cluster has 33833 voxels
+ Filled 472 voxels in small holes; now have 34305 voxels
+ Filled 2 voxels in large holes; now have 34307 voxels
+ Clustering voxels ...
+ Largest cluster has 34304 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 162282 voxels
+ Mask now has 34326 voxels
++ 34326 voxels in the mask [out of 196608: 17.46%]
++ first 13 x-planes are zero [from R]
++ last 14 x-planes are zero [from L]
++ first 5 y-planes are zero [from P]
++ last 7 y-planes are zero [from A]
++ first 0 z-planes are zero [from I]
++ last 6 z-planes are zero [from S]
++ applying mask to original data
++ Writing masked data
++ Output dataset ./__tt_vr_base_min_outlier_ts_ns+orig.BRIK
++ 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_ns+orig
#++ Applying threshold of 560.000000 on /mnt/d/Fizza/84/lmci/sub-01/subject_results/group.lmci/subj.sub_001/sub_001.results/__tt_vr_base_min_outlier_ts_ns+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix ./__tt_vr_base_min_outlier_ts_ns_wt -a ./__tt_vr_base_min_outlier_ts_ns+orig -expr 'min(1,(a/560.000000))'
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tt_vr_base_min_outlier_ts_ns_wt+orig.BRIK
#++ Aligning anat data to epi data
#Script is running (command trimmed):
3dAllineate -lpc -wtprefix ./__tt_sub-01_T2_ns_al_junk_wtal -weight ./__tt_vr_base_min_outlier_ts_ns_wt+orig -source ./__tt_sub-01_T2_ns+orig -prefix ./sub-01_T2_al_junk -base ./__tt_vr_base_min_outlier_ts_ns+orig -cmass -1Dmatrix_save ./sub-01_T2_al_junk_mat.aff12.1D -master BASE -mast_dxyz 0.859375 -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -twobest 11 -twopass -VERB -maxrot 45 -maxshf 40 -fineblur 1 -source_automask+2
++ 3dAllineate: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Option '-cmass' enables center-of-mass code = 7 = +xyz
++ Source dataset: ./__tt_sub-01_T2_ns+orig.HEAD
++ Base dataset: ./__tt_vr_base_min_outlier_ts_ns+orig.HEAD
++ Loading datasets into memory
++ 582046 voxels in -source_automask+2
++ Zero-pad: ybot=3 ytop=1
++ Zero-pad: zbot=8 ztop=2
++ 34326 voxels [13.6%] in weight mask
++ Output dataset ./__tt_sub-01_T2_ns_al_junk_wtal+orig.BRIK
++ Number of points for matching = 34326
++ Local correlation: blok type = 'TOHD(17.731)'
++ base center of mass = 31.008 30.749 31.796 (index)
+ source center of mass = 125.670 110.495 22.058 (index)
+ source-target CM = 1.588 0.083 -1.774 (xyz)
+ estimated center of mass shifts = 1.588 0.083 -1.774
++ shift param auto-range: -67.9..71.1 -73.8..74.0 -64.0..60.4
+ Range param#4 [z-angle] = -6.000000 .. 6.000000 center = 0.000000
+ Range param#5 [x-angle] = -6.000000 .. 6.000000 center = 0.000000
+ Range param#6 [y-angle] = -6.000000 .. 6.000000 center = 0.000000
+ Range param#1 [x-shift] = -8.411812 .. 11.588188 center = 1.588188
+ Range param#2 [y-shift] = -9.917183 .. 10.082817 center = 0.082817
+ Range param#3 [z-shift] = -11.774208 .. 8.225792 center = -1.774208
+ Range param#4 [z-angle] = -45.000000 .. 45.000000 center = 0.000000
+ Range param#5 [x-angle] = -45.000000 .. 45.000000 center = 0.000000
+ Range param#6 [y-angle] = -45.000000 .. 45.000000 center = 0.000000
+ Range param#1 [x-shift] = -38.411812 .. 41.588188 center = 1.588188
+ Range param#2 [y-shift] = -39.917183 .. 40.082817 center = 0.082817
+ Range param#3 [z-shift] = -41.774208 .. 38.225792 center = -1.774208
+ 12 free parameters
++ Normalized (unitless) convergence radius = 0.0000088
++ Final parameter search ranges:
+ x-shift = -38.412 .. 41.588
+ y-shift = -39.917 .. 40.083
+ z-shift = -41.774 .. 38.226
+ z-angle = -45.000 .. 45.000
+ x-angle = -45.000 .. 45.000
+ y-angle = -45.000 .. 45.000
+ x-scale = 0.711 .. 1.406
+ y-scale = 0.711 .. 1.406
+ z-scale = 0.711 .. 1.406
+ y/x-shear = -0.111 .. 0.111
+ z/x-shear = -0.111 .. 0.111
+ z/y-shear = -0.111 .. 0.111
++ changing output grid spacing to 0.8594 mm
++ OpenMP thread count = 15
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed =======
+ source mask has 582046 [out of 2883584] voxels
+ base mask has 46092 [out of 252416] voxels
++ ========== sub-brick #0 ========== [total CPU to here=0.0 s]
++ *** Coarse pass begins ***
+ * Enter alignment setup routine
+ - copying base image
+ - copying source image
+ - Smoothing base; radius=4.00
+ - Smoothing source; radius=4.00
+ !source mask fill: ubot=0 usiz=193
+ - copying weight image
+ - using 34326 points from base image [use_all=2]
+ * Exit alignment setup routine
+ - Search for coarse starting parameters
+ 28018 total points stored in 57 'TOHD(18.1766)' bloks (0 duplicates)
+ - number of free params = 6
+ - Test (64+101)*64 params [top5=*o+-.]:#*[#1=-0.0537038] **[#2=-0.0924275] *o+.o.+*[#9=-0.0927428] *-.--++*[#34=-0.102243] **[#35=-0.110514] *+o-*[#162=-0.121928] *-+oo++*[#307=-0.122239] **[#314=-0.12401] **[#316=-0.124288] **[#1025=-0.142832] *o+o*[#1066=-0.1586] *o+o*[#1194=-0.170135] *+.-+.$o-o.-+ + - best 88 costs found:
o= 0 v=-0.170135: -5.08 26.75 4.89 -7.50 30.00 -7.50 [grid]
o= 1 v=-0.169554: -6.95 14.22 -3.93 4.39 33.35 4.11 [rand]
o= 2 v=-0.164478: -6.95 14.22 0.38 -4.39 33.35 -4.11 [rand]
o= 3 v=-0.159376: -2.49 6.31 6.02 -4.32 22.85 -18.95 [rand]
o= 4 v=-0.158674: -6.95 14.22 -3.93 -4.39 33.35 4.11 [rand]
o= 5 v=-0.158600: -5.08 6.75 4.89 -7.50 30.00 -7.50 [grid]
o= 6 v=-0.157360: -6.95 14.22 0.38 -4.39 33.35 4.11 [rand]
o= 7 v=-0.154848: -6.95 14.22 0.38 4.39 33.35 4.11 [rand]
o= 8 v=-0.154526: -6.95 14.22 -3.93 4.39 33.35 -4.11 [rand]
o= 9 v=-0.152506: 8.25 6.75 -8.44 7.50 30.00 -30.00 [grid]
o=10 v=-0.151971: 8.25 26.75 -8.44 -7.50 30.00 -7.50 [grid]
o=11 v=-0.151498: -6.95 14.22 0.38 4.39 33.35 -4.11 [rand]
o=12 v=-0.150625: 8.25 6.75 -8.44 -7.50 30.00 -30.00 [grid]
o=13 v=-0.149131: -5.08 6.75 -8.44 -7.50 30.00 30.00 [grid]
o=14 v=-0.149112: 8.25 26.75 4.89 7.50 30.00 -7.50 [grid]
o=15 v=-0.148997: 13.19 4.64 -5.67 24.53 29.49 -26.10 [rand]
o=16 v=-0.148900: -10.01 4.64 -5.67 -24.53 29.49 26.10 [rand]
o=17 v=-0.148545: -12.62 9.54 3.06 -15.99 13.53 29.93 [rand]
o=18 v=-0.147946: -5.08 6.75 4.89 -30.00 30.00 7.50 [grid]
o=19 v=-0.147941: 8.25 -6.58 4.89 30.00 7.50 -30.00 [grid]
o=20 v=-0.147146: 10.13 14.22 0.38 4.39 33.35 -4.11 [rand]
o=21 v=-0.146407: 8.25 26.75 4.89 7.50 30.00 7.50 [grid]
o=22 v=-0.146336: 5.67 6.31 6.02 4.32 22.85 18.95 [rand]
o=23 v=-0.143939: -5.08 6.75 4.89 -30.00 30.00 -30.00 [grid]
o=24 v=-0.143712: 8.25 26.75 4.89 -7.50 30.00 7.50 [grid]
o=25 v=-0.143051: -5.30 9.16 1.71 -42.18 25.76 19.54 [rand]
o=26 v=-0.142832: 8.25 6.75 4.89 7.50 30.00 7.50 [grid]
o=27 v=-0.142762: -5.08 26.75 4.89 -7.50 30.00 -30.00 [grid]
o=28 v=-0.140643: 10.13 14.22 -3.93 4.39 33.35 -4.11 [rand]
o=29 v=-0.139643: -5.08 6.75 4.89 7.50 30.00 -30.00 [grid]
o=30 v=-0.139241: 8.25 6.75 4.89 7.50 30.00 -7.50 [grid]
o=31 v=-0.138668: 8.25 6.75 4.89 30.00 7.50 -30.00 [grid]
o=32 v=-0.137947: 8.25 6.75 4.89 30.00 30.00 30.00 [grid]
o=33 v=-0.137818: 10.13 14.22 0.38 4.39 33.35 4.11 [rand]
o=34 v=-0.137670: -6.95 14.22 -3.93 -4.39 33.35 -4.11 [rand]
o=35 v=-0.137187: -13.37 11.24 8.68 -35.95 25.02 2.65 [rand]
o=36 v=-0.136904: -5.08 6.75 4.89 -7.50 30.00 -30.00 [grid]
o=37 v=-0.136402: -5.08 6.75 -8.44 7.50 30.00 7.50 [grid]
o=38 v=-0.135600: -5.08 26.75 4.89 7.50 30.00 -30.00 [grid]
o=39 v=-0.135578: 9.48 -13.09 16.15 4.53 -27.86 -39.72 [rand]
o=40 v=-0.135154: 10.13 14.22 0.38 -4.39 33.35 4.11 [rand]
o=41 v=-0.135144: 8.25 26.75 4.89 -7.50 30.00 -30.00 [grid]
o=42 v=-0.134615: -2.49 6.31 6.02 4.32 22.85 -18.95 [rand]
o=43 v=-0.134605: 8.47 9.16 1.71 42.18 25.76 -19.54 [rand]
o=44 v=-0.134233: 8.25 6.75 4.89 30.00 30.00 -7.50 [grid]
o=45 v=-0.134148: 10.13 14.22 0.38 -4.39 33.35 -4.11 [rand]
o=46 v=-0.132644: -5.08 6.75 4.89 -30.00 30.00 -7.50 [grid]
o=47 v=-0.132638: -5.08 26.75 -8.44 7.50 30.00 7.50 [grid]
o=48 v=-0.132472: 7.57 3.49 22.75 -29.81 -4.26 -23.54 [rand]
o=49 v=-0.132472: 8.25 6.75 4.89 -7.50 30.00 7.50 [grid]
o=50 v=-0.131968: -5.08 26.75 -8.44 30.00 30.00 -30.00 [grid]
o=51 v=-0.131961: 10.13 14.22 -3.93 -4.39 33.35 -4.11 [rand]
o=52 v=-0.131290: -13.37 11.24 8.68 -35.95 25.02 -2.65 [rand]
o=53 v=-0.129676: 11.84 -8.76 13.86 7.51 -21.00 -38.82 [rand]
o=54 v=-0.128911: 10.13 14.22 -3.93 -4.39 33.35 4.11 [rand]
o=55 v=-0.127863: -5.08 26.75 -8.44 7.50 30.00 -7.50 [grid]
o=56 v=-0.127654: -10.01 4.64 2.12 -24.53 29.49 -26.10 [rand]
o=57 v=-0.127340: -5.30 9.16 1.71 -42.18 25.76 -19.54 [rand]
o=58 v=-0.126897: -8.23 24.84 -13.16 3.10 34.36 2.55 [rand]
o=59 v=-0.126301: -16.91 -5.77 12.82 -16.04 3.33 12.13 [rand]
o=60 v=-0.126214: 8.25 6.75 -8.44 -7.50 30.00 -7.50 [grid]
o=61 v=-0.126189: 5.67 6.31 -9.57 -4.32 22.85 -18.95 [rand]
o=62 v=-0.126031: -10.01 4.64 2.12 -24.53 29.49 26.10 [rand]
o=63 v=-0.125915: 15.79 9.54 3.06 15.99 13.53 -29.93 [rand]
o=64 v=-0.125838: 8.25 -6.58 24.89 7.50 -30.00 -30.00 [grid]
o=65 v=-0.125797: -5.08 26.75 4.89 7.50 30.00 30.00 [grid]
o=66 v=-0.125647: 8.25 -6.58 -8.44 7.50 30.00 -30.00 [grid]
o=67 v=-0.125081: 11.41 24.84 -13.16 -3.10 34.36 -2.55 [rand]
o=68 v=-0.124951: 8.25 26.75 4.89 7.50 30.00 30.00 [grid]
o=69 v=-0.124288: -5.08 -6.58 24.89 -7.50 -7.50 -7.50 [grid]
o=70 v=-0.124268: 9.48 -13.09 16.15 -4.53 -27.86 -39.72 [rand]
o=71 v=-0.124028: 8.25 26.75 4.89 30.00 7.50 -30.00 [grid]
o=72 v=-0.124010: -5.08 6.75 24.89 -7.50 -7.50 -7.50 [grid]
o=73 v=-0.123835: -5.08 26.75 4.89 7.50 30.00 -7.50 [grid]
o=74 v=-0.123567: 8.25 26.75 4.89 7.50 30.00 -30.00 [grid]
o=75 v=-0.123223: 13.19 4.64 2.12 24.53 29.49 -26.10 [rand]
o=76 v=-0.122997: 8.47 9.16 1.71 42.18 25.76 19.54 [rand]
o=77 v=-0.122959: 5.67 6.31 6.02 -4.32 22.85 18.95 [rand]
o=78 v=-0.122328: 8.25 6.75 4.89 -7.50 7.50 -30.00 [grid]
o=79 v=-0.122239: 8.25 -6.58 24.89 7.50 -7.50 -7.50 [grid]
o=80 v=-0.121928: -5.08 26.75 4.89 7.50 7.50 -7.50 [grid]
o=81 v=-0.121909: 8.25 -6.58 24.89 7.50 -7.50 7.50 [grid]
o=82 v=-0.121378: 5.67 -6.14 -9.57 4.32 22.85 -18.95 [rand]
o=83 v=-0.120824: -10.01 -4.48 -5.67 -24.53 29.49 26.10 [rand]
o=84 v=-0.120608: -5.08 6.75 24.89 -7.50 -7.50 7.50 [grid]
o=85 v=-0.120205: -16.91 -5.77 12.82 -16.04 -3.33 12.13 [rand]
o=86 v=-0.119451: -5.08 6.75 4.89 -7.50 30.00 7.50 [grid]
o=87 v=-0.119382: -5.08 6.75 -8.44 7.50 30.00 30.00 [grid]
+ - A little optimization:*[#10569=-0.190933] *[#10573=-0.195518] *[#10576=-0.203965] *[#10577=-0.215471] *[#10578=-0.220469] *[#10583=-0.221385] *[#10585=-0.222533] *[#10588=-0.224152] *[#10593=-0.224873] *[#10594=-0.226073] *[#10595=-0.226992] *[#10597=-0.227072] *[#10598=-0.227184] *[#10599=-0.227189] *[#10601=-0.227316] *[#10604=-0.227434] *[#10608=-0.227456] *[#10609=-0.227485] *[#10610=-0.227502] ..*[#10680=-0.227913] *[#10683=-0.233312] *[#10685=-0.234255] *[#10688=-0.235027] *[#10694=-0.237418] *[#10695=-0.23772] *[#10698=-0.238006] *[#10701=-0.238244] *[#10704=-0.238246] *[#10705=-0.238308] *[#10708=-0.238649] *[#10710=-0.238774] *[#10711=-0.239078] *[#10712=-0.239357] *[#10713=-0.23953] *[#10714=-0.239605] *[#10715=-0.239677] *[#10716=-0.239724] *[#10717=-0.23979] *[#10718=-0.239926] *[#10721=-0.240129] *[#10722=-0.240244] *[#10724=-0.240332] *[#10731=-0.240373] ....*[#10963=-0.240594] *[#10964=-0.240729] *[#10967=-0.240736] *[#10970=-0.240857] .....*[#11267=-0.241301] *[#11268=-0.242355] *[#11269=-0.242892] *[#11276=-0.243506] *[#11277=-0.243647] *[#11279=-0.243667] *[#11284=-0.243719] *[#11286=-0.243742] .............................................................................
+ - costs of the above after a little optimization:
o= 0 v=-0.227502: -2.32 21.69 3.42 -6.11 29.93 -6.55 [grid] [f=51]
o= 1 v=-0.193999: -0.51 13.94 -1.59 5.33 32.98 6.19 [rand] [f=52]
o= 2 v=-0.240373: 0.12 19.99 1.61 -2.99 32.75 -3.09 [rand] [f=67]
o= 3 v=-0.201214: -3.01 11.62 6.98 -3.81 23.11 -18.38 [rand] [f=52]
o= 4 v=-0.226510: 2.51 19.64 -1.58 -4.14 38.35 1.88 [rand] [f=54]
o= 5 v=-0.204641: -6.35 11.15 5.74 -8.34 23.60 -6.67 [grid] [f=69]
o= 6 v=-0.240857: 0.18 20.89 1.06 -3.21 34.00 -2.38 [rand] [f=63]
o= 7 v=-0.192918: -0.49 14.67 -2.89 5.39 38.20 6.50 [rand] [f=57]
o= 8 v=-0.212693: 0.64 16.03 -2.76 -6.06 37.64 7.09 [rand] [f=62]
o= 9 v=-0.175430: 7.72 8.39 -7.45 12.09 30.80 -30.02 [grid] [f=43]
o=10 v=-0.229175: 2.18 19.31 -3.63 1.21 43.31 -5.19 [grid] [f=83]
*o=11 v=-0.243742: 1.34 20.67 1.04 0.91 34.75 -4.19 [rand] [f=67]
o=12 v=-0.180627: 5.76 9.65 -7.99 -5.48 36.65 -28.00 [grid] [f=62]
o=13 v=-0.200162: -4.52 12.17 -7.00 -7.62 40.36 23.72 [grid] [f=78]
o=14 v=-0.234218: 2.31 22.48 0.78 6.68 33.26 -6.36 [grid] [f=78]
o=15 v=-0.169478: 9.39 5.23 -2.24 25.58 29.59 -25.37 [rand] [f=66]
o=16 v=-0.187309: -9.73 8.84 -4.55 -18.20 29.31 31.25 [rand] [f=58]
o=17 v=-0.176154: -11.14 3.88 3.24 -17.03 14.72 27.77 [rand] [f=52]
o=18 v=-0.179783: -7.97 11.46 3.49 -25.43 31.19 6.64 [grid] [f=52]
o=19 v=-0.172018: 9.54 -1.35 5.06 30.51 9.23 -29.79 [grid] [f=44]
o=20 v=-0.232127: 2.13 20.35 -0.88 0.89 37.52 -4.84 [rand] [f=83]
o=21 v=-0.232549: 1.57 22.36 2.28 -0.07 30.69 -4.54 [grid] [f=79]
o=22 v=-0.156362: 6.58 6.90 6.78 5.08 23.75 19.13 [rand] [f=49]
o=23 v=-0.160857: -5.81 7.67 6.11 -24.33 24.35 -30.55 [grid] [f=43]
o=24 v=-0.224041: 2.91 21.91 -2.88 -3.98 40.67 1.15 [grid] [f=83]
o=25 v=-0.164066: -6.45 11.39 4.59 -44.93 25.69 16.35 [rand] [f=60]
o=26 v=-0.173874: 8.36 6.10 1.80 7.58 27.34 3.28 [grid] [f=58]
o=27 v=-0.152285: -5.13 22.79 4.88 -7.67 30.20 -30.12 [grid] [f=33]
o=28 v=-0.231381: 1.17 18.86 0.67 5.03 36.06 -8.64 [rand] [f=64]
o=29 v=-0.194334: -2.56 16.79 6.27 0.31 22.60 -15.54 [grid] [f=83]
o=30 v=-0.181250: 8.64 5.82 1.93 9.91 26.13 -2.00 [grid] [f=59]
o=31 v=-0.176641: 10.53 -0.50 5.41 30.32 8.62 -29.02 [grid] [f=50]
o=32 v=-0.161069: 5.47 8.01 5.09 30.39 29.50 30.60 [grid] [f=66]
o=33 v=-0.233369: 1.03 22.94 1.59 -2.34 32.41 -2.37 [rand] [f=77]
o=34 v=-0.198255: -6.47 13.51 4.69 -7.88 25.61 -7.21 [rand] [f=53]
o=35 v=-0.168694: -7.11 11.14 8.36 -35.23 24.95 3.63 [rand] [f=63]
o=36 v=-0.194964: -2.29 13.24 5.13 -2.55 25.99 -23.44 [grid] [f=83]
o=37 v=-0.174058: -5.47 10.43 -2.68 2.88 34.05 11.53 [grid] [f=83]
o=38 v=-0.211217: 2.84 20.80 4.09 8.37 26.50 -16.26 [grid] [f=67]
o=39 v=-0.158703: 9.35 -13.31 16.87 3.79 -23.74 -40.95 [rand] [f=53]
o=40 v=-0.234964: 0.08 19.11 0.69 -4.43 35.38 -1.37 [rand] [f=67]
o=41 v=-0.172423: 4.19 17.05 5.03 -7.30 27.40 -29.85 [grid] [f=82]
o=42 v=-0.211261: 1.53 19.55 5.28 3.21 24.20 -18.31 [rand] [f=53]
o=43 v=-0.149434: 5.03 10.24 2.38 43.47 24.50 -21.27 [rand] [f=48]
o=44 v=-0.157623: 8.25 7.30 4.48 28.48 26.18 -10.54 [grid] [f=64]
o=45 v=-0.229365: 0.38 18.57 0.46 -5.29 34.90 -0.05 [rand] [f=73]
o=46 v=-0.158141: -5.68 10.96 5.94 -30.03 29.29 -7.71 [grid] [f=37]
o=47 v=-0.172223: -2.90 21.49 -7.10 6.76 40.52 5.33 [grid] [f=56]
o=48 v=-0.140589: 7.55 3.80 20.74 -25.40 -4.60 -23.90 [rand] [f=71]
o=49 v=-0.150954: 9.58 8.70 2.88 -4.98 34.05 4.28 [grid] [f=42]
o=50 v=-0.142877: -4.06 26.24 -8.25 29.56 33.94 -30.06 [grid] [f=48]
o=51 v=-0.241170: -0.23 20.71 0.74 0.64 34.80 -5.21 [rand] [f=61]
o=52 v=-0.165117: -4.33 11.95 10.05 -35.64 25.53 1.05 [rand] [f=73]
o=53 v=-0.168976: 12.15 -9.18 15.42 8.89 -14.18 -34.56 [rand] [f=61]
o=54 v=-0.227081: 2.30 19.55 -0.76 -3.07 37.32 -0.53 [rand] [f=69]
o=55 v=-0.174819: -2.47 27.37 -3.23 8.84 31.79 -8.05 [grid] [f=80]
o=56 v=-0.163562: -6.57 9.07 5.34 -26.17 26.99 -28.67 [rand] [f=77]
o=57 v=-0.148553: -4.56 11.11 7.61 -41.68 21.90 -20.68 [rand] [f=51]
o=58 v=-0.236456: 0.03 21.39 -0.39 -2.24 37.08 -4.66 [rand] [f=73]
o=59 v=-0.172149: -12.15 -2.69 11.42 -19.64 2.97 12.62 [rand] [f=51]
o=60 v=-0.233110: 0.90 21.33 -1.03 6.50 38.77 -9.80 [grid] [f=65]
o=61 v=-0.160161: 7.44 14.50 -11.40 -0.60 29.15 -23.47 [rand] [f=46]
o=62 v=-0.192260: -10.41 9.00 1.64 -25.19 25.62 17.92 [rand] [f=49]
o=63 v=-0.179107: 12.24 0.66 1.86 17.97 12.50 -27.22 [rand] [f=56]
o=64 v=-0.163071: 8.77 -11.35 24.35 7.10 -28.90 -30.49 [grid] [f=43]
o=65 v=-0.162104: -1.36 20.86 -0.61 -3.14 31.91 38.34 [grid] [f=58]
o=66 v=-0.152611: 9.25 -3.98 -4.64 7.44 30.08 -29.02 [grid] [f=53]
o=67 v=-0.229587: 1.73 24.71 -4.93 -0.33 43.92 -4.06 [rand] [f=79]
o=68 v=-0.146625: 4.26 27.72 2.26 6.61 29.69 27.99 [grid] [f=52]
o=69 v=-0.195415: -1.19 0.30 17.38 -6.01 -0.97 -11.13 [grid] [f=61]
o=70 v=-0.165471: 9.16 -14.10 17.81 2.84 -24.46 -37.34 [rand] [f=78]
o=71 v=-0.154140: 9.88 20.04 7.27 27.61 8.61 -24.71 [grid] [f=66]
o=72 v=-0.198329: -0.28 7.03 17.60 -7.82 -0.27 -6.93 [grid] [f=53]
o=73 v=-0.232412: 1.75 22.20 2.03 4.53 31.19 -6.90 [grid] [f=72]
o=74 v=-0.195836: 2.19 20.03 3.72 8.15 23.83 -30.70 [grid] [f=54]
o=75 v=-0.174654: 9.22 6.74 -0.17 24.14 26.68 -24.42 [rand] [f=48]
o=76 v=-0.170241: 6.27 6.95 5.14 35.96 34.27 31.18 [rand] [f=60]
o=77 v=-0.154568: 5.76 7.18 6.85 3.11 22.37 18.43 [rand] [f=60]
o=78 v=-0.174632: 5.02 15.67 7.13 -8.32 8.66 -30.29 [grid] [f=54]
o=79 v=-0.189141: 5.97 -0.36 20.83 11.66 -7.08 -3.40 [grid] [f=57]
o=80 v=-0.158802: -5.15 25.64 5.47 8.29 12.37 -7.60 [grid] [f=56]
o=81 v=-0.171913: 6.07 -4.23 22.13 13.36 -9.07 1.58 [grid] [f=78]
o=82 v=-0.169715: 8.11 2.23 -2.70 12.72 23.63 -24.02 [rand] [f=83]
o=83 v=-0.162784: -9.04 -0.51 -2.08 -18.38 26.06 22.92 [rand] [f=58]
o=84 v=-0.177089: -4.34 2.11 18.91 -13.57 -5.99 2.24 [grid] [f=52]
o=85 v=-0.170597: -11.06 -4.90 11.70 -16.49 1.55 9.17 [rand] [f=83]
o=86 v=-0.191685: -9.09 7.38 0.14 -9.47 27.63 6.92 [grid] [f=54]
o=87 v=-0.188804: -6.16 9.51 -8.36 2.45 43.88 24.92 [grid] [f=52]
+ - saving #11 for use with twobest
+ - skip #51 for twobest: too close to set #11
+ - skip # 6 for twobest: too close to set #11
+ - skip # 2 for twobest: too close to set #11
+ - skip #58 for twobest: too close to set #11
+ - skip #40 for twobest: too close to set # 6
+ - saving #14 for use with twobest
+ - skip #33 for twobest: too close to set #11
+ - saving #60 for use with twobest
+ - skip #21 for twobest: too close to set #11
+ - skip #73 for twobest: too close to set #11
+ - skip #20 for twobest: too close to set #11
+ - skip #28 for twobest: too close to set #11
+ - saving #67 for use with twobest
+ - skip #45 for twobest: too close to set # 6
+ - saving #10 for use with twobest
+ - skip # 0 for twobest: too close to set # 6
+ - skip #54 for twobest: too close to set #11
+ - skip # 4 for twobest: too close to set # 6
+ - skip #24 for twobest: too close to set #54
+ - saving # 8 for use with twobest
+ - saving #42 for use with twobest
+ - saving #38 for use with twobest
+ - saving # 5 for use with twobest
+ - saving # 3 for use with twobest
+ - saving #13 for use with twobest
+ - saving #72 for use with twobest
+ - skip #34 for twobest: too close to set # 5
+ - saving #74 for use with twobest
+ - saving #69 for use with twobest
+ - saving #36 for use with twobest
+ - saving #29 for use with twobest
+ - saving # 1 for use with twobest
+ - saving # 7 for use with twobest
+ - saving #62 for use with twobest
+ - saving #86 for use with twobest
+ - saving #79 for use with twobest
+ - saving #87 for use with twobest
+ - saving #16 for use with twobest
+ - saving #30 for use with twobest
+ - saving #12 for use with twobest
+ - saving #18 for use with twobest
+ - saving #63 for use with twobest
+ - saving #84 for use with twobest
+ - saving #31 for use with twobest
+ - Coarse startup search net CPU time = 0.0 s
++ Start refinement #1 on 12 coarse parameter sets
+ * Enter alignment setup routine
+ - Smoothing base; radius=3.11
+ - Smoothing source; radius=3.11
+ !source mask fill: ubot=0 usiz=193
+ - retaining old weight image
+ - using 34326 points from base image [use_all=2]
+ * Exit alignment setup routine
+ 28132 total points stored in 59 'TOHD(18.0018)' bloks (0 duplicates)
+ - param set #1 has cost=-0.217041 [o=11 t=0]
+ -- Parameters = 1.4919 19.7102 1.5336 1.0152 34.4039 -4.3551 0.9988 0.9965 0.9956 0.0001 -0.0016 0.0123
+ - param set #2 has cost=-0.198780 [o=14 t=1]
+ -- Parameters = 2.3000 22.3660 0.9797 6.5886 33.1346 -6.3542 0.9994 0.9992 0.9990 -0.0003 0.0120 -0.0004
+ - param set #3 has cost=-0.202410 [o=60 t=2]
+ -- Parameters = 0.9233 21.3786 -0.7322 6.2310 38.8866 -9.6387 0.9932 0.9976 0.9987 0.0001 0.0128 0.0002
+ - param set #4 has cost=-0.206742 [o=67 t=3]
+ -- Parameters = 1.7887 23.4337 -4.0335 0.1005 44.7511 -3.7651 0.9977 0.9814 0.9942 -0.0002 -0.0031 0.0109
+ - param set #5 has cost=-0.229821 [o=10 t=4]
+ -- Parameters = 2.1825 20.2306 -3.1678 2.3910 44.5816 -5.9605 0.9640 0.9468 0.9991 0.0106 0.0169 -0.0041
+ - param set #6 has cost=-0.215201 [o=8 t=5]
+ -- Parameters = 1.0247 18.6527 -2.2708 -6.6375 42.3562 3.0951 0.9938 0.9653 1.0058 -0.0052 -0.0027 0.0079
+ - param set #7 has cost=-0.188788 [o=42 t=6]
+ -- Parameters = 1.3376 18.7496 5.3136 2.8654 25.2754 -13.4990 1.0016 0.9872 0.9953 -0.0020 0.0001 0.0012
+ - param set #8 has cost=-0.198281 [o=38 t=7]
+ -- Parameters = 2.2043 19.6331 3.5703 5.6795 28.7715 -7.0430 0.9980 0.9997 1.0040 0.0010 0.0086 0.0086
+ - param set #9 has cost=-0.189359 [o=5 t=8]
+ -- Parameters = -5.6147 10.9415 8.6923 -9.6692 23.1722 -7.4127 0.9800 0.9937 0.9657 -0.0002 0.0059 -0.0004
+ - param set #10 has cost=-0.190914 [o=3 t=9]
+ -- Parameters = -2.0009 12.3410 8.9828 -4.1965 23.8652 -15.9540 0.9893 0.9829 0.9587 0.0141 -0.0080 0.0074
+ - param set #11 has cost=-0.164249 [o=13 t=10]
+ -- Parameters = -3.5063 12.6355 -6.5377 -7.9132 40.5667 24.3664 1.0023 1.0045 1.0346 0.0005 0.0002 0.0001
+ - param set #12 has cost=-0.103204 [o=-1 t=-1]
+ -- Parameters = 11.2303 2.4634 -5.8075 7.0177 -9.2111 -1.0937 0.9846 1.0162 0.9402 0.0010 0.0008 0.0050
+ - sorting parameter sets by cost
+ - scanning for distances from #1
+ --- dist(#2,#1) = 0.113
+ --- dist(#3,#1) = 0.101
+ --- dist(#4,#1) = 0.0902
+ --- dist(#5,#1) = 0.0731
+ --- dist(#6,#1) = 0.127
+ --- dist(#7,#1) = 0.176
+ --- dist(#8,#1) = 0.23
+ --- dist(#9,#1) = 0.238
+ --- dist(#10,#1) = 0.215
+ --- dist(#11,#1) = 0.337
+ --- dist(#12,#1) = 0.598
++ Start refinement #2 on 12 coarse parameter sets
+ * Enter alignment setup routine
+ - Smoothing base; radius=2.42
+ - Smoothing source; radius=2.42
+ !source mask fill: ubot=0 usiz=193
+ - retaining old weight image
+ - using 34326 points from base image [use_all=2]
+ * Exit alignment setup routine
+ 28444 total points stored in 61 'TOHD(17.8953)' bloks (0 duplicates)
+ - param set #1 has cost=-0.199049 [o=10 t=4]
+ -- Parameters = 2.0922 20.5262 -3.1896 2.5934 44.5438 -6.1031 0.9619 0.9356 1.0026 0.0100 0.0163 0.0064
+ - param set #2 has cost=-0.186526 [o=11 t=0]
+ -- Parameters = 1.6490 19.9451 1.6394 0.9973 34.4982 -4.0115 1.0032 0.9848 0.9851 -0.0037 -0.0008 0.0199
+ - param set #3 has cost=-0.185564 [o=8 t=5]
+ -- Parameters = 0.8516 18.9223 -2.4750 -6.7573 42.3991 3.2239 0.9954 0.9587 1.0068 -0.0057 -0.0024 0.0169
+ - param set #4 has cost=-0.197546 [o=67 t=3]
+ -- Parameters = 1.7634 21.0452 -3.1571 0.8941 44.9477 -3.6397 0.9706 0.9345 1.0054 -0.0138 -0.0144 0.0053
+ - param set #5 has cost=-0.174128 [o=60 t=2]
+ -- Parameters = 1.2949 20.1338 -0.5084 5.9951 39.6742 -10.0607 0.9703 0.9877 0.9940 0.0020 0.0146 0.0034
+ - param set #6 has cost=-0.188162 [o=14 t=1]
+ -- Parameters = 2.6558 20.0340 1.0166 5.0313 32.4825 -5.9341 0.9696 0.9359 1.0058 -0.0033 0.0118 0.0007
+ - param set #7 has cost=-0.177312 [o=38 t=7]
+ -- Parameters = 2.1234 19.2648 2.6305 5.1372 29.0916 -5.8648 0.9974 0.9787 1.0117 0.0033 0.0096 0.0185
+ - param set #8 has cost=-0.176159 [o=3 t=9]
+ -- Parameters = -1.6310 13.3068 10.1799 -4.5839 24.6532 -16.3536 0.9886 0.9663 0.9321 0.0188 -0.0091 0.0068
+ - param set #9 has cost=-0.168258 [o=5 t=8]
+ -- Parameters = -5.5647 10.8746 9.6254 -9.4702 22.9935 -7.4966 0.9850 0.9882 0.9496 0.0024 0.0183 -0.0032
+ - param set #10 has cost=-0.163694 [o=42 t=6]
+ -- Parameters = 1.5203 18.7084 4.6272 2.8119 25.7092 -13.4385 1.0037 0.9938 0.9944 -0.0008 -0.0006 0.0068
+ - param set #11 has cost=-0.137330 [o=13 t=10]
+ -- Parameters = -3.4243 12.6560 -6.4525 -7.9766 40.6094 24.4128 1.0030 1.0030 1.0321 0.0005 0.0091 -0.0002
+ - param set #12 has cost=-0.096858 [o=-1 t=-1]
+ -- Parameters = 13.1995 2.2431 -3.8765 6.8148 -6.3382 -2.7890 0.9398 1.0262 0.9188 0.0015 -0.0027 0.0045
+ - sorting parameter sets by cost
+ - scanning for distances from #1
+ --- dist(#2,#1) = 0.138
+ --- dist(#3,#1) = 0.134
+ --- dist(#4,#1) = 0.112
+ --- dist(#5,#1) = 0.104
+ --- dist(#6,#1) = 0.172
+ --- dist(#7,#1) = 0.221
+ --- dist(#8,#1) = 0.0748
+ --- dist(#9,#1) = 0.239
+ --- dist(#10,#1) = 0.209
+ --- dist(#11,#1) = 0.339
+ --- dist(#12,#1) = 0.565
++ Start refinement #3 on 12 coarse parameter sets
+ * Enter alignment setup routine
+ - Smoothing base; radius=1.88
+ - Smoothing source; radius=1.88
+ !source mask fill: ubot=0 usiz=193
+ - retaining old weight image
+ - using 34326 points from base image [use_all=2]
+ * Exit alignment setup routine
+ 28393 total points stored in 61 'TOHD(17.8305)' bloks (0 duplicates)
+ - param set #1 has cost=-0.180284 [o=10 t=4]
+ -- Parameters = 1.8997 21.5120 -3.5567 2.2601 44.1911 -6.2064 0.9678 0.8901 1.0094 0.0124 0.0207 0.0062
+ - param set #2 has cost=-0.181916 [o=67 t=3]
+ -- Parameters = 2.4966 21.9252 -3.5682 -0.6011 44.9356 -3.2038 0.9519 0.9092 1.0139 -0.0161 -0.0159 0.0037
+ - param set #3 has cost=-0.170162 [o=14 t=1]
+ -- Parameters = 2.7623 19.9597 1.0896 5.0918 31.8441 -5.5823 0.9700 0.9308 1.0097 -0.0034 0.0115 0.0060
+ - param set #4 has cost=-0.165740 [o=11 t=0]
+ -- Parameters = 1.4298 20.0315 1.7301 0.9736 34.0985 -3.8231 0.9997 0.9801 0.9880 -0.0043 0.0009 0.0195
+ - param set #5 has cost=-0.169773 [o=8 t=5]
+ -- Parameters = 1.1882 19.7998 -3.5577 -6.3946 40.4395 3.1909 0.9852 0.9142 1.0357 0.0021 0.0010 0.0169
+ - param set #6 has cost=-0.159882 [o=38 t=7]
+ -- Parameters = 2.0328 19.3722 2.3327 4.9372 29.0505 -5.2802 0.9901 0.9781 1.0195 0.0019 0.0110 0.0221
+ - param set #7 has cost=-0.160942 [o=3 t=9]
+ -- Parameters = -1.7903 13.2371 10.2740 -4.4282 25.6398 -15.1370 0.9949 0.9682 0.9210 0.0165 -0.0007 0.0078
+ - param set #8 has cost=-0.154917 [o=60 t=2]
+ -- Parameters = 1.3895 18.1229 0.1127 5.6802 39.3602 -10.0449 0.9697 0.9821 0.9976 0.0022 0.0149 0.0038
+ - param set #9 has cost=-0.150715 [o=5 t=8]
+ -- Parameters = -5.4833 11.0274 11.6833 -9.6978 22.9013 -7.1567 0.9706 0.9827 0.9124 -0.0063 0.0237 -0.0121
+ - param set #10 has cost=-0.146688 [o=42 t=6]
+ -- Parameters = 1.9717 18.9198 4.5569 2.2357 26.0944 -12.9801 0.9997 0.9781 0.9829 -0.0016 -0.0215 -0.0029
+ - param set #11 has cost=-0.121670 [o=13 t=10]
+ -- Parameters = -3.1873 12.2717 -6.6321 -7.8744 40.9137 27.0924 1.0034 1.0140 1.0313 0.0016 0.0090 -0.0007
+ - param set #12 has cost=-0.087996 [o=-1 t=-1]
+ -- Parameters = 13.2609 2.4258 -3.7211 6.8468 -6.2142 -6.1301 0.9373 1.0228 0.9156 -0.0007 -0.0039 0.0058
+ - sorting parameter sets by cost
+ - scanning for distances from #1
+ --- dist(#2,#1) = 0.165
+ --- dist(#3,#1) = 0.145
+ --- dist(#4,#1) = 0.082
+ --- dist(#5,#1) = 0.12
+ --- dist(#6,#1) = 0.214
+ --- dist(#7,#1) = 0.177
+ --- dist(#8,#1) = 0.138
+ --- dist(#9,#1) = 0.245
+ --- dist(#10,#1) = 0.209
+ --- dist(#11,#1) = 0.337
+ --- dist(#12,#1) = 0.568
+ - Total coarse refinement net CPU time = 0.0 s; 3914 funcs
++ *** Fine pass begins ***
+ * Enter alignment setup routine
+ - Smoothing base; radius=1.00
+ - Smoothing source; radius=1.00
+ !source mask fill: ubot=0 usiz=193
+ - retaining old weight image
+ * Exit alignment setup routine
++ Picking best parameter set out of 13 cases
+ 28212 total points stored in 61 'TOHD(17.7591)' bloks (0 duplicates)
+ - cost(#1)=-0.170158 * [o=67 t=3]
+ -- Parameters = 2.4966 21.9252 -3.5682 -0.6011 44.9356 -3.2038 0.9519 0.9092 1.0139 -0.0161 -0.0159 0.0037
+ - cost(#2)=-0.168228 [o=10 t=4]
+ -- Parameters = 1.8997 21.5120 -3.5567 2.2601 44.1911 -6.2064 0.9678 0.8901 1.0094 0.0124 0.0207 0.0062
+ - cost(#3)=-0.161015 [o=14 t=1]
+ -- Parameters = 2.7623 19.9597 1.0896 5.0918 31.8441 -5.5823 0.9700 0.9308 1.0097 -0.0034 0.0115 0.0060
+ - cost(#4)=-0.158801 [o=8 t=5]
+ -- Parameters = 1.1882 19.7998 -3.5577 -6.3946 40.4395 3.1909 0.9852 0.9142 1.0357 0.0021 0.0010 0.0169
+ - cost(#5)=-0.154445 [o=11 t=0]
+ -- Parameters = 1.4298 20.0315 1.7301 0.9736 34.0985 -3.8231 0.9997 0.9801 0.9880 -0.0043 0.0009 0.0195
+ - cost(#6)=-0.150981 [o=3 t=9]
+ -- Parameters = -1.7903 13.2371 10.2740 -4.4282 25.6398 -15.1370 0.9949 0.9682 0.9210 0.0165 -0.0007 0.0078
+ - cost(#7)=-0.150202 [o=38 t=7]
+ -- Parameters = 2.0328 19.3722 2.3327 4.9372 29.0505 -5.2802 0.9901 0.9781 1.0195 0.0019 0.0110 0.0221
+ - cost(#8)=-0.142180 [o=60 t=2]
+ -- Parameters = 1.3895 18.1229 0.1127 5.6802 39.3602 -10.0449 0.9697 0.9821 0.9976 0.0022 0.0149 0.0038
+ - cost(#9)=-0.145518 [o=5 t=8]
+ -- Parameters = -5.4833 11.0274 11.6833 -9.6978 22.9013 -7.1567 0.9706 0.9827 0.9124 -0.0063 0.0237 -0.0121
+ - cost(#10)=-0.135891 [o=42 t=6]
+ -- Parameters = 1.9717 18.9198 4.5569 2.2357 26.0944 -12.9801 0.9997 0.9781 0.9829 -0.0016 -0.0215 -0.0029
+ - cost(#11)=-0.107056 [o=13 t=10]
+ -- Parameters = -3.1873 12.2717 -6.6321 -7.8744 40.9137 27.0924 1.0034 1.0140 1.0313 0.0016 0.0090 -0.0007
+ - cost(#12)=-0.084030 [o=-1 t=-1]
+ -- Parameters = 13.2609 2.4258 -3.7211 6.8468 -6.2142 -6.1301 0.9373 1.0228 0.9156 -0.0007 -0.0039 0.0058
+ - cost(#13)=0.044940 [o=-2 t=-2]
+ -- Parameters = 1.5882 0.0828 -1.7742 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
+ -num_rtb 99 ==> refine all 13 cases
+ - cost(#1)=-0.177218 * [o=67 t=3]
+ -- Parameters = 2.4116 22.8823 -3.5832 -1.3864 44.8807 -2.7220 0.9457 0.8791 1.0122 -0.0197 0.0042 0.0188
+ - cost(#2)=-0.171144 [o=10 t=4]
+ -- Parameters = 1.9778 21.7598 -3.5440 2.3891 43.7427 -6.9359 0.9633 0.8821 1.0121 0.0107 0.0222 -0.0048
+ - cost(#3)=-0.162493 [o=14 t=1]
+ -- Parameters = 3.0191 20.3502 1.3731 4.8033 31.7619 -5.1135 0.9709 0.9187 1.0061 -0.0018 0.0097 0.0040
+ - cost(#4)=-0.165667 [o=8 t=5]
+ -- Parameters = 1.1570 20.4447 -3.3595 -6.3814 41.8253 3.0629 0.9829 0.9045 1.0323 -0.0027 0.0014 0.0245
+ - cost(#5)=-0.162689 [o=11 t=0]
+ -- Parameters = 1.3966 20.2290 2.0521 1.4744 32.8896 -3.6381 0.9947 0.9284 0.9925 -0.0009 0.0016 0.0233
+ - cost(#6)=-0.151391 [o=3 t=9]
+ -- Parameters = -1.8124 13.2925 10.2904 -4.3615 25.4656 -15.2556 0.9953 0.9645 0.9218 0.0158 0.0051 0.0067
+ - cost(#7)=-0.150408 [o=38 t=7]
+ -- Parameters = 2.0851 19.3588 2.3651 4.9841 28.9645 -5.3125 0.9914 0.9778 1.0204 0.0018 0.0111 0.0138
+ - cost(#8)=-0.143699 [o=60 t=2]
+ -- Parameters = 1.6085 18.2304 0.4936 5.5937 39.0348 -9.6024 0.9702 0.9829 1.0013 0.0023 0.0069 0.0049
+ - cost(#9)=-0.151261 [o=5 t=8]
+ -- Parameters = -5.2992 10.8733 12.4038 -9.3184 22.2238 -7.5544 0.9718 0.9301 0.9163 -0.0003 0.0269 -0.0200
+ - cost(#10)=-0.137220 [o=42 t=6]
+ -- Parameters = 2.3170 19.0447 4.3686 1.8780 26.2745 -12.1215 0.9963 0.9741 0.9829 -0.0031 -0.0290 -0.0072
+ - cost(#11)=-0.108296 [o=13 t=10]
+ -- Parameters = -3.1703 12.3614 -6.2052 -7.9168 40.9409 27.0739 1.0014 1.0139 1.0493 0.0023 0.0080 0.0000
+ - cost(#12)=-0.084508 [o=-1 t=-1]
+ -- Parameters = 13.1495 2.3533 -3.5932 6.7965 -6.1784 -6.0334 0.9414 1.0238 0.9133 -0.0010 -0.0096 0.0060
+ - cost(#13)=-0.077424 [o=-2 t=-2]
+ -- Parameters = 12.7325 -0.3817 -3.5222 3.8353 -6.8251 2.6358 0.9722 1.0317 0.9505 -0.0010 -0.0015 0.0165
+ - case #1 [o=67 t=3] is now the best
+ - Initial cost = -0.177218
+ - Initial fine Parameters = 2.4116 22.8823 -3.5832 -1.3864 44.8807 -2.7220 0.9457 0.8791 1.0122 -0.0197 0.0042 0.0188
+ - Finalish cost = -0.180345 ; 976 funcs
+ - ini Finalish Parameters = 2.4367 23.4304 -3.8663 -1.8201 44.7827 -2.4261 0.9464 0.8669 1.0172 -0.0189 -0.0015 0.0354
+ - Final cost = -0.180526 ; 1465 funcs
+ Final fine fit Parameters:
x-shift= 2.4649 y-shift= 23.4237 z-shift= -3.9296 ... enorm= 23.8786 mm
z-angle= -1.9623 x-angle= 44.7904 y-angle= -2.2242 ... total= 44.9214 deg
x-scale= 0.9468 y-scale= 0.8669 z-scale= 1.0194 ... vol3D= 0.8367 = base bigger than source
y/x-shear= -0.0204 z/x-shear= -0.0065 z/y-shear= 0.0387
*+ WARNING: Parameter x-angle = 44.79038 is close to edge of its search range -45.00000 .. 45.00000
+ - Fine net CPU time = 0.0 s
++ Computing output image
++ image warp: parameters = 2.4649 23.4237 -3.9296 -1.9623 44.7904 -2.2242 0.9468 0.8669 1.0194 -0.0204 -0.0065 0.0387
++ Unloading unneeded data
++ Output dataset ./sub-01_T2_al_junk+orig.BRIK
++ Wrote -1Dmatrix_save ./sub-01_T2_al_junk_mat.aff12.1D
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 10.5
++ ###########################################################
++ # PLEASE check results VISUALLY for alignment quality #
++ ###########################################################
#++ Creating final output: skullstripped anat data
copying from dataset /mnt/d/Fizza/84/lmci/sub-01/subject_results/group.lmci/subj.sub_001/sub_001.results/__tt_sub-01_T2_ns+orig to /mnt/d/Fizza/84/lmci/sub-01/subject_results/group.lmci/subj.sub_001/sub_001.results/sub-01_T2_ns+orig
#Script is running (command trimmed):
3dcopy ./__tt_sub-01_T2_ns+orig sub-01_T2_ns
++ 3dcopy: AFNI version=AFNI_21.2.04 (Jul 28 2021) [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 sub-01_T2+orig -save_skullstrip \
-suffix _al_junk -epi vr_base_min_outlier+orig -epi_base 0 -epi_strip \
3dAutomask -giant_move -volreg off -tshift off" \
./sub-01_T2_al_junk+orig

#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_vr_base_min_outlier*
#Script is running:
\rm -f ./__tt_sub-01_T2*

# Finished alignment successfully

@auto_tlrc -base MNI_avg152T1+tlrc -input sub-01_T2_ns+orig -no_ss -OK_maxite
Center distance of 39.825324 mm
Padding ...
++ 3dZeropad: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ output dataset: ./__ats_tmp__ref_MNI_avg152T1_15pad+tlrc.BRIK
Resampling ...
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__resamp_step+orig.BRIK
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__resamp+tlrc.BRIK
Clipping -0.000100 646.000100 ...
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__ats_tmp___rs_sub-01_T2_ns+tlrc.BRIK
++ 3drefit: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___rs_sub-01_T2_ns+tlrc.HEAD
+ changing dataset view code
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_21.2.04 (Jul 28 2021) [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_21.2.04 (Jul 28 2021) [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 (cubic final interpolation) ...
++ 3dWarpDrive: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: RW Cox
++ Initial scale factor set to 0.30/137.00=4.6e+02
RMS[0] = 0.360247 0.190097 ITER = 13/50
0.360247

Warping has converged.

mv: 'sub-01_T2_ns.Xaff12.1D' and 'sub-01_T2_ns.Xaff12.1D' are the same file
++ 3dcopy: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ 3dWarp: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: RW Cox
Applying brain mask
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__reg_braintlrcstep+orig.BRIK
++ 3dWarp: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: RW Cox
++ 3drename: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ THD_rename_dataset_files: rename __ats_tmp___pad15_sub-01_T2_ns+orig.HEAD -> __ats_tmp___pad15_sub-01_T2_ns.skl+orig.HEAD
++ THD_rename_dataset_files: rename __ats_tmp___pad15_sub-01_T2_ns+orig.BRIK -> __ats_tmp___pad15_sub-01_T2_ns.skl+orig.BRIK
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp___pad15_sub-01_T2_ns+orig.BRIK
Unpadding ...
++ 3dZeropad: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ output dataset: ./__ats_tmp___upad15_sub-01_T2_ns+orig.BRIK
++ 3drefit: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad15_sub-01_T2_ns+orig
*+ WARNING: Changing the space of an ORIG view dataset may cause confusion!
*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space).
*+ WARNING: Consider changing the view of the dataset to TLRC view also
++ 3drefit processed 1 datasets
Changing view of transformed anatomy
++ 3drefit: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad15_sub-01_T2_ns+orig.HEAD
+ changing dataset view code
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
Setting parent with 3drefit -wset sub-01_T2_ns+orig __ats_tmp___upad15_sub-01_T2_ns+tlrc
++ 3drefit: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad15_sub-01_T2_ns+tlrc
+ setting Warp parent
++ 3drefit processed 1 datasets
++ 3drename: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Warning: ignoring +tlrc on new_prefix.
++ THD_rename_dataset_files: rename __ats_tmp___upad15_sub-01_T2_ns+tlrc.HEAD -> sub-01_T2_ns+tlrc.HEAD
++ THD_rename_dataset_files: rename __ats_tmp___upad15_sub-01_T2_ns+tlrc.BRIK -> sub-01_T2_ns+tlrc.BRIK
Cleanup ...
cat_matvec sub-01_T2_ns+tlrc::WARP_DATA -I
if ( ! -f sub-01_T2_ns+tlrc.HEAD ) then
foreach run ( 01 )
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.sub_001.r01.tshift+orig
++ 3dvolreg: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: RW Cox
++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK
++ Reading input dataset ./pb01.sub_001.r01.tshift+orig.BRIK
++ Edging: x=3 y=3 z=2
++ Creating mask for -maxdisp
+ Automask has 37507 voxels
+ 5583 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 197 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..
++ CPU time for realignment=0 s [=0 s/sub-brick]
++ Min : roll=-1.056 pitch=-0.705 yaw=-1.262 dS=-1.159 dL=-1.032 dP=-0.591
++ Mean: roll=-0.113 pitch=-0.007 yaw=-0.314 dS=+0.051 dL=-0.305 dP=-0.063
++ Max : roll=+0.446 pitch=+0.898 yaw=+0.358 dS=+0.852 dL=+0.374 dP=+0.409
++ Max displacements (mm) for each sub-brick:
3.20(0.00) 3.05(0.34) 3.13(0.46) 3.14(0.21) 3.19(0.28) 3.08(0.21) 3.15(0.10) 3.10(0.11) 3.05(0.11) 3.04(0.03) 2.95(0.15) 3.07(0.19) 2.95(0.15) 2.28(1.02) 2.24(0.30) 1.95(0.45) 1.54(0.44) 1.70(0.37) 1.81(0.41) 1.77(1.24) 2.18(1.09) 1.95(0.53) 1.95(0.09) 1.90(0.16) 1.97(0.23) 1.87(0.32) 2.20(0.41) 1.91(0.44) 1.28(0.65) 1.65(0.47) 1.74(0.22) 1.60(0.44) 1.62(0.25) 1.65(0.23) 1.65(0.11) 1.96(0.42) 2.04(0.42) 1.99(0.68) 2.56(1.40) 2.08(0.84) 1.96(0.47) 2.19(1.09) 1.78(0.49) 1.86(0.71) 2.20(0.35) 2.37(0.58) 2.44(0.63) 2.27(0.31) 2.00(0.47) 2.19(0.37) 2.35(0.42) 2.07(0.28) 2.02(0.19) 1.99(0.14) 1.91(0.52) 1.77(0.22) 1.54(0.36) 1.33(0.48) 1.31(0.34) 1.16(0.29) 1.00(0.22) 0.87(0.44) 0.69(0.57) 0.42(0.54) 1.01(0.88) 0.65(0.51) 0.28(0.48) 0.55(0.40) 0.50(0.12) 0.29(0.26) 0.00(0.29) 0.59(0.59) 0.62(0.09) 0.30(0.38) 0.56(0.27) 0.68(0.14) 0.66(0.15) 0.81(0.28) 1.10(0.58) 0.88(0.59) 0.94(1.27) 0.96(0.35) 0.96(0.16) 0.98(0.22) 1.04(0.66) 0.62(0.60) 0.75(0.20) 0.98(0.29) 0.73(0.68) 1.07(0.61) 0.99(0.52) 0.90(0.37) 0.69(0.24) 0.78(0.69) 0.37(0.61) 0.64(0.60) 0.90(0.35) 0.92(0.29) 0.77(0.30) 0.64(0.31) 0.85(0.40) 0.74(0.27) 0.48(0.28) 0.77(0.39) 0.88(0.29) 0.83(0.30) 0.89(0.49) 1.00(0.45) 0.84(0.37) 0.98(0.18) 1.06(0.47) 1.19(0.43) 1.14(0.11) 1.24(0.26) 1.19(0.21) 1.20(0.21) 1.08(0.41) 1.46(0.49) 1.50(0.20) 1.23(0.48) 1.22(0.13) 1.51(0.43) 1.32(0.25) 1.25(0.16) 1.35(0.21) 1.16(0.39) 1.19(0.33) 1.21(0.15) 1.18(0.11) 1.21(0.14) 1.21(0.66) 1.46(0.37) 1.34(0.26) 1.35(0.15) 1.30(0.19) 1.55(0.31) 1.72(0.46) 1.24(1.21) 1.24(0.67) 1.36(0.13) 1.37(0.22) 1.19(0.26) 1.17(0.16) 1.07(0.61) 1.08(0.51) 1.20(1.27) 1.30(0.52) 1.31(0.09) 1.21(0.71) 0.83(1.22) 0.91(1.27) 1.01(0.54) 1.15(0.26) 0.96(0.40) 0.61(0.77) 0.91(0.63) 0.58(0.55) 0.51(0.25) 0.67(0.23) 0.69(0.29) 0.58(0.22) 0.59(0.06) 0.64(0.27) 0.67(0.50) 0.80(0.69) 0.78(0.09) 0.73(0.19) 0.58(0.34) 0.58(0.09) 0.59(0.08) 0.74(0.17) 0.63(0.25) 0.58(0.24) 0.61(0.11) 0.66(0.10) 0.61(0.14) 0.63(0.04) 0.57(0.18) 0.63(0.16) 0.72(0.14) 0.56(0.34) 0.64(0.39) 0.63(0.04) 0.68(0.17) 0.56(0.34) 0.48(0.33) 0.65(0.40) 0.55(0.21) 0.57(0.25) 0.93(0.41) 0.79(0.38) 0.95(0.19) 0.79(0.41) 0.95(0.23) 0.92(0.15) 1.11(0.23) 1.19(0.13)
++ Max displacement in automask = 3.20 (mm) at sub-brick 0
++ Max delta displ in automask = 1.40 (mm) at sub-brick 38
++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK
3dcalc -overwrite -a pb01.sub_001.r01.tshift+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: input 'a' is not used in the expression
++ Output dataset ./rm.epi.all1+orig.BRIK
cat_matvec -ONELINE sub-01_T2_ns+tlrc::WARP_DATA -I sub-01_T2_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D
3dAllineate -base sub-01_T2_ns+tlrc -input pb01.sub_001.r01.tshift+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r01
++ 3dAllineate: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./pb01.sub_001.r01.tshift+orig.HEAD
++ Base dataset: ./sub-01_T2_ns+tlrc.HEAD
++ Loading datasets into memory
++ NOTE: base and source coordinate systems have different handedness
+ Orientations: base=Right handed (LPI); source=Left handed (RPI)
+ - It is nothing to worry about: 3dAllineate aligns based on coordinates.
+ - But it is always important to check the alignment visually to be sure.
*+ WARNING: center of mass shifts (-cmass) are turned off, but would be large
*+ WARNING: - at least one is more than 20% of search range
+ -cmass x y z shifts = -1.905 -27.558 -5.700
+ shift search range is +/- = 57.780 69.336 57.780
+ 3.3% 39.7% 9.9%
++ master dataset for output = base
++ changing output grid spacing to 3.0000 mm
++ OpenMP thread count = 15
++ ========== Applying transformation to 197 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..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196
++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 9.7
++ ###########################################################
+
++ ***********************************************************
*+ WARNING: -cmass was turned off, but might have been needed :(
+ Please check your results - PLEASE PLEASE PLEASE
++ ***********************************************************
3dAllineate -base sub-01_T2_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r01
++ 3dAllineate: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ NOTE: base and source coordinate systems have different handedness
+ Orientations: base=Right handed (LPI); source=Left handed (RPI)
+ - It is nothing to worry about: 3dAllineate aligns based on coordinates.
+ - But it is always important to check the alignment visually to be sure.
*+ WARNING: center of mass shifts (-cmass) are turned off, but would be TERRIBLY large!
*+ WARNING: - at least one is more than 50% of search range
+ -cmass x y z shifts = -0.583 -39.194 -4.784
+ shift search range is +/- = 57.780 69.336 57.780
+ 1.0% 56.5% 8.3%
++ Output dataset ./rm.epi.1.r01+tlrc.BRIK
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 9.1
+
++ ***********************************************************
*+ WARNING: -cmass was turned off, but might have been needed :(
+ Please check your results - PLEASE PLEASE PLEASE
++ ***********************************************************
3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc
++ 3dTstat: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.epi.min.r01+tlrc.BRIK
end
cat dfile.r01.1D
1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -collapse_cols euclidean_norm -write motion_sub_001_enorm.1D
3dcopy rm.epi.min.r01+tlrc mask_epi_extents
++ 3dcopy: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
foreach run ( 01 )
3dcalc -a rm.epi.nomask.r01+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.sub_001.r01.volreg
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.sub_001.r01.volreg+tlrc.BRIK
end
cat_matvec -ONELINE sub-01_T2_ns+tlrc::WARP_DATA -I sub-01_T2_al_junk_mat.aff12.1D -I
3dAllineate -base sub-01_T2_ns+tlrc -input vr_base_min_outlier+orig -1Dmatrix_apply mat.basewarp.aff12.1D -mast_dxyz 3 -prefix final_epi_vr_base_min_outlier
++ 3dAllineate: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./vr_base_min_outlier+orig.HEAD
++ Base dataset: ./sub-01_T2_ns+tlrc.HEAD
++ Loading datasets into memory
++ NOTE: base and source coordinate systems have different handedness
+ Orientations: base=Right handed (LPI); source=Left handed (RPI)
+ - It is nothing to worry about: 3dAllineate aligns based on coordinates.
+ - But it is always important to check the alignment visually to be sure.
*+ WARNING: center of mass shifts (-cmass) are turned off, but would be large
*+ WARNING: - at least one is more than 20% of search range
+ -cmass x y z shifts = -2.221 -27.773 -5.578
+ shift search range is +/- = 57.780 69.336 57.780
+ 3.8% 40.1% 9.7%
++ master dataset for output = base
++ changing output grid spacing to 3.0000 mm
++ OpenMP thread count = 15
++ ========== Applying transformation to 1 sub-bricks ==========
++ Output dataset ./final_epi_vr_base_min_outlier+tlrc.BRIK
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 2.6
++ ###########################################################
+
++ ***********************************************************
*+ WARNING: -cmass was turned off, but might have been needed :(
+ Please check your results - PLEASE PLEASE PLEASE
++ ***********************************************************
3dcopy sub-01_T2_ns+tlrc anat_final.sub_001
++ 3dcopy: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
3dAllineate -base final_epi_vr_base_min_outlier+tlrc -allcostX -input anat_final.sub_001+tlrc
tee out.allcostX.txt
++ 3dAllineate: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./anat_final.sub_001+tlrc.HEAD
++ Base dataset: ./final_epi_vr_base_min_outlier+tlrc.HEAD
++ Loading datasets into memory
++ Local correlation: blok type = 'TOHD(15.531)'
*+ WARNING: center of mass shifts (-cmass) are turned off, but would be large
*+ WARNING: - at least one is more than 20% of search range
+ -cmass x y z shifts = 0.644 -25.373 -9.088
+ shift search range is +/- = 68.373 78.003 75.114
+ 0.9% 32.5% 12.1%
*+ WARNING: No output dataset will be calculated
++ OpenMP thread count = 15
+ initial 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
++ allcost output: init #0
ls = 0.440408
sp = 0.393019
mi = 2.56612
crM = 0.254798
nmi = 0.897856
je = 2.56612
hel = -0.0497571
crA = 0.505806
crU = 0.473532
lss = 0.559592
lpc = 0.100955
lpa = 0.899045
lpc+ = 0.434514
lpa+ = 1.2326
++ Output dataset ./volumized+tlrc.BRIK
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 3.0
++ ###########################################################
+
++ ***********************************************************
*+ WARNING: -cmass was turned off, but might have been needed :(
+ Please check your results - PLEASE PLEASE PLEASE
++ ***********************************************************
3dAllineate -source sub-01_T2+orig -master anat_final.sub_001+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped
++ 3dAllineate: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ -1Dmatrix_apply: converting input 3x4 array to 1 row of 12 numbers
++ Source dataset: ./sub-01_T2+orig.HEAD
++ Base dataset: (not given)
++ Loading datasets into memory
+ -cmass x y z shifts = 0.000 0.000 0.000
+ shift search range is +/- = 70.344 70.344 55.212
++ OpenMP thread count = 15
++ ========== Applying transformation to 1 sub-bricks ==========
++ wsinc5 interpolation setup:
+ taper function = Min sidelobe 3 term
+ taper cut point = 0.000
+ window radius = 5 voxels
+ window shape = Cubical
+ The above can be altered via the AFNI_WSINC5_* environment variables.
+ (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.)
+ wsinc5 CUBE(5) mask has 1000 points
++ Output dataset ./anat_w_skull_warped+tlrc.BRIK
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 2.7
++ ###########################################################
foreach run ( 01 )
3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.sub_001.r01.blur pb02.sub_001.r01.volreg+tlrc
++ 3dmerge: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ default -1dindex = 0
++ default -1tindex = 1
Program 3dmerge
3dmerge: edit and combine 3D datasets, by RW Cox
++ editing input dataset in memory (102.1 MB) ...................................................................................................................................................................................................
-- Wrote edited dataset: ./pb03.sub_001.r01.blur+tlrc.BRIK
end
foreach run ( 01 )
3dAutomask -prefix rm.mask_r01 pb03.sub_001.r01.blur+tlrc
++ 3dAutomask: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset pb03.sub_001.r01.blur+tlrc
++ Forming automask
+ Fixed clip level = 171.307098
+ Used gradual clip level = 95.401291 .. 186.063248
+ Number voxels above clip level = 57686
+ Clustering voxels ...
+ Largest cluster has 57597 voxels
+ Clustering voxels ...
+ Largest cluster has 57103 voxels
+ Filled 224 voxels in small holes; now have 57327 voxels
+ Filled 3 voxels in large holes; now have 57330 voxels
+ Clustering voxels ...
+ Largest cluster has 57326 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 214250 voxels
+ Mask now has 57383 voxels
++ 57383 voxels in the mask [out of 271633: 21.13%]
++ first 8 x-planes are zero [from L]
++ last 7 x-planes are zero [from R]
++ first 5 y-planes are zero [from P]
++ last 20 y-planes are zero [from A]
++ first 0 z-planes are zero [from I]
++ last 2 z-planes are zero [from S]
++ Output dataset ./rm.mask_r01+tlrc.BRIK
++ CPU time = 0.000000 sec
end
3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub_001
++ processing 1 input dataset(s), NN=2...
++ padding all datasets by 0 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 57383 survived, 214250 were zero
++ writing result full_mask.sub_001...
++ Output dataset ./full_mask.sub_001+tlrc.BRIK
3dresample -master full_mask.sub_001+tlrc -input sub-01_T2_ns+tlrc -prefix rm.resam.anat
3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub_001
++ no -frac option: defaulting to -union
++ processing 1 input dataset(s), NN=2...
++ padding all datasets by 5 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 72271 survived, 199362 were zero
++ filled 0 holes (0 voxels)
++ writing result mask_anat.sub_001...
++ Output dataset ./mask_anat.sub_001+tlrc.BRIK
3dmask_tool -input full_mask.sub_001+tlrc mask_anat.sub_001+tlrc -inter -prefix mask_epi_anat.sub_001
++ processing 2 input dataset(s), NN=2...
++ padding all datasets by 0 (for dilations)
++ frac 1 over 2 volumes gives min count 2
++ voxel limits: 44802 clipped, 42426 survived, 184405 were zero
++ writing result mask_epi_anat.sub_001...
++ Output dataset ./mask_epi_anat.sub_001+tlrc.BRIK
3dABoverlap -no_automask full_mask.sub_001+tlrc mask_anat.sub_001+tlrc
tee out.mask_ae_overlap.txt
++ 3dABoverlap: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
#A=./full_mask.sub_001+tlrc.BRIK B=./mask_anat.sub_001+tlrc.BRIK
#A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A)
57383 72271 87228 42426 14957 29845 26.0652 41.2960 1.0355 1.7663 0.5855
3ddot -dodice full_mask.sub_001+tlrc mask_anat.sub_001+tlrc
tee out.mask_ae_dice.txt
0.65445
3dresample -master full_mask.sub_001+tlrc -prefix ./rm.resam.group -input /home/fizza/abin/MNI_avg152T1+tlrc
3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group
++ no -frac option: defaulting to -union
++ processing 1 input dataset(s), NN=2...
++ padding all datasets by 5 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 73409 survived, 198224 were zero
++ filled 0 holes (0 voxels)
++ writing result mask_group...
++ Output dataset ./mask_group+tlrc.BRIK
3ddot -dodice mask_anat.sub_001+tlrc mask_group+tlrc
tee out.mask_at_dice.txt
0.954352
foreach run ( 01 )
3dTstat -prefix rm.mean_r01 pb03.sub_001.r01.blur+tlrc
++ 3dTstat: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.mean_r01+tlrc.BRIK
3dcalc -a pb03.sub_001.r01.blur+tlrc -b rm.mean_r01+tlrc -c mask_epi_extents+tlrc -expr c * min(200, a/b*100)*step(a)*step(b) -prefix pb04.sub_001.r01.scale
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb04.sub_001.r01.scale+tlrc.BRIK