echo auto-generated by afni_proc.py, Thu Feb 2 10:52:53 2023 auto-generated by afni_proc.py, Thu Feb 2 10:52:53 2023 echo (version 7.50, December 16, 2022) (version 7.50, December 16, 2022) echo execution started: `date` date execution started: Thu 02 Feb 2023 10:52:54 AM IST afni -ver Precompiled binary linux_ubuntu_16_64: Jan 18 2023 (Version AFNI_23.0.01 'Commodus') afni_history -check_date 14 Nov 2022 -- is current: afni_history as new as: 14 Nov 2022 most recent entry is: 17 Jan 2023 if ( 0 ) then which tedana /home/taliw/.local/bin/tedana if ( 0 ) then if ( 0 > 0 ) then set subj = SM327_all4runs endif set output_dir = SM327_all4runs.results if ( -d SM327_all4runs.results ) then set runs = ( `count -digits 2 1 1` ) count -digits 2 1 1 set echo_list = ( `count -digits 2 1 12` ) count -digits 2 1 12 set echo_times = ( 12.0 31.7 51.4 ) set fave_echo = 02 mkdir -p SM327_all4runs.results mkdir SM327_all4runs.results/stimuli cp ms327_faces_allruns.txt SM327_all4runs.results/stimuli 3dcopy anatSS.T1W.nii SM327_all4runs.results/anatSS.T1W ++ 3dcopy: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] 3dcopy /home/taliw/abin/MNI152_2009_template_SSW.nii.gz SM327_all4runs.results/MNI152_2009_template_SSW.nii.gz ++ 3dcopy: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] 3dcopy anatQQ.T1W.nii SM327_all4runs.results/anatQQ.T1W ++ 3dcopy: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] 3dcopy anatQQ.T1W.aff12.1D SM327_all4runs.results/anatQQ.T1W.aff12.1D ++ 3dcopy: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] 3dcopy anatQQ.T1W_WARP.nii SM327_all4runs.results/anatQQ.T1W_WARP.nii ++ 3dcopy: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] 3dTcat -prefix SM327_all4runs.results/pb00.SM327_all4runs.r01.e01.tcat epi_run1_face_echo_001+orig[0..$] ++ 3dTcat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ elapsed time = 1.0 s 3dTcat -prefix SM327_all4runs.results/pb00.SM327_all4runs.r01.e02.tcat epi_run1_face_echo_002+orig[0..$] ++ 3dTcat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ elapsed time = 0.8 s 3dTcat -prefix SM327_all4runs.results/pb00.SM327_all4runs.r01.e03.tcat epi_run1_face_echo_003+orig[0..$] ++ 3dTcat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ elapsed time = 0.8 s 3dTcat -prefix SM327_all4runs.results/pb00.SM327_all4runs.r01.e04.tcat epi_run2_face_echo_001+orig[0..$] ++ 3dTcat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ elapsed time = 0.7 s 3dTcat -prefix SM327_all4runs.results/pb00.SM327_all4runs.r01.e05.tcat epi_run2_face_echo_002+orig[0..$] ++ 3dTcat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ elapsed time = 0.8 s 3dTcat -prefix SM327_all4runs.results/pb00.SM327_all4runs.r01.e06.tcat epi_run2_face_echo_003+orig[0..$] ++ 3dTcat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ elapsed time = 1.0 s 3dTcat -prefix SM327_all4runs.results/pb00.SM327_all4runs.r01.e07.tcat epi_run3_face_echo_001+orig[0..$] ++ 3dTcat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ elapsed time = 1.1 s 3dTcat -prefix SM327_all4runs.results/pb00.SM327_all4runs.r01.e08.tcat epi_run3_face_echo_002+orig[0..$] ++ 3dTcat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ elapsed time = 1.4 s 3dTcat -prefix SM327_all4runs.results/pb00.SM327_all4runs.r01.e09.tcat epi_run3_face_echo_003+orig[0..$] ++ 3dTcat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ elapsed time = 1.3 s 3dTcat -prefix SM327_all4runs.results/pb00.SM327_all4runs.r01.e10.tcat epi_run4_face_echo_001+orig[0..$] ++ 3dTcat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ elapsed time = 0.9 s 3dTcat -prefix SM327_all4runs.results/pb00.SM327_all4runs.r01.e11.tcat epi_run4_face_echo_002+orig[0..$] ++ 3dTcat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ elapsed time = 0.7 s 3dTcat -prefix SM327_all4runs.results/pb00.SM327_all4runs.r01.e12.tcat epi_run4_face_echo_003+orig[0..$] ++ 3dTcat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ elapsed time = 1.0 s set tr_counts = ( 466 ) cd SM327_all4runs.results @radial_correlate -nfirst 0 -polort 4 -do_clean yes -rdir radcor.pb00.tcat pb00.SM327_all4runs.r01.e02.tcat+orig.HEAD ++ 3dTcat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ elapsed time = 1.3 s ++ 3dAutomask: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Emperor Zhark *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./epi.r01+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:./epi.r01+orig.BRIK is 7.042221 degrees from plumb. *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./radcor.20.r01.automask+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:./radcor.20.r01.automask+orig.BRIK is 7.042221 degrees from plumb. -- detrend -polort 4, new eset = det.r01 ++ 3dTproject: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Cox the Algebraic (Linear) *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./epi.r01+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:./epi.r01+orig.BRIK is 7.042221 degrees from plumb. ++ Setting up regressors ++ 1 Blocks * 5 polynomials -- 5 polort regressors ++ 466 retained time points MINUS 5 regressors ==> 461 D.O.F. left ++ no -mask option ==> processing all 464640 voxels in dataset *+ WARNING: 3dTproject input data :: 6072 vectors are constant -- running correlation on dataset pb00.SM327_all4runs.r01.e02.tcat+orig.HEAD ... ++ merge blur: rad 20, FWHM 40 ++ 3dmerge: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./det.r01+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:./det.r01+orig.BRIK is 7.042221 degrees from plumb. ++ default -1dindex = 0 ++ default -1tindex = 1 ++ Oblique dataset:./det.r01+orig.BRIK is 7.042221 degrees from plumb. Program 3dmerge 3dmerge: edit and combine 3D datasets, by RW Cox ++ editing input dataset in memory (826.0 MB) .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. -- Wrote edited dataset: ./sphere.mean.20.r01+orig.BRIK ++ 3dTcorrelate: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./sphere.mean.20.r01+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:./sphere.mean.20.r01+orig.BRIK is 7.042221 degrees from plumb. ++ Oblique dataset:./det.r01+orig.BRIK is 7.042221 degrees from plumb. ++ Wrote dataset: ./radcor.20.r01.corr+orig.BRIK ++ 3dbucket: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ---- done ++ have do_clean, cleaning up... tee out.vlines.pb00.tcat.txt find_variance_lines.tcsh -polort 4 -nerode 2 -rdir vlines.pb00.tcat pb00.SM327_all4runs.r01.e02.tcat+orig.HEAD ++ have nslices : 60 ++ copying pb00.SM327_all4runs.r01.e02.tcat+orig.HEAD[0..$] to ts.0.orig.r01.nii.gz ++ 3dTcat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ elapsed time = 23.0 s ++ creating automask from first dset ++ 3dAutomask: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Emperor Zhark *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/ts.0.orig.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/ts.0.orig.r01.nii.gz is 7.042221 degrees from plumb. ++ Loading dataset ts.0.orig.r01.nii.gz ++ Forming automask + Fixed clip level = 2016.242432 + Used gradual clip level = 1533.045898 .. 2265.296875 + Number voxels above clip level = 83664 + Clustering voxels ... + Largest cluster has 82284 voxels + Clustering voxels ... + Largest cluster has 78672 voxels + Filled 980 voxels in small holes; now have 79652 voxels + Filled 5 voxels in large holes; now have 79657 voxels + Clustering voxels ... + Largest cluster has 79644 voxels + Clustering non-brain voxels ... + Clustering voxels ... + Largest cluster has 384853 voxels + Mask now has 79787 voxels ++ 79787 voxels in the mask [out of 464640: 17.17%] ++ first 18 x-planes are zero [from R] ++ last 16 x-planes are zero [from L] ++ first 13 y-planes are zero [from A] ++ last 10 y-planes are zero [from P] ++ first 0 z-planes are zero [from I] ++ last 3 z-planes are zero [from S] ++ Output dataset ./mask.nii.gz ++ CPU time = 0.000000 sec -- will apply mask mask.nii.gz ++ eroding mask.nii.gz by 2 voxels ++ no -frac option: defaulting to -union ++ processing 1 input dataset(s), NN=2... ++ padding all datasets by 0 (for dilations) *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/tmp.mask.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/tmp.mask.nii.gz is 7.042221 degrees from plumb. ++ frac 0 over 1 volumes gives min count 0 ++ voxel limits: 0 clipped, 53744 survived, 410896 were zero ++ writing result mask.nii.gz... ++ Output dataset ./mask.nii.gz ++ requiring 5 voxels in mask columns ++ 3dLocalstat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Emperor Zhark *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/mask.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/mask.nii.gz is 7.042221 degrees from plumb. ++ Number of voxels in mask = 53744 ++ Oblique dataset:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/mask.nii.gz is 7.042221 degrees from plumb. ++ Neighborhood comprises 121 voxels ++ Start sub-brick [0] ++ Output dataset ./tmp.mask.col.count.nii.gz ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./mask.nii.gz -- detrend -polort 4, new eset = ts.1.det.r01.nii.gz ++ 3dTproject: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Cox the Algebraic (Linear) *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/ts.0.orig.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/ts.0.orig.r01.nii.gz is 7.042221 degrees from plumb. ++ Setting up regressors ++ 1 Blocks * 5 polynomials -- 5 polort regressors ++ 466 retained time points MINUS 5 regressors ==> 461 D.O.F. left ++ no -mask option ==> processing all 464640 voxels in dataset *+ WARNING: 3dTproject input data :: 6072 vectors are constant ++ 3dTstat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/ts.1.det.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/ts.1.det.r01.nii.gz is 7.042221 degrees from plumb. ++ Output dataset ./tmp.stdev.nii.gz ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./var.0.orig.r01.nii.gz *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/mask.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/mask.nii.gz is 7.042221 degrees from plumb. ++ Oblique dataset:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.0.orig.r01.nii.gz is 7.042221 degrees from plumb. ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./var.1.scale.r01.nii.gz ++ 3dLocalstat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Emperor Zhark *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/mask.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/mask.nii.gz is 7.042221 degrees from plumb. ++ Number of voxels in mask = 53573 ++ Oblique dataset:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 7.042221 degrees from plumb. ++ Neighborhood comprises 121 voxels ++ Start sub-brick [0] ++ Output dataset ./proj.r01.nii.gz ++ Neighborhood definition (NN=3) accepted *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/proj.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/proj.r01.nii.gz is 7.042221 degrees from plumb. ++ User input stat threshold: -1 ++ User input stat threshold: 0.95 ++ Data volume: [0] 'MEAN' ++ Threshold volume: [0] 'MEAN' ++ How many sides to this stat? 0 ++ Looks like clustering is *not* being performed on a stat value; won't worry about sidedness, then. ++ Opt code: 2sided,-1,0.95,NN3 *+ WARNING: No mask being used? That *could* be OK, but thought I'd let you know... ++ Threshold volume [0] does *not* appear to be a stat! ++ Sorting clusters by size. # # Cluster report #[ Dataset prefix = proj.r01.nii.gz ] #[ Threshold vol = [0] 'MEAN' ] #[ Supplement dat vol = [0] 'MEAN' ] #[ Option summary = 2sided,-1,0.95,NN3 ] #[ Threshold value(s) = left-tail thr=-1.000000; right-tail thr=0.950000 ] #[ Aux. stat. info. = not a stat! ] #[ Nvoxel threshold = 0; Volume threshold = 0.000 ] #[ Single voxel volume = 15.625 (microliters) ] #[ Neighbor type, NN = 3 ] #[ Voxel datum type = float ] #[ Voxel dimensions = 2.500 mm X 2.500 mm X 2.500 mm ] #[ Coordinates Order = RAI ] #[ Mean and SEM based on signed voxel intensities ] # #Volume CM RL CM AP CM IS minRL maxRL minAP maxAP minIS maxIS Mean SEM Max Int MI RL MI AP MI IS #------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ------- ------- ------- ----- ----- ----- 936 -20.8 -72.9 -38.4 -43.5 -6.0 -87.9 -52.9 -58.2 -10.7 0.9844 5.3e-04 1 -43.5 -60.4 -55.7 568 -47.9 22.7 -61.0 -58.5 -26.0 -7.9 49.6 -85.7 -28.2 0.977 6.6e-04 1 -46.0 34.6 -75.7 382 21.7 -72.2 -40.4 9.0 36.5 -85.4 -52.9 -58.2 -23.2 0.9874 7.1e-04 1 34.0 -60.4 -55.7 367 3.1 -76.2 -35.9 -1.0 9.0 -87.9 -67.9 -53.2 -13.2 0.9768 8.0e-04 1 -1.0 -77.9 -53.2 284 30.8 45.1 -65.7 19.0 44.0 34.6 52.1 -93.2 -43.2 0.9778 9.0e-04 1 31.5 47.1 -78.2 42 50.5 23.7 -58.3 49.0 51.5 22.1 24.6 -75.7 -38.2 0.9561 6.5e-04 0.9626 51.5 24.6 -73.2 36 43.3 -40.5 -40.5 41.5 46.5 -45.4 -35.4 -53.2 -30.7 0.9778 0.0021 1 46.5 -35.4 -45.7 23 -6.0 53.0 -67.0 -6.0 -6.0 52.1 54.6 -83.2 -48.2 0.9677 0.005 1 -6.0 54.6 -78.2 21 -56.0 -15.2 -65.5 -56.0 -56.0 -17.9 -12.9 -73.2 -55.7 1. 0 1 -56.0 -15.4 -73.2 16 54.0 9.6 -54.4 54.0 54.0 9.6 9.6 -73.2 -35.7 0.9527 2.6e-05 0.9527 54.0 9.6 -45.7 15 11.5 54.6 -70.7 11.5 11.5 54.6 54.6 -88.2 -53.2 0.9774 0 0.9774 11.5 54.6 -88.2 15 -11.0 54.6 -65.7 -11.0 -11.0 54.6 54.6 -83.2 -48.2 0.9947 0 0.9947 -11.0 54.6 -83.2 12 29.0 -60.4 -41.9 29.0 29.0 -60.4 -60.4 -55.7 -28.2 0.9539 0 0.9539 29.0 -60.4 -55.7 9 1.5 54.6 -73.2 1.5 1.5 54.6 54.6 -83.2 -63.2 1 0 1 1.5 54.6 -83.2 7 39.0 -50.4 -43.2 39.0 39.0 -50.4 -50.4 -50.7 -35.7 1 0 1 39.0 -50.4 -50.7 7 -46.0 -45.4 -40.7 -46.0 -46.0 -45.4 -45.4 -48.2 -33.2 0.9871 5.6e-05 0.9871 -46.0 -45.4 -48.2 6 56.5 4.6 -64.4 56.5 56.5 4.6 4.6 -70.7 -58.2 0.9856 1.9e-05 0.9856 56.5 4.6 -58.2 5 6.5 57.1 -80.7 6.5 6.5 57.1 57.1 -85.7 -75.7 1 0 1 6.5 57.1 -85.7 5 56.5 -0.4 -65.7 56.5 56.5 -0.4 -0.4 -70.7 -60.7 1 0 1 56.5 -0.4 -70.7 #------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ------- ------- ------- ----- ----- ----- # 2756 -8.8 -35.1 -47.3 0.9809 3.1e-04 -43.50 -60.40 -59.40 -46.00 34.60 -59.40 34.00 -60.40 -59.40 -1.00 -77.90 -59.40 31.50 47.10 -59.40 51.50 24.60 -59.40 46.50 -35.40 -59.40 -6.00 54.60 -59.40 -56.00 -15.40 -59.40 54.00 9.60 -59.40 11.50 54.60 -59.40 -11.00 54.60 -59.40 29.00 -60.40 -59.40 1.50 54.60 -59.40 39.00 -50.40 -59.40 -46.00 -45.40 -59.40 56.50 4.60 -59.40 6.50 57.10 -59.40 56.50 -0.40 -59.40 -- evaluating intersection... ++ 3dMean: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ WARNING: Have only 1 dset. *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/proj.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/proj.r01.nii.gz is 7.042221 degrees from plumb. ++ Neighborhood definition (NN=3) accepted *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/proj.min.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/proj.min.nii.gz is 7.042221 degrees from plumb. ++ User input stat threshold: -1 ++ User input stat threshold: 0.95 ++ Data volume: [0] 'MEAN' ++ Threshold volume: [0] 'MEAN' ++ How many sides to this stat? 0 ++ Looks like clustering is *not* being performed on a stat value; won't worry about sidedness, then. ++ Opt code: 2sided,-1,0.95,NN3 *+ WARNING: No mask being used? That *could* be OK, but thought I'd let you know... ++ Threshold volume [0] does *not* appear to be a stat! ++ Sorting clusters by size. # # Cluster report #[ Dataset prefix = proj.min.nii.gz ] #[ Threshold vol = [0] 'MEAN' ] #[ Supplement dat vol = [0] 'MEAN' ] #[ Option summary = 2sided,-1,0.95,NN3 ] #[ Threshold value(s) = left-tail thr=-1.000000; right-tail thr=0.950000 ] #[ Aux. stat. info. = not a stat! ] #[ Nvoxel threshold = 0; Volume threshold = 0.000 ] #[ Single voxel volume = 15.625 (microliters) ] #[ Neighbor type, NN = 3 ] #[ Voxel datum type = float ] #[ Voxel dimensions = 2.500 mm X 2.500 mm X 2.500 mm ] #[ Coordinates Order = RAI ] #[ Mean and SEM based on signed voxel intensities ] # #Volume CM RL CM AP CM IS minRL maxRL minAP maxAP minIS maxIS Mean SEM Max Int MI RL MI AP MI IS #------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ------- ------- ------- ----- ----- ----- 936 -20.8 -72.9 -38.4 -43.5 -6.0 -87.9 -52.9 -58.2 -10.7 0.9844 5.3e-04 1 -43.5 -60.4 -55.7 568 -47.9 22.7 -61.0 -58.5 -26.0 -7.9 49.6 -85.7 -28.2 0.977 6.6e-04 1 -46.0 34.6 -75.7 382 21.7 -72.2 -40.4 9.0 36.5 -85.4 -52.9 -58.2 -23.2 0.9874 7.1e-04 1 34.0 -60.4 -55.7 367 3.1 -76.2 -35.9 -1.0 9.0 -87.9 -67.9 -53.2 -13.2 0.9768 8.0e-04 1 -1.0 -77.9 -53.2 284 30.8 45.1 -65.7 19.0 44.0 34.6 52.1 -93.2 -43.2 0.9778 9.0e-04 1 31.5 47.1 -78.2 42 50.5 23.7 -58.3 49.0 51.5 22.1 24.6 -75.7 -38.2 0.9561 6.5e-04 0.9626 51.5 24.6 -73.2 36 43.3 -40.5 -40.5 41.5 46.5 -45.4 -35.4 -53.2 -30.7 0.9778 0.0021 1 46.5 -35.4 -45.7 23 -6.0 53.0 -67.0 -6.0 -6.0 52.1 54.6 -83.2 -48.2 0.9677 0.005 1 -6.0 54.6 -78.2 21 -56.0 -15.2 -65.5 -56.0 -56.0 -17.9 -12.9 -73.2 -55.7 1. 0 1 -56.0 -15.4 -73.2 16 54.0 9.6 -54.4 54.0 54.0 9.6 9.6 -73.2 -35.7 0.9527 2.6e-05 0.9527 54.0 9.6 -45.7 15 11.5 54.6 -70.7 11.5 11.5 54.6 54.6 -88.2 -53.2 0.9774 0 0.9774 11.5 54.6 -88.2 15 -11.0 54.6 -65.7 -11.0 -11.0 54.6 54.6 -83.2 -48.2 0.9947 0 0.9947 -11.0 54.6 -83.2 12 29.0 -60.4 -41.9 29.0 29.0 -60.4 -60.4 -55.7 -28.2 0.9539 0 0.9539 29.0 -60.4 -55.7 9 1.5 54.6 -73.2 1.5 1.5 54.6 54.6 -83.2 -63.2 1 0 1 1.5 54.6 -83.2 7 39.0 -50.4 -43.2 39.0 39.0 -50.4 -50.4 -50.7 -35.7 1 0 1 39.0 -50.4 -50.7 7 -46.0 -45.4 -40.7 -46.0 -46.0 -45.4 -45.4 -48.2 -33.2 0.9871 5.6e-05 0.9871 -46.0 -45.4 -48.2 6 56.5 4.6 -64.4 56.5 56.5 4.6 4.6 -70.7 -58.2 0.9856 1.9e-05 0.9856 56.5 4.6 -58.2 5 6.5 57.1 -80.7 6.5 6.5 57.1 57.1 -85.7 -75.7 1 0 1 6.5 57.1 -85.7 5 56.5 -0.4 -65.7 56.5 56.5 -0.4 -0.4 -70.7 -60.7 1 0 1 56.5 -0.4 -70.7 #------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ------- ------- ------- ----- ----- ----- # 2756 -8.8 -35.1 -47.3 0.9809 3.1e-04 -43.50 -60.40 -59.40 -46.00 34.60 -59.40 34.00 -60.40 -59.40 -1.00 -77.90 -59.40 31.50 47.10 -59.40 51.50 24.60 -59.40 46.50 -35.40 -59.40 -6.00 54.60 -59.40 -56.00 -15.40 -59.40 54.00 9.60 -59.40 11.50 54.60 -59.40 -11.00 54.60 -59.40 29.00 -60.40 -59.40 1.50 54.60 -59.40 39.00 -50.40 -59.40 -46.00 -45.40 -59.40 56.50 4.60 -59.40 6.50 57.10 -59.40 56.50 -0.40 -59.40 ++ Check about making images ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands *+ WARNING: input 'a' is not used in the expression ++ Symbol k using predefined value ++ Symbol x using predefined value ++ Symbol y using predefined value ++ Output dataset ./__tmp_dash_line.nii.gz ++ olay_alpha has known value: Yes ++ My command: @chauffeur_afni -ulay var.1.scale.r01.nii.gz -olay __tmp_dash_line.nii.gz -pbar_posonly -cbar Reds_and_Blues_Inv -func_range 1 -set_subbricks 0 0 0 -thr_olay 0.5 -olay_alpha Yes -olay_boxed Yes -set_dicom_xyz -43.50 -60.40 -59.40 -opacity 9 -blowup 4 -no_cor -no_axi -montx 1 -monty 1 -prefix img_r01_01 -set_xhairs OFF -label_mode 0 ++ Using AFNI ver : AFNI_23.0.01 ++ chauffeur ver : 6.52 ------------------ start of optionizing ------------------ ++ Found input file: var.1.scale.r01.nii.gz ++ Found input file: __tmp_dash_line.nii.gz ++ Using blowup factor: 4 ++ Using opacity: 9 ++ Making temporary work directory to copy vis files: ./__tmp_chauf_Ns86AUXMAD2 ++ Converted 0 to labels ++ Final subbrick indices: 0 0 0 ++ Copy ulay to visualize (volumetric) within user's range: *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 7.042221 degrees from plumb. *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 7.042221 degrees from plumb. ++ Ulay to be visualized within user range: [0%, 98%] -> [0.000000, 1.000000] ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_Ns86AUXMAD2/tmp_ulay.nii ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_Ns86AUXMAD2/tmp_olay.nii ++ User-entered function range value value (1) ++ Dimensions (xyzt): 88 88 60 1 ++ (initial) Slice spacing ordered (x,y,z) is: 88 88 60 ++ Will have user's chosen: SET_DICOM_XYZ -43.50 -60.40 -59.40 ------------------- end of optionizing ------------------- -- trying to start Xvfb :92 [1] 2538850 +/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/__tmp_chauf_Ns86AUXMAD2++ Writing one 352x240 image to filter '/usr/bin/pnmtopng -compression 9 > ./img_r01_01.sag.png' pnmtopng: 216 colors found AFNI QUITTs! +++ Command Echo: afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=1x1:88:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=1x1:88:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=1x1:60:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1.000000 -com SET_FUNC_RANGE 1 -com SET_THRESHNEW 0.5 * -com SET_FUNC_ALPHA Yes -com SET_FUNC_BOXED Yes -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ -43.50 -60.40 -59.40 -com SAVE_PNG sagittalimage ./img_r01_01.sag blowup=4 -com QUITT ./__tmp_chauf_Ns86AUXMAD2 +* Removing temporary image directory './__tmp_chauf_Ns86AUXMAD2'. [1] Done Xvfb :92 -screen 0 1024x768x24 ++ DONE (good exit) see: ./img_r01_01* ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands *+ WARNING: input 'a' is not used in the expression ++ Symbol k using predefined value ++ Symbol x using predefined value ++ Symbol y using predefined value ++ Output dataset ./__tmp_dash_line.nii.gz ++ olay_alpha has known value: Yes ++ My command: @chauffeur_afni -ulay var.1.scale.r01.nii.gz -olay __tmp_dash_line.nii.gz -pbar_posonly -cbar Reds_and_Blues_Inv -func_range 1 -set_subbricks 0 0 0 -thr_olay 0.5 -olay_alpha Yes -olay_boxed Yes -set_dicom_xyz -46.00 34.60 -59.40 -opacity 9 -blowup 4 -no_cor -no_axi -montx 1 -monty 1 -prefix img_r01_02 -set_xhairs OFF -label_mode 0 ++ Using AFNI ver : AFNI_23.0.01 ++ chauffeur ver : 6.52 ------------------ start of optionizing ------------------ ++ Found input file: var.1.scale.r01.nii.gz ++ Found input file: __tmp_dash_line.nii.gz ++ Using blowup factor: 4 ++ Using opacity: 9 ++ Making temporary work directory to copy vis files: ./__tmp_chauf_0YC3l7i0ktG ++ Converted 0 to labels ++ Final subbrick indices: 0 0 0 ++ Copy ulay to visualize (volumetric) within user's range: *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 7.042221 degrees from plumb. *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 7.042221 degrees from plumb. ++ Ulay to be visualized within user range: [0%, 98%] -> [0.000000, 1.000000] ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_0YC3l7i0ktG/tmp_ulay.nii ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_0YC3l7i0ktG/tmp_olay.nii ++ User-entered function range value value (1) ++ Dimensions (xyzt): 88 88 60 1 ++ (initial) Slice spacing ordered (x,y,z) is: 88 88 60 ++ Will have user's chosen: SET_DICOM_XYZ -46.00 34.60 -59.40 ------------------- end of optionizing ------------------- -- trying to start Xvfb :35 [1] 2538953 +/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/__tmp_chauf_0YC3l7i0ktG++ Writing one 352x240 image to filter '/usr/bin/pnmtopng -compression 9 > ./img_r01_02.sag.png' pnmtopng: 218 colors found AFNI QUITTs! +++ Command Echo: afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=1x1:88:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=1x1:88:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=1x1:60:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1.000000 -com SET_FUNC_RANGE 1 -com SET_THRESHNEW 0.5 * -com SET_FUNC_ALPHA Yes -com SET_FUNC_BOXED Yes -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ -46.00 34.60 -59.40 -com SAVE_PNG sagittalimage ./img_r01_02.sag blowup=4 -com QUITT ./__tmp_chauf_0YC3l7i0ktG +* Removing temporary image directory './__tmp_chauf_0YC3l7i0ktG'. [1] Done Xvfb :35 -screen 0 1024x768x24 ++ DONE (good exit) see: ./img_r01_02* ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands *+ WARNING: input 'a' is not used in the expression ++ Symbol k using predefined value ++ Symbol x using predefined value ++ Symbol y using predefined value ++ Output dataset ./__tmp_dash_line.nii.gz ++ olay_alpha has known value: Yes ++ My command: @chauffeur_afni -ulay var.1.scale.r01.nii.gz -olay __tmp_dash_line.nii.gz -pbar_posonly -cbar Reds_and_Blues_Inv -func_range 1 -set_subbricks 0 0 0 -thr_olay 0.5 -olay_alpha Yes -olay_boxed Yes -set_dicom_xyz 34.00 -60.40 -59.40 -opacity 9 -blowup 4 -no_cor -no_axi -montx 1 -monty 1 -prefix img_r01_03 -set_xhairs OFF -label_mode 0 ++ Using AFNI ver : AFNI_23.0.01 ++ chauffeur ver : 6.52 ------------------ start of optionizing ------------------ ++ Found input file: var.1.scale.r01.nii.gz ++ Found input file: __tmp_dash_line.nii.gz ++ Using blowup factor: 4 ++ Using opacity: 9 ++ Making temporary work directory to copy vis files: ./__tmp_chauf_oUlJ1i6s2GH ++ Converted 0 to labels ++ Final subbrick indices: 0 0 0 ++ Copy ulay to visualize (volumetric) within user's range: *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 7.042221 degrees from plumb. *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 7.042221 degrees from plumb. ++ Ulay to be visualized within user range: [0%, 98%] -> [0.000000, 1.000000] ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_oUlJ1i6s2GH/tmp_ulay.nii ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_oUlJ1i6s2GH/tmp_olay.nii ++ User-entered function range value value (1) ++ Dimensions (xyzt): 88 88 60 1 ++ (initial) Slice spacing ordered (x,y,z) is: 88 88 60 ++ Will have user's chosen: SET_DICOM_XYZ 34.00 -60.40 -59.40 ------------------- end of optionizing ------------------- -- trying to start Xvfb :868 [1] 2539057 +/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/__tmp_chauf_oUlJ1i6s2GH++ Writing one 352x240 image to filter '/usr/bin/pnmtopng -compression 9 > ./img_r01_03.sag.png' pnmtopng: 218 colors found AFNI QUITTs! +++ Command Echo: afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=1x1:88:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=1x1:88:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=1x1:60:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1.000000 -com SET_FUNC_RANGE 1 -com SET_THRESHNEW 0.5 * -com SET_FUNC_ALPHA Yes -com SET_FUNC_BOXED Yes -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 34.00 -60.40 -59.40 -com SAVE_PNG sagittalimage ./img_r01_03.sag blowup=4 -com QUITT ./__tmp_chauf_oUlJ1i6s2GH +* Removing temporary image directory './__tmp_chauf_oUlJ1i6s2GH'. [1] Done Xvfb :868 -screen 0 1024x768x24 ++ DONE (good exit) see: ./img_r01_03* ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands *+ WARNING: input 'a' is not used in the expression ++ Symbol k using predefined value ++ Symbol x using predefined value ++ Symbol y using predefined value ++ Output dataset ./__tmp_dash_line.nii.gz ++ olay_alpha has known value: Yes ++ My command: @chauffeur_afni -ulay var.1.scale.r01.nii.gz -olay __tmp_dash_line.nii.gz -pbar_posonly -cbar Reds_and_Blues_Inv -func_range 1 -set_subbricks 0 0 0 -thr_olay 0.5 -olay_alpha Yes -olay_boxed Yes -set_dicom_xyz -1.00 -77.90 -59.40 -opacity 9 -blowup 4 -no_cor -no_axi -montx 1 -monty 1 -prefix img_r01_04 -set_xhairs OFF -label_mode 0 ++ Using AFNI ver : AFNI_23.0.01 ++ chauffeur ver : 6.52 ------------------ start of optionizing ------------------ ++ Found input file: var.1.scale.r01.nii.gz ++ Found input file: __tmp_dash_line.nii.gz ++ Using blowup factor: 4 ++ Using opacity: 9 ++ Making temporary work directory to copy vis files: ./__tmp_chauf_g4pJy33Up7d ++ Converted 0 to labels ++ Final subbrick indices: 0 0 0 ++ Copy ulay to visualize (volumetric) within user's range: *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 7.042221 degrees from plumb. *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 7.042221 degrees from plumb. ++ Ulay to be visualized within user range: [0%, 98%] -> [0.000000, 1.000000] ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_g4pJy33Up7d/tmp_ulay.nii ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_g4pJy33Up7d/tmp_olay.nii ++ User-entered function range value value (1) ++ Dimensions (xyzt): 88 88 60 1 ++ (initial) Slice spacing ordered (x,y,z) is: 88 88 60 ++ Will have user's chosen: SET_DICOM_XYZ -1.00 -77.90 -59.40 ------------------- end of optionizing ------------------- -- trying to start Xvfb :368 [1] 2539160 +/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/__tmp_chauf_g4pJy33Up7d++ Writing one 352x240 image to filter '/usr/bin/pnmtopng -compression 9 > ./img_r01_04.sag.png' pnmtopng: 217 colors found AFNI QUITTs! +++ Command Echo: afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=1x1:88:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=1x1:88:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=1x1:60:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1.000000 -com SET_FUNC_RANGE 1 -com SET_THRESHNEW 0.5 * -com SET_FUNC_ALPHA Yes -com SET_FUNC_BOXED Yes -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ -1.00 -77.90 -59.40 -com SAVE_PNG sagittalimage ./img_r01_04.sag blowup=4 -com QUITT ./__tmp_chauf_g4pJy33Up7d +* Removing temporary image directory './__tmp_chauf_g4pJy33Up7d'. [1] Done Xvfb :368 -screen 0 1024x768x24 ++ DONE (good exit) see: ./img_r01_04* ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands *+ WARNING: input 'a' is not used in the expression ++ Symbol k using predefined value ++ Symbol x using predefined value ++ Symbol y using predefined value ++ Output dataset ./__tmp_dash_line.nii.gz ++ olay_alpha has known value: Yes ++ My command: @chauffeur_afni -ulay var.1.scale.r01.nii.gz -olay __tmp_dash_line.nii.gz -pbar_posonly -cbar Reds_and_Blues_Inv -func_range 1 -set_subbricks 0 0 0 -thr_olay 0.5 -olay_alpha Yes -olay_boxed Yes -set_dicom_xyz 31.50 47.10 -59.40 -opacity 9 -blowup 4 -no_cor -no_axi -montx 1 -monty 1 -prefix img_r01_05 -set_xhairs OFF -label_mode 0 ++ Using AFNI ver : AFNI_23.0.01 ++ chauffeur ver : 6.52 ------------------ start of optionizing ------------------ ++ Found input file: var.1.scale.r01.nii.gz ++ Found input file: __tmp_dash_line.nii.gz ++ Using blowup factor: 4 ++ Using opacity: 9 ++ Making temporary work directory to copy vis files: ./__tmp_chauf_VbEmeG4kOJS ++ Converted 0 to labels ++ Final subbrick indices: 0 0 0 ++ Copy ulay to visualize (volumetric) within user's range: *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 7.042221 degrees from plumb. *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 7.042221 degrees from plumb. ++ Ulay to be visualized within user range: [0%, 98%] -> [0.000000, 1.000000] ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_VbEmeG4kOJS/tmp_ulay.nii ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_VbEmeG4kOJS/tmp_olay.nii ++ User-entered function range value value (1) ++ Dimensions (xyzt): 88 88 60 1 ++ (initial) Slice spacing ordered (x,y,z) is: 88 88 60 ++ Will have user's chosen: SET_DICOM_XYZ 31.50 47.10 -59.40 ------------------- end of optionizing ------------------- -- trying to start Xvfb :968 [1] 2539265 +/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/__tmp_chauf_VbEmeG4kOJS++ Writing one 352x240 image to filter '/usr/bin/pnmtopng -compression 9 > ./img_r01_05.sag.png' pnmtopng: 217 colors found AFNI QUITTs! +++ Command Echo: afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=1x1:88:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=1x1:88:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=1x1:60:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1.000000 -com SET_FUNC_RANGE 1 -com SET_THRESHNEW 0.5 * -com SET_FUNC_ALPHA Yes -com SET_FUNC_BOXED Yes -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 31.50 47.10 -59.40 -com SAVE_PNG sagittalimage ./img_r01_05.sag blowup=4 -com QUITT ./__tmp_chauf_VbEmeG4kOJS +* Removing temporary image directory './__tmp_chauf_VbEmeG4kOJS'. [1] Done Xvfb :968 -screen 0 1024x768x24 ++ DONE (good exit) see: ./img_r01_05* ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands *+ WARNING: input 'a' is not used in the expression ++ Symbol k using predefined value ++ Symbol x using predefined value ++ Symbol y using predefined value ++ Output dataset ./__tmp_dash_line.nii.gz ++ olay_alpha has known value: Yes ++ My command: @chauffeur_afni -ulay var.1.scale.r01.nii.gz -olay __tmp_dash_line.nii.gz -pbar_posonly -cbar Reds_and_Blues_Inv -func_range 1 -set_subbricks 0 0 0 -thr_olay 0.5 -olay_alpha Yes -olay_boxed Yes -set_dicom_xyz 51.50 24.60 -59.40 -opacity 9 -blowup 4 -no_cor -no_axi -montx 1 -monty 1 -prefix img_r01_06 -set_xhairs OFF -label_mode 0 ++ Using AFNI ver : AFNI_23.0.01 ++ chauffeur ver : 6.52 ------------------ start of optionizing ------------------ ++ Found input file: var.1.scale.r01.nii.gz ++ Found input file: __tmp_dash_line.nii.gz ++ Using blowup factor: 4 ++ Using opacity: 9 ++ Making temporary work directory to copy vis files: ./__tmp_chauf_pJyVHyO680h ++ Converted 0 to labels ++ Final subbrick indices: 0 0 0 ++ Copy ulay to visualize (volumetric) within user's range: *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 7.042221 degrees from plumb. *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 7.042221 degrees from plumb. ++ Ulay to be visualized within user range: [0%, 98%] -> [0.000000, 1.000000] ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_pJyVHyO680h/tmp_ulay.nii ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_pJyVHyO680h/tmp_olay.nii ++ User-entered function range value value (1) ++ Dimensions (xyzt): 88 88 60 1 ++ (initial) Slice spacing ordered (x,y,z) is: 88 88 60 ++ Will have user's chosen: SET_DICOM_XYZ 51.50 24.60 -59.40 ------------------- end of optionizing ------------------- -- trying to start Xvfb :351 [1] 2539372 +/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/__tmp_chauf_pJyVHyO680h++ Writing one 352x240 image to filter '/usr/bin/pnmtopng -compression 9 > ./img_r01_06.sag.png' pnmtopng: 217 colors found AFNI QUITTs! +++ Command Echo: afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=1x1:88:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=1x1:88:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=1x1:60:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1.000000 -com SET_FUNC_RANGE 1 -com SET_THRESHNEW 0.5 * -com SET_FUNC_ALPHA Yes -com SET_FUNC_BOXED Yes -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 51.50 24.60 -59.40 -com SAVE_PNG sagittalimage ./img_r01_06.sag blowup=4 -com QUITT ./__tmp_chauf_pJyVHyO680h +* Removing temporary image directory './__tmp_chauf_pJyVHyO680h'. [1] Done Xvfb :351 -screen 0 1024x768x24 ++ DONE (good exit) see: ./img_r01_06* ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands *+ WARNING: input 'a' is not used in the expression ++ Symbol k using predefined value ++ Symbol x using predefined value ++ Symbol y using predefined value ++ Output dataset ./__tmp_dash_line.nii.gz ++ olay_alpha has known value: Yes ++ My command: @chauffeur_afni -ulay var.1.scale.r01.nii.gz -olay __tmp_dash_line.nii.gz -pbar_posonly -cbar Reds_and_Blues_Inv -func_range 1 -set_subbricks 0 0 0 -thr_olay 0.5 -olay_alpha Yes -olay_boxed Yes -set_dicom_xyz 46.50 -35.40 -59.40 -opacity 9 -blowup 4 -no_cor -no_axi -montx 1 -monty 1 -prefix img_r01_07 -set_xhairs OFF -label_mode 0 ++ Using AFNI ver : AFNI_23.0.01 ++ chauffeur ver : 6.52 ------------------ start of optionizing ------------------ ++ Found input file: var.1.scale.r01.nii.gz ++ Found input file: __tmp_dash_line.nii.gz ++ Using blowup factor: 4 ++ Using opacity: 9 ++ Making temporary work directory to copy vis files: ./__tmp_chauf_Mdlk7ABIo86 ++ Converted 0 to labels ++ Final subbrick indices: 0 0 0 ++ Copy ulay to visualize (volumetric) within user's range: *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 7.042221 degrees from plumb. *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz, 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:/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 7.042221 degrees from plumb. ++ Ulay to be visualized within user range: [0%, 98%] -> [0.000000, 1.000000] ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_Mdlk7ABIo86/tmp_ulay.nii ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_Mdlk7ABIo86/tmp_olay.nii ++ User-entered function range value value (1) ++ Dimensions (xyzt): 88 88 60 1 ++ (initial) Slice spacing ordered (x,y,z) is: 88 88 60 ++ Will have user's chosen: SET_DICOM_XYZ 46.50 -35.40 -59.40 ------------------- end of optionizing ------------------- -- trying to start Xvfb :376 [1] 2539477 +/home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vlines.pb00.tcat/__tmp_chauf_Mdlk7ABIo86++ Writing one 352x240 image to filter '/usr/bin/pnmtopng -compression 9 > ./img_r01_07.sag.png' pnmtopng: 217 colors found AFNI QUITTs! +++ Command Echo: afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=1x1:88:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=1x1:88:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=1x1:60:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1.000000 -com SET_FUNC_RANGE 1 -com SET_THRESHNEW 0.5 * -com SET_FUNC_ALPHA Yes -com SET_FUNC_BOXED Yes -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 46.50 -35.40 -59.40 -com SAVE_PNG sagittalimage ./img_r01_07.sag blowup=4 -com QUITT ./__tmp_chauf_Mdlk7ABIo86 +* Removing temporary image directory './__tmp_chauf_Mdlk7ABIo86'. [1] Done Xvfb :376 -screen 0 1024x768x24 ++ DONE (good exit) see: ./img_r01_07* +++ Transforming all input to rgb for a good reason +++ Writing image to QC_var_lines.jpg +++ Arranging 7 images (each 352x240) into a 7x1 matrix. You can view image QC_var_lines.jpg with: aiv QC_var_lines.jpg ++ have do_clean, removing time series... == found questionable regions across inputs: 19 found questionable intersected regions : 19 =============== bad_coords.inter.txt =============== -43.50 -60.40 -59.40 -46.00 34.60 -59.40 34.00 -60.40 -59.40 -1.00 -77.90 -59.40 31.50 47.10 -59.40 51.50 24.60 -59.40 46.50 -35.40 -59.40 -6.00 54.60 -59.40 -56.00 -15.40 -59.40 54.00 9.60 -59.40 11.50 54.60 -59.40 -11.00 54.60 -59.40 29.00 -60.40 -59.40 1.50 54.60 -59.40 39.00 -50.40 -59.40 -46.00 -45.40 -59.40 56.50 4.60 -59.40 6.50 57.10 -59.40 56.50 -0.40 -59.40 =============== bad_coords.r01.txt =============== -43.50 -60.40 -59.40 -46.00 34.60 -59.40 34.00 -60.40 -59.40 -1.00 -77.90 -59.40 31.50 47.10 -59.40 51.50 24.60 -59.40 46.50 -35.40 -59.40 -6.00 54.60 -59.40 -56.00 -15.40 -59.40 54.00 9.60 -59.40 11.50 54.60 -59.40 -11.00 54.60 -59.40 29.00 -60.40 -59.40 1.50 54.60 -59.40 39.00 -50.40 -59.40 -46.00 -45.40 -59.40 56.50 4.60 -59.40 6.50 57.10 -59.40 56.50 -0.40 -59.40 touch out.pre_ss_warn.txt foreach run ( 01 ) 3dToutcount -automask -fraction -polort 4 -legendre pb00.SM327_all4runs.r01.e02.tcat+orig ++ 3dToutcount: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.SM327_all4runs.r01.e02.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.SM327_all4runs.r01.e02.tcat+orig.BRIK is 7.042221 degrees from plumb. ++ 79787 voxels passed mask/clip 1deval -a outcount.r01.1D -expr 1-step(a-0.05) 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 cat rm.out.cen.r01.1D set minindex = `3dTstat -argmin -prefix - outcount_rall.1D\'` 3dTstat -argmin -prefix - outcount_rall.1D' ++ 3dTstat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [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 466 -index_to_run_tr 108 set minoutrun = 01 set minouttr = 108 echo min outlier: run 01, TR 108 tee out.min_outlier.txt min outlier: run 01, TR 108 foreach run ( 01 ) foreach eind ( 01 02 03 04 05 06 07 08 09 10 11 12 ) 3dDespike -NEW -nomask -prefix pb01.SM327_all4runs.r01.e01.despike pb00.SM327_all4runs.r01.e01.tcat+orig ++ 3dDespike: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.SM327_all4runs.r01.e01.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.SM327_all4runs.r01.e01.tcat+orig.BRIK is 7.042221 degrees from plumb. ++ Input dataset is in short format, but output will be in float format ++ ignoring first 0 time points, using last 466 ++ using 466 time points => -corder 16 ++ Loading dataset pb00.SM327_all4runs.r01.e01.tcat+orig ++ processing all 464640 voxels in dataset ++ Procesing time series with NEW model fit algorithm ++ smash edit thresholds: 3.1 .. 5.0 MADs + [ 3.457% .. 0.072% of normal distribution] + [ 8.839% .. 3.125% of Laplace distribution] ++ start OpenMP thread #10 ++ start OpenMP thread #1 ++ start OpenMP thread #7 ++ start OpenMP thread #4 ++ start OpenMP thread #0 ++ start OpenMP thread #11 ++ start OpenMP thread #3 ++ start OpenMP thread #9 ++ start OpenMP thread #8 ++ start OpenMP thread #6 ++ start OpenMP thread #12 ++ start OpenMP thread #5 ++ start OpenMP thread #2 ++ start OpenMP thread #14 ++ start OpenMP thread #13 ...................................................................................................................................................................................................... ++ Elapsed despike time = 3s 371ms ++ FINAL: 213692688 data points, 10801731 edits [5.055%], 3620866 big edits [1.694%] ++ Output dataset ./pb01.SM327_all4runs.r01.e01.despike+orig.BRIK end 3dDespike -NEW -nomask -prefix pb01.SM327_all4runs.r01.e02.despike pb00.SM327_all4runs.r01.e02.tcat+orig ++ 3dDespike: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.SM327_all4runs.r01.e02.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.SM327_all4runs.r01.e02.tcat+orig.BRIK is 7.042221 degrees from plumb. ++ Input dataset is in short format, but output will be in float format ++ ignoring first 0 time points, using last 466 ++ using 466 time points => -corder 16 ++ Loading dataset pb00.SM327_all4runs.r01.e02.tcat+orig ++ processing all 464640 voxels in dataset ++ Procesing time series with NEW model fit algorithm ++ smash edit thresholds: 3.1 .. 5.0 MADs + [ 3.457% .. 0.072% of normal distribution] + [ 8.839% .. 3.125% of Laplace distribution] ++ start OpenMP thread #2 ++ start OpenMP thread #7 ++ start OpenMP thread #9 ++ start OpenMP thread #0 ++ start OpenMP thread #8 ++ start OpenMP thread #6 ++ start OpenMP thread #3 ++ start OpenMP thread #1 ++ start OpenMP thread #4 ++ start OpenMP thread #10 ++ start OpenMP thread #14 ++ start OpenMP thread #11 ++ start OpenMP thread #12 ++ start OpenMP thread #5 ++ start OpenMP thread #13 ...................................................................................................................................................................................................... ++ Elapsed despike time = 3s 352ms ++ FINAL: 213692688 data points, 10906497 edits [5.104%], 3736136 big edits [1.748%] ++ Output dataset ./pb01.SM327_all4runs.r01.e02.despike+orig.BRIK end 3dDespike -NEW -nomask -prefix pb01.SM327_all4runs.r01.e03.despike pb00.SM327_all4runs.r01.e03.tcat+orig ++ 3dDespike: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.SM327_all4runs.r01.e03.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.SM327_all4runs.r01.e03.tcat+orig.BRIK is 7.042221 degrees from plumb. ++ Input dataset is in short format, but output will be in float format ++ ignoring first 0 time points, using last 466 ++ using 466 time points => -corder 16 ++ Loading dataset pb00.SM327_all4runs.r01.e03.tcat+orig ++ processing all 464640 voxels in dataset ++ Procesing time series with NEW model fit algorithm ++ smash edit thresholds: 3.1 .. 5.0 MADs + [ 3.457% .. 0.072% of normal distribution] + [ 8.839% .. 3.125% of Laplace distribution] ++ start OpenMP thread #7 ++ start OpenMP thread #11 ++ start OpenMP thread #13 ++ start OpenMP thread #14 ++ start OpenMP thread #1 ++ start OpenMP thread #5 ++ start OpenMP thread #8 ++ start OpenMP thread #0 ++ start OpenMP thread #12 ++ start OpenMP thread #2 ++ start OpenMP thread #3 ++ start OpenMP thread #6 ++ start OpenMP thread #4 ++ start OpenMP thread #10 ++ start OpenMP thread #9 ...................................................................................................................................................................................................... ++ Elapsed despike time = 3s 324ms ++ FINAL: 213692688 data points, 12457306 edits [5.830%], 5734715 big edits [2.684%] ++ Output dataset ./pb01.SM327_all4runs.r01.e03.despike+orig.BRIK end 3dDespike -NEW -nomask -prefix pb01.SM327_all4runs.r01.e04.despike pb00.SM327_all4runs.r01.e04.tcat+orig ++ 3dDespike: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.SM327_all4runs.r01.e04.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.SM327_all4runs.r01.e04.tcat+orig.BRIK is 7.042221 degrees from plumb. ++ Input dataset is in short format, but output will be in float format ++ ignoring first 0 time points, using last 466 ++ using 466 time points => -corder 16 ++ Loading dataset pb00.SM327_all4runs.r01.e04.tcat+orig ++ processing all 464640 voxels in dataset ++ Procesing time series with NEW model fit algorithm ++ smash edit thresholds: 3.1 .. 5.0 MADs + [ 3.457% .. 0.072% of normal distribution] + [ 8.839% .. 3.125% of Laplace distribution] ++ start OpenMP thread #0 ++ start OpenMP thread #8 ++ start OpenMP thread #13 ++ start OpenMP thread #6 ++ start OpenMP thread #14 ++ start OpenMP thread #2 ++ start OpenMP thread #5 ++ start OpenMP thread #11 ++ start OpenMP thread #1 ++ start OpenMP thread #12 ++ start OpenMP thread #9 ++ start OpenMP thread #3 ++ start OpenMP thread #10 ++ start OpenMP thread #4 ++ start OpenMP thread #7 ...................................................................................................................................................................................................... ++ Elapsed despike time = 3s 338ms ++ FINAL: 213692688 data points, 9233243 edits [4.321%], 2132705 big edits [0.998%] ++ Output dataset ./pb01.SM327_all4runs.r01.e04.despike+orig.BRIK end 3dDespike -NEW -nomask -prefix pb01.SM327_all4runs.r01.e05.despike pb00.SM327_all4runs.r01.e05.tcat+orig ++ 3dDespike: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.SM327_all4runs.r01.e05.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.SM327_all4runs.r01.e05.tcat+orig.BRIK is 7.042221 degrees from plumb. ++ Input dataset is in short format, but output will be in float format ++ ignoring first 0 time points, using last 466 ++ using 466 time points => -corder 16 ++ Loading dataset pb00.SM327_all4runs.r01.e05.tcat+orig ++ processing all 464640 voxels in dataset ++ Procesing time series with NEW model fit algorithm ++ smash edit thresholds: 3.1 .. 5.0 MADs + [ 3.457% .. 0.072% of normal distribution] + [ 8.839% .. 3.125% of Laplace distribution] ++ start OpenMP thread #1 ++ start OpenMP thread #14 ++ start OpenMP thread #2 ++ start OpenMP thread #11 ++ start OpenMP thread #12 ++ start OpenMP thread #8 ++ start OpenMP thread #7 ++ start OpenMP thread #13 ++ start OpenMP thread #9 ++ start OpenMP thread #3 ++ start OpenMP thread #6 ++ start OpenMP thread #4 ++ start OpenMP thread #5 ++ start OpenMP thread #10 ++ start OpenMP thread #0 ...................................................................................................................................................................................................... ++ Elapsed despike time = 3s 308ms ++ FINAL: 213692688 data points, 11019345 edits [5.157%], 3776703 big edits [1.767%] ++ Output dataset ./pb01.SM327_all4runs.r01.e05.despike+orig.BRIK end 3dDespike -NEW -nomask -prefix pb01.SM327_all4runs.r01.e06.despike pb00.SM327_all4runs.r01.e06.tcat+orig ++ 3dDespike: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.SM327_all4runs.r01.e06.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.SM327_all4runs.r01.e06.tcat+orig.BRIK is 7.042221 degrees from plumb. ++ Input dataset is in short format, but output will be in float format ++ ignoring first 0 time points, using last 466 ++ using 466 time points => -corder 16 ++ Loading dataset pb00.SM327_all4runs.r01.e06.tcat+orig ++ processing all 464640 voxels in dataset ++ Procesing time series with NEW model fit algorithm ++ smash edit thresholds: 3.1 .. 5.0 MADs + [ 3.457% .. 0.072% of normal distribution] + [ 8.839% .. 3.125% of Laplace distribution] ++ start OpenMP thread #9 ++ start OpenMP thread #6 ++ start OpenMP thread #11 ++ start OpenMP thread #2 ++ start OpenMP thread #8 ++ start OpenMP thread #0 ++ start OpenMP thread #14 ++ start OpenMP thread #12 ++ start OpenMP thread #4 ++ start OpenMP thread #7 ++ start OpenMP thread #1 ++ start OpenMP thread #10 ++ start OpenMP thread #13 ++ start OpenMP thread #5 ++ start OpenMP thread #3 ...................................................................................................................................................................................................... ++ Elapsed despike time = 3s 303ms ++ FINAL: 213692688 data points, 12188131 edits [5.704%], 5409070 big edits [2.531%] ++ Output dataset ./pb01.SM327_all4runs.r01.e06.despike+orig.BRIK end 3dDespike -NEW -nomask -prefix pb01.SM327_all4runs.r01.e07.despike pb00.SM327_all4runs.r01.e07.tcat+orig ++ 3dDespike: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.SM327_all4runs.r01.e07.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.SM327_all4runs.r01.e07.tcat+orig.BRIK is 7.042221 degrees from plumb. ++ Input dataset is in short format, but output will be in float format ++ ignoring first 0 time points, using last 466 ++ using 466 time points => -corder 16 ++ Loading dataset pb00.SM327_all4runs.r01.e07.tcat+orig ++ processing all 464640 voxels in dataset ++ Procesing time series with NEW model fit algorithm ++ smash edit thresholds: 3.1 .. 5.0 MADs + [ 3.457% .. 0.072% of normal distribution] + [ 8.839% .. 3.125% of Laplace distribution] ++ start OpenMP thread #11 ++ start OpenMP thread #1 ++ start OpenMP thread #2 ++ start OpenMP thread #10 ++ start OpenMP thread #8 ++ start OpenMP thread #14 ++ start OpenMP thread #3 ++ start OpenMP thread #6 ++ start OpenMP thread #12 ++ start OpenMP thread #9 ++ start OpenMP thread #5 ++ start OpenMP thread #13 ++ start OpenMP thread #0 ++ start OpenMP thread #4 ++ start OpenMP thread #7 ...................................................................................................................................................................................................... ++ Elapsed despike time = 3s 821ms ++ FINAL: 213692688 data points, 13613005 edits [6.370%], 6467981 big edits [3.027%] ++ Output dataset ./pb01.SM327_all4runs.r01.e07.despike+orig.BRIK end 3dDespike -NEW -nomask -prefix pb01.SM327_all4runs.r01.e08.despike pb00.SM327_all4runs.r01.e08.tcat+orig ++ 3dDespike: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.SM327_all4runs.r01.e08.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.SM327_all4runs.r01.e08.tcat+orig.BRIK is 7.042221 degrees from plumb. ++ Input dataset is in short format, but output will be in float format ++ ignoring first 0 time points, using last 466 ++ using 466 time points => -corder 16 ++ Loading dataset pb00.SM327_all4runs.r01.e08.tcat+orig ++ processing all 464640 voxels in dataset ++ Procesing time series with NEW model fit algorithm ++ smash edit thresholds: 3.1 .. 5.0 MADs + [ 3.457% .. 0.072% of normal distribution] + [ 8.839% .. 3.125% of Laplace distribution] ++ start OpenMP thread #8 ++ start OpenMP thread #7 ++ start OpenMP thread #12 ++ start OpenMP thread #14 ++ start OpenMP thread #6 ++ start OpenMP thread #1 ++ start OpenMP thread #3 ++ start OpenMP thread #2 ++ start OpenMP thread #4 ++ start OpenMP thread #0 ++ start OpenMP thread #5 ++ start OpenMP thread #13 ++ start OpenMP thread #9 ++ start OpenMP thread #10 ++ start OpenMP thread #11 ...................................................................................................................................................................................................... ++ Elapsed despike time = 3s 796ms ++ FINAL: 213692688 data points, 13143318 edits [6.151%], 6367554 big edits [2.980%] ++ Output dataset ./pb01.SM327_all4runs.r01.e08.despike+orig.BRIK end 3dDespike -NEW -nomask -prefix pb01.SM327_all4runs.r01.e09.despike pb00.SM327_all4runs.r01.e09.tcat+orig ++ 3dDespike: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.SM327_all4runs.r01.e09.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.SM327_all4runs.r01.e09.tcat+orig.BRIK is 7.042221 degrees from plumb. ++ Input dataset is in short format, but output will be in float format ++ ignoring first 0 time points, using last 466 ++ using 466 time points => -corder 16 ++ Loading dataset pb00.SM327_all4runs.r01.e09.tcat+orig ++ processing all 464640 voxels in dataset ++ Procesing time series with NEW model fit algorithm ++ smash edit thresholds: 3.1 .. 5.0 MADs + [ 3.457% .. 0.072% of normal distribution] + [ 8.839% .. 3.125% of Laplace distribution] ++ start OpenMP thread #6 ++ start OpenMP thread #0 ++ start OpenMP thread #13 ++ start OpenMP thread #14 ++ start OpenMP thread #1 ++ start OpenMP thread #7 ++ start OpenMP thread #5 ++ start OpenMP thread #9 ++ start OpenMP thread #10 ++ start OpenMP thread #4 ++ start OpenMP thread #2 ++ start OpenMP thread #8 ++ start OpenMP thread #12 ++ start OpenMP thread #3 ++ start OpenMP thread #11 ...................................................................................................................................................................................................... ++ Elapsed despike time = 3s 807ms ++ FINAL: 213692688 data points, 13696968 edits [6.410%], 7160868 big edits [3.351%] ++ Output dataset ./pb01.SM327_all4runs.r01.e09.despike+orig.BRIK end 3dDespike -NEW -nomask -prefix pb01.SM327_all4runs.r01.e10.despike pb00.SM327_all4runs.r01.e10.tcat+orig ++ 3dDespike: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.SM327_all4runs.r01.e10.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.SM327_all4runs.r01.e10.tcat+orig.BRIK is 7.042221 degrees from plumb. ++ Input dataset is in short format, but output will be in float format ++ ignoring first 0 time points, using last 466 ++ using 466 time points => -corder 16 ++ Loading dataset pb00.SM327_all4runs.r01.e10.tcat+orig ++ processing all 464640 voxels in dataset ++ Procesing time series with NEW model fit algorithm ++ smash edit thresholds: 3.1 .. 5.0 MADs + [ 3.457% .. 0.072% of normal distribution] + [ 8.839% .. 3.125% of Laplace distribution] ++ start OpenMP thread #8 ++ start OpenMP thread #3 ++ start OpenMP thread #11 ++ start OpenMP thread #14 ++ start OpenMP thread #9 ++ start OpenMP thread #5 ++ start OpenMP thread #1 ++ start OpenMP thread #13 ++ start OpenMP thread #7 ++ start OpenMP thread #10 ++ start OpenMP thread #0 ++ start OpenMP thread #4 ++ start OpenMP thread #12 ++ start OpenMP thread #2 ++ start OpenMP thread #6 ...................................................................................................................................................................................................... ++ Elapsed despike time = 4s 23ms ++ FINAL: 213692688 data points, 21141343 edits [9.893%], 14031057 big edits [6.566%] ++ Output dataset ./pb01.SM327_all4runs.r01.e10.despike+orig.BRIK end 3dDespike -NEW -nomask -prefix pb01.SM327_all4runs.r01.e11.despike pb00.SM327_all4runs.r01.e11.tcat+orig ++ 3dDespike: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.SM327_all4runs.r01.e11.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.SM327_all4runs.r01.e11.tcat+orig.BRIK is 7.042221 degrees from plumb. ++ Input dataset is in short format, but output will be in float format ++ ignoring first 0 time points, using last 466 ++ using 466 time points => -corder 16 ++ Loading dataset pb00.SM327_all4runs.r01.e11.tcat+orig ++ processing all 464640 voxels in dataset ++ Procesing time series with NEW model fit algorithm ++ smash edit thresholds: 3.1 .. 5.0 MADs + [ 3.457% .. 0.072% of normal distribution] + [ 8.839% .. 3.125% of Laplace distribution] ++ start OpenMP thread #0 ++ start OpenMP thread #12 ++ start OpenMP thread #6 ++ start OpenMP thread #14 ++ start OpenMP thread #10 ++ start OpenMP thread #4 ++ start OpenMP thread #7 ++ start OpenMP thread #1 ++ start OpenMP thread #11 ++ start OpenMP thread #2 ++ start OpenMP thread #3 ++ start OpenMP thread #13 ++ start OpenMP thread #8 ++ start OpenMP thread #5 ++ start OpenMP thread #9 ...................................................................................................................................................................................................... ++ Elapsed despike time = 4s 31ms ++ FINAL: 213692688 data points, 22337999 edits [10.453%], 16027032 big edits [7.500%] ++ Output dataset ./pb01.SM327_all4runs.r01.e11.despike+orig.BRIK end 3dDespike -NEW -nomask -prefix pb01.SM327_all4runs.r01.e12.despike pb00.SM327_all4runs.r01.e12.tcat+orig ++ 3dDespike: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.SM327_all4runs.r01.e12.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.SM327_all4runs.r01.e12.tcat+orig.BRIK is 7.042221 degrees from plumb. ++ Input dataset is in short format, but output will be in float format ++ ignoring first 0 time points, using last 466 ++ using 466 time points => -corder 16 ++ Loading dataset pb00.SM327_all4runs.r01.e12.tcat+orig ++ processing all 464640 voxels in dataset ++ Procesing time series with NEW model fit algorithm ++ smash edit thresholds: 3.1 .. 5.0 MADs + [ 3.457% .. 0.072% of normal distribution] + [ 8.839% .. 3.125% of Laplace distribution] ++ start OpenMP thread #0 ++ start OpenMP thread #1 ++ start OpenMP thread #10 ++ start OpenMP thread #14 ++ start OpenMP thread #11 ++ start OpenMP thread #6 ++ start OpenMP thread #5 ++ start OpenMP thread #3 ++ start OpenMP thread #8 ++ start OpenMP thread #2 ++ start OpenMP thread #7 ++ start OpenMP thread #12 ++ start OpenMP thread #9 ++ start OpenMP thread #4 ++ start OpenMP thread #13 ...................................................................................................................................................................................................... ++ Elapsed despike time = 4s 2ms ++ FINAL: 213692688 data points, 20591617 edits [9.636%], 14189788 big edits [6.640%] ++ Output dataset ./pb01.SM327_all4runs.r01.e12.despike+orig.BRIK end end foreach run ( 01 ) foreach eind ( 01 02 03 04 05 06 07 08 09 10 11 12 ) 3dTshift -tzero 0 -quintic -prefix pb02.SM327_all4runs.r01.e01.tshift pb01.SM327_all4runs.r01.e01.despike+orig ++ 3dTshift: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.SM327_all4runs.r01.e01.despike+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb01.SM327_all4runs.r01.e01.despike+orig.BRIK is 7.042221 degrees from plumb. ++ updating time offset to 0 end 3dTshift -tzero 0 -quintic -prefix pb02.SM327_all4runs.r01.e02.tshift pb01.SM327_all4runs.r01.e02.despike+orig ++ 3dTshift: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.SM327_all4runs.r01.e02.despike+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb01.SM327_all4runs.r01.e02.despike+orig.BRIK is 7.042221 degrees from plumb. ++ updating time offset to 0 end 3dTshift -tzero 0 -quintic -prefix pb02.SM327_all4runs.r01.e03.tshift pb01.SM327_all4runs.r01.e03.despike+orig ++ 3dTshift: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.SM327_all4runs.r01.e03.despike+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb01.SM327_all4runs.r01.e03.despike+orig.BRIK is 7.042221 degrees from plumb. ++ updating time offset to 0 end 3dTshift -tzero 0 -quintic -prefix pb02.SM327_all4runs.r01.e04.tshift pb01.SM327_all4runs.r01.e04.despike+orig ++ 3dTshift: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.SM327_all4runs.r01.e04.despike+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb01.SM327_all4runs.r01.e04.despike+orig.BRIK is 7.042221 degrees from plumb. ++ updating time offset to 0 end 3dTshift -tzero 0 -quintic -prefix pb02.SM327_all4runs.r01.e05.tshift pb01.SM327_all4runs.r01.e05.despike+orig ++ 3dTshift: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.SM327_all4runs.r01.e05.despike+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb01.SM327_all4runs.r01.e05.despike+orig.BRIK is 7.042221 degrees from plumb. ++ updating time offset to 0 end 3dTshift -tzero 0 -quintic -prefix pb02.SM327_all4runs.r01.e06.tshift pb01.SM327_all4runs.r01.e06.despike+orig ++ 3dTshift: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.SM327_all4runs.r01.e06.despike+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb01.SM327_all4runs.r01.e06.despike+orig.BRIK is 7.042221 degrees from plumb. ++ updating time offset to 0 end 3dTshift -tzero 0 -quintic -prefix pb02.SM327_all4runs.r01.e07.tshift pb01.SM327_all4runs.r01.e07.despike+orig ++ 3dTshift: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.SM327_all4runs.r01.e07.despike+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb01.SM327_all4runs.r01.e07.despike+orig.BRIK is 7.042221 degrees from plumb. ++ updating time offset to 0 end 3dTshift -tzero 0 -quintic -prefix pb02.SM327_all4runs.r01.e08.tshift pb01.SM327_all4runs.r01.e08.despike+orig ++ 3dTshift: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.SM327_all4runs.r01.e08.despike+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb01.SM327_all4runs.r01.e08.despike+orig.BRIK is 7.042221 degrees from plumb. ++ updating time offset to 0 end 3dTshift -tzero 0 -quintic -prefix pb02.SM327_all4runs.r01.e09.tshift pb01.SM327_all4runs.r01.e09.despike+orig ++ 3dTshift: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.SM327_all4runs.r01.e09.despike+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb01.SM327_all4runs.r01.e09.despike+orig.BRIK is 7.042221 degrees from plumb. ++ updating time offset to 0 end 3dTshift -tzero 0 -quintic -prefix pb02.SM327_all4runs.r01.e10.tshift pb01.SM327_all4runs.r01.e10.despike+orig ++ 3dTshift: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.SM327_all4runs.r01.e10.despike+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb01.SM327_all4runs.r01.e10.despike+orig.BRIK is 7.042221 degrees from plumb. ++ updating time offset to 0 end 3dTshift -tzero 0 -quintic -prefix pb02.SM327_all4runs.r01.e11.tshift pb01.SM327_all4runs.r01.e11.despike+orig ++ 3dTshift: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.SM327_all4runs.r01.e11.despike+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb01.SM327_all4runs.r01.e11.despike+orig.BRIK is 7.042221 degrees from plumb. ++ updating time offset to 0 end 3dTshift -tzero 0 -quintic -prefix pb02.SM327_all4runs.r01.e12.tshift pb01.SM327_all4runs.r01.e12.despike+orig ++ 3dTshift: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.SM327_all4runs.r01.e12.despike+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb01.SM327_all4runs.r01.e12.despike+orig.BRIK is 7.042221 degrees from plumb. ++ updating time offset to 0 end end 3dbucket -prefix vr_base_min_outlier pb02.SM327_all4runs.r01.e02.tshift+orig[108] ++ 3dbucket: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] align_epi_anat.py -anat2epi -anat anatSS.T1W+orig -suffix _al_junk -epi vr_base_min_outlier+orig -epi_base 0 -epi_strip 3dAutomask -anat_has_skull no -giant_move -volreg off -tshift off #++ align_epi_anat version: 1.63 #++ 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 ./anatSS.T1W+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_anatSS.T1W* #Script is running (command trimmed): 3dcopy ./anatSS.T1W+orig ./__tt_anatSS.T1W+orig ++ 3dcopy: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] #Script is running (command trimmed): 3dinfo ./__tt_anatSS.T1W+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique' #++ Dataset /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/__tt_anatSS.T1W+orig is not oblique #Script is running (command trimmed): 3dinfo ./vr_base_min_outlier+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique' #++ Dataset /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/vr_base_min_outlier+orig is ***oblique**** #Script is running (command trimmed): 3dAttribute DELTA ./__tt_anatSS.T1W+orig #++ Spacing for anat to oblique epi alignment is 0.937513 #++ Matching obliquity of anat to epi #Script is running (command trimmed): 3dWarp -verb -card2oblique ./vr_base_min_outlier+orig -prefix ./__tt_anatSS.T1W_ob -newgrid 0.937513 ./__tt_anatSS.T1W+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./__tt_anatSS.T1W_obla2e_mat.1D ++ 3dWarp: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: RW Cox #++ using 0th sub-brick because only one found #Script is running (command trimmed): 3dbucket -prefix ./__tt_vr_base_min_outlier_ts ./vr_base_min_outlier+orig'[0]' ++ 3dbucket: AFNI version=AFNI_23.0.01 (Jan 18 2023) [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_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Emperor Zhark *+ 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 7.042221 degrees from plumb. ++ Loading dataset ./__tt_vr_base_min_outlier_ts+orig ++ Forming automask + Fixed clip level = 2040.955566 + Used gradual clip level = 1537.926880 .. 2294.705811 + Number voxels above clip level = 83627 + Clustering voxels ... + Largest cluster has 82272 voxels + Clustering voxels ... + Largest cluster has 78470 voxels + Filled 1002 voxels in small holes; now have 79472 voxels + Filled 10 voxels in large holes; now have 79482 voxels + Clustering voxels ... + Largest cluster has 79467 voxels + Clustering non-brain voxels ... + Clustering voxels ... + Largest cluster has 385125 voxels + Mask now has 79515 voxels ++ 79515 voxels in the mask [out of 464640: 17.11%] ++ first 18 x-planes are zero [from R] ++ last 16 x-planes are zero [from L] ++ first 13 y-planes are zero [from A] ++ last 9 y-planes are zero [from P] ++ first 0 z-planes are zero [from I] ++ last 3 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 6483.738281 on /home/taliw/data/Candies/SM327/afni/SM327_all4runs.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/6483.738281))' ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands #++ Aligning anat data to epi data #Script is running (command trimmed): 3dAllineate -lpc -wtprefix ./__tt_anatSS.T1W_ob_al_junk_wtal -weight ./__tt_vr_base_min_outlier_ts_ns_wt+orig -source ./__tt_anatSS.T1W_ob+orig -prefix ./__tt_anatSS.T1W_ob_temp_al_junk -base ./__tt_vr_base_min_outlier_ts_ns+orig -cmass -1Dmatrix_save ./anatSS.T1W_al_junk_e2a_only_mat.aff12.1D -master BASE -mast_dxyz 0.937513 -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_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./__tt_vr_base_min_outlier_ts_ns_wt+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_ns_wt+orig.BRIK is 7.042221 degrees from plumb. ++ Oblique dataset:./__tt_vr_base_min_outlier_ts_ns+orig.BRIK is 7.042221 degrees from plumb. ++ Option '-cmass' enables center-of-mass code = 7 = +xyz ++ Source dataset: ./__tt_anatSS.T1W_ob+orig.HEAD ++ Base dataset: ./__tt_vr_base_min_outlier_ts_ns+orig.HEAD ++ Loading datasets into memory ++ 1673389 voxels in -source_automask+2 ++ largeness ==> set -twobest 29 ++ Zero-pad: ybot=0 ytop=2 ++ Zero-pad: zbot=11 ztop=8 ++ 79514 voxels [12.7%] in weight mask ++ Number of points for matching = 79514 ++ Local correlation: blok type = 'TOHD(12.9425)' ++ base center of mass = 44.637 49.116 44.059 (index) + source center of mass = 87.690 165.681 163.907 (index) + source-target CM = 0.226 5.165 -5.764 (xyz) + estimated center of mass shifts = 0.226 5.165 -5.764 ++ shift param auto-range: -69.6..70.0 -66.3..76.6 -68.4..56.8 + 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] = -9.774185 .. 10.225815 center = 0.225815 + Range param#2 [y-shift] = -4.834969 .. 15.165031 center = 5.165031 + Range param#3 [z-shift] = -15.763626 .. 4.236374 center = -5.763626 + 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] = -39.774185 .. 40.225815 center = 0.225815 + Range param#2 [y-shift] = -34.834969 .. 45.165031 center = 5.165031 + Range param#3 [z-shift] = -45.763626 .. 34.236374 center = -5.763626 + 12 free parameters ++ Normalized (unitless) convergence radius = 0.0000088 ++ Final parameter search ranges: + x-shift = -39.774 .. 40.226 + y-shift = -34.835 .. 45.165 + z-shift = -45.764 .. 34.236 + 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 0.9375 mm ++ OpenMP thread count = 15 ++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed ======= + source mask has 1673389 [out of 15043392] voxels + base mask has 100501 [out of 625680] 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=2.50 + - Smoothing source; radius=2.50 + !source mask fill: ubot=112.297 usiz=488.908 + - copying weight image + - using 79514 points from base image [use_all=2] + * Exit alignment setup routine + - Search for coarse starting parameters + 68181 total points stored in 132 'TOHD(13.1817)' bloks (0 duplicates) + - number of free params = 6 + - Test (64+191)*64 params [top5=*o+-.]:#*[#1=-0.05437] **[#2=-0.0695303] *++..*[#10=-0.113345] *-+o+..$+.. + - best 88 costs found: o= 0 v=-0.113345: -6.44 11.83 0.90 -7.50 7.50 7.50 [grid] o= 1 v=-0.074378: -6.44 -1.50 0.90 -7.50 -7.50 7.50 [grid] o= 2 v=-0.072577: -18.27 11.02 8.83 -16.04 -3.33 12.13 [rand] o= 3 v=-0.072438: 6.89 11.83 0.90 7.50 7.50 -7.50 [grid] o= 4 v=-0.071607: 2.63 -8.93 4.17 -5.34 -3.42 -10.89 [rand] o= 5 v=-0.069589: -2.18 -8.93 4.17 5.34 -3.42 10.89 [rand] o= 6 v=-0.069530: -6.44 11.83 0.90 7.50 7.50 7.50 [grid] o= 7 v=-0.068049: -27.63 32.78 -15.58 -16.34 19.59 25.89 [rand] o= 8 v=-0.066233: -6.44 11.83 0.90 -7.50 7.50 -7.50 [grid] o= 9 v=-0.065499: 28.08 32.78 -15.58 16.34 19.59 -25.89 [rand] o=10 v=-0.064781: 2.63 19.26 4.17 5.34 3.42 -10.89 [rand] o=11 v=-0.064434: 29.18 -31.57 1.23 37.17 -30.77 -19.93 [rand] o=12 v=-0.063843: 18.72 11.02 8.83 16.04 -3.33 -12.13 [rand] o=13 v=-0.063593: -18.27 -0.69 8.83 -16.04 -3.33 12.13 [rand] o=14 v=-0.063371: -2.18 19.26 4.17 -5.34 3.42 -10.89 [rand] o=15 v=-0.063058: 2.63 19.26 4.17 -5.34 3.42 -10.89 [rand] o=16 v=-0.062240: -6.44 11.83 0.90 -30.00 7.50 -7.50 [grid] o=17 v=-0.061810: -8.52 42.44 -13.87 29.17 22.04 11.69 [rand] o=18 v=-0.061311: 26.89 -1.50 0.90 7.50 -7.50 -30.00 [grid] o=19 v=-0.061144: 6.89 11.83 0.90 -7.50 7.50 -7.50 [grid] o=20 v=-0.060972: 15.38 41.46 -21.98 13.02 24.31 -24.93 [rand] o=21 v=-0.060866: 6.89 -1.50 0.90 7.50 -7.50 -7.50 [grid] o=22 v=-0.060393: 18.72 11.02 8.83 16.04 3.33 -12.13 [rand] o=23 v=-0.060187: -18.27 11.02 8.83 -16.04 3.33 12.13 [rand] o=24 v=-0.059850: 27.08 -29.87 -12.32 42.20 -39.43 -22.96 [rand] o=25 v=-0.058423: 8.97 42.44 -13.87 29.17 22.04 -11.69 [rand] o=26 v=-0.057865: -18.11 31.31 -11.81 6.51 20.18 7.56 [rand] o=27 v=-0.057523: -26.44 11.83 0.90 -30.00 7.50 7.50 [grid] o=28 v=-0.057450: -6.44 31.83 -12.43 -7.50 30.00 -7.50 [grid] o=29 v=-0.056245: -3.91 29.29 -8.39 -26.16 25.44 -13.47 [rand] o=30 v=-0.056102: -6.44 31.83 0.90 -7.50 7.50 7.50 [grid] o=31 v=-0.056003: -27.63 32.78 -15.58 16.34 19.59 25.89 [rand] o=32 v=-0.055996: 6.89 -1.50 0.90 -7.50 -7.50 -7.50 [grid] o=33 v=-0.055925: -34.10 21.75 -14.37 16.34 8.64 40.54 [rand] o=34 v=-0.055298: -34.63 40.84 -20.01 40.22 24.26 41.52 [rand] o=35 v=-0.054994: -6.44 -1.50 0.90 7.50 -7.50 7.50 [grid] o=36 v=-0.054803: -3.36 41.37 -22.34 -36.12 41.59 -17.14 [rand] o=37 v=-0.054720: -18.11 31.31 -11.81 -6.51 20.18 7.56 [rand] o=38 v=-0.054487: 18.72 -0.69 8.83 16.04 -3.33 -12.13 [rand] o=39 v=-0.054370: 6.89 11.83 0.90 7.50 7.50 7.50 [grid] o=40 v=-0.054200: 2.67 1.46 15.22 -11.43 -3.92 -7.36 [rand] o=41 v=-0.053942: -3.91 29.29 -8.39 26.16 25.44 13.47 [rand] o=42 v=-0.053912: -2.22 1.46 15.22 -11.43 -3.92 -7.36 [rand] o=43 v=-0.053899: -36.65 24.26 4.89 -39.85 8.62 -5.87 [rand] o=44 v=-0.053382: -26.44 -1.50 0.90 -7.50 -7.50 30.00 [grid] o=45 v=-0.053310: 2.63 19.26 4.17 5.34 3.42 10.89 [rand] o=46 v=-0.053265: -6.44 -1.50 0.90 -30.00 -7.50 -7.50 [grid] o=47 v=-0.053232: -18.27 11.02 8.83 16.04 -3.33 12.13 [rand] o=48 v=-0.052877: -2.22 1.46 15.22 11.43 -3.92 7.36 [rand] o=49 v=-0.052749: 24.18 -26.27 -21.84 23.87 -39.87 -34.71 [rand] o=50 v=-0.052466: -19.26 -11.51 -3.16 30.54 -19.59 20.03 [rand] o=51 v=-0.052350: 11.52 -28.97 -11.74 4.11 -32.66 -25.74 [rand] o=52 v=-0.052295: 26.89 -21.50 0.90 -7.50 -7.50 -30.00 [grid] o=53 v=-0.052278: -36.32 42.89 -16.97 -5.37 -26.45 -20.44 [rand] o=54 v=-0.052102: 25.55 33.83 -29.75 42.33 22.93 -32.02 [rand] o=55 v=-0.052059: -31.96 40.32 -11.70 24.11 16.02 33.42 [rand] o=56 v=-0.052048: -33.60 34.67 -18.72 -31.95 9.87 34.85 [rand] o=57 v=-0.051997: 19.72 -11.51 -3.16 30.54 -19.59 -20.03 [rand] o=58 v=-0.051719: 31.80 -1.24 4.28 2.62 -10.20 -32.31 [rand] o=59 v=-0.051714: -2.22 8.87 15.22 -11.43 -3.92 -7.36 [rand] o=60 v=-0.051637: -34.97 39.86 -27.34 -18.41 40.28 -7.49 [rand] o=61 v=-0.051615: -28.73 41.90 -12.75 -37.17 30.77 19.93 [rand] o=62 v=-0.051481: -14.93 41.46 -21.98 13.02 24.31 24.93 [rand] o=63 v=-0.051341: 26.89 11.83 -12.43 7.50 -7.50 -30.00 [grid] o=64 v=-0.051214: -6.62 0.39 13.13 13.42 -4.00 14.01 [rand] o=65 v=-0.051183: 6.89 -21.50 0.90 7.50 -30.00 -7.50 [grid] o=66 v=-0.051176: -2.18 19.26 4.17 5.34 3.42 10.89 [rand] o=67 v=-0.051077: -18.11 31.31 0.28 -6.51 20.18 7.56 [rand] o=68 v=-0.051022: -34.97 39.86 15.81 -18.41 -40.28 -7.49 [rand] o=69 v=-0.050892: -2.18 19.26 4.17 5.34 -3.42 10.89 [rand] o=70 v=-0.050874: 17.75 -23.96 13.25 22.81 -23.42 -9.07 [rand] o=71 v=-0.050644: -6.44 -21.50 0.90 -7.50 -30.00 7.50 [grid] o=72 v=-0.050611: 10.55 -23.65 9.25 -30.67 -17.79 -20.52 [rand] o=73 v=-0.050579: -6.44 11.83 0.90 30.00 -7.50 7.50 [grid] o=74 v=-0.050371: 32.66 19.51 -11.36 8.22 9.03 -36.72 [rand] o=75 v=-0.050312: 7.07 9.94 13.13 -13.42 4.00 -14.01 [rand] o=76 v=-0.050188: -6.44 31.83 -12.43 -7.50 7.50 7.50 [grid] o=77 v=-0.050050: 8.97 42.44 -13.87 -29.17 22.04 -11.69 [rand] o=78 v=-0.049982: -8.52 42.44 2.34 29.17 22.04 11.69 [rand] o=79 v=-0.049901: -6.44 -21.50 0.90 30.00 -30.00 7.50 [grid] o=80 v=-0.049862: -35.38 0.75 31.11 -37.76 -24.22 -3.86 [rand] o=81 v=-0.049836: 18.72 11.02 8.83 -16.04 3.33 -12.13 [rand] o=82 v=-0.049734: 26.89 11.83 -12.43 30.00 -7.50 -30.00 [grid] o=83 v=-0.049647: -19.68 -21.62 10.64 -4.90 -12.23 16.79 [rand] o=84 v=-0.049496: -26.08 31.12 -23.56 15.82 17.65 37.25 [rand] o=85 v=-0.049405: -2.18 -8.93 4.17 -5.34 -3.42 -10.89 [rand] o=86 v=-0.049177: -26.44 -1.50 0.90 -30.00 -7.50 7.50 [grid] o=87 v=-0.049076: -3.91 29.29 -3.14 26.16 25.44 13.47 [rand] + - A little optimization:*[#16325=-0.126301] *[#16329=-0.130518] *[#16332=-0.13218] *[#16333=-0.138448] *[#16335=-0.139357] *[#16336=-0.157072] *[#16337=-0.186214] *[#16341=-0.194793] *[#16342=-0.197002] *[#16344=-0.210592] *[#16345=-0.234924] *[#16346=-0.259781] *[#16348=-0.267577] *[#16350=-0.28196] *[#16351=-0.287935] *[#16352=-0.303563] *[#16353=-0.33338] *[#16356=-0.347597] *[#16358=-0.36133] *[#16359=-0.371919] *[#16362=-0.388314] *[#16363=-0.399625] *[#16365=-0.402448] *[#16366=-0.413547] *[#16368=-0.414895] *[#16369=-0.420043] *[#16372=-0.434104] *[#16378=-0.434838] *[#16379=-0.436003] *[#16381=-0.436391] *[#16382=-0.436437] *[#16383=-0.437009] *[#16386=-0.437397] *[#16389=-0.437453] *[#16392=-0.437616] *[#16395=-0.437633] ...................................*[#18795=-0.437659] ..................................................... + - costs of the above after a little optimization: o= 0 v=-0.437633: -1.33 4.83 1.96 -0.57 2.20 1.02 [grid] [f=75] o= 1 v=-0.437166: -1.41 4.79 1.99 -0.61 2.12 1.15 [grid] [f=83] o= 2 v=-0.335910: -2.18 4.13 1.44 -1.62 2.65 3.20 [rand] [f=83] o= 3 v=-0.437181: -1.24 4.77 1.95 -0.54 2.18 0.84 [grid] [f=83] o= 4 v=-0.206206: 0.51 1.98 4.40 2.45 -2.55 1.39 [rand] [f=83] o= 5 v=-0.437133: -1.28 4.72 1.91 -0.57 2.21 0.95 [rand] [f=83] o= 6 v=-0.436628: -1.22 4.81 1.96 -0.43 2.15 0.81 [grid] [f=83] o= 7 v=-0.077078: -27.69 33.67 -12.84 -15.14 20.08 24.95 [rand] [f=63] o= 8 v=-0.436668: -1.48 4.75 2.02 -0.65 2.10 1.17 [grid] [f=83] o= 9 v=-0.079576: 27.53 32.08 -14.36 23.29 15.51 -27.18 [rand] [f=50] o=10 v=-0.108292: 2.40 19.63 0.57 1.60 6.13 -2.50 [rand] [f=83] o=11 v=-0.066881: 29.54 -31.96 0.42 36.34 -27.29 -20.55 [rand] [f=42] o=12 v=-0.078373: 13.06 10.39 10.07 13.99 -2.90 -11.01 [rand] [f=55] o=13 v=-0.095468: -16.53 4.11 7.12 -14.55 -4.16 5.62 [rand] [f=83] o=14 v=-0.122537: -2.42 15.23 1.15 -2.21 5.02 1.19 [rand] [f=83] o=15 v=-0.087713: 3.53 17.35 4.86 -0.21 5.07 -10.04 [rand] [f=46] o=16 v=-0.085675: -7.75 15.09 -0.83 -25.97 5.59 -4.46 [grid] [f=83] o=17 v=-0.064931: -8.48 43.72 -13.68 28.96 21.94 11.38 [rand] [f=33] o=18 v=-0.069632: 24.16 -1.96 1.13 7.38 -9.39 -30.11 [grid] [f=77] o=19 v=-0.088613: 10.67 11.31 1.56 -7.96 5.00 -6.22 [grid] [f=57] o=20 v=-0.081742: 16.59 41.42 -18.75 15.13 25.94 -21.70 [rand] [f=47] o=21 v=-0.437083: -1.32 4.69 2.02 -0.57 2.08 0.97 [grid] [f=83] o=22 v=-0.081606: 18.72 10.27 5.76 12.41 1.34 -13.04 [rand] [f=72] o=23 v=-0.346935: -2.13 6.16 1.90 -2.30 2.75 0.83 [rand] [f=83] o=24 v=-0.072550: 26.54 -31.92 -5.48 43.11 -39.06 -20.05 [rand] [f=79] o=25 v=-0.070962: 9.82 35.81 -16.54 24.01 23.30 -12.72 [rand] [f=59] o=26 v=-0.086005: -15.92 37.43 -11.01 4.94 21.62 11.27 [rand] [f=43] o=27 v=-0.089357: -20.81 12.22 1.57 -27.56 4.41 7.51 [grid] [f=54] o=28 v=-0.111963: -4.71 37.70 -15.18 -6.27 25.01 1.11 [grid] [f=80] o=29 v=-0.072517: -2.29 33.88 -9.37 -28.76 24.39 -12.82 [rand] [f=53] o=30 v=-0.110632: -7.02 29.91 -7.30 -8.21 16.37 3.15 [grid] [f=68] o=31 v=-0.067085: -27.73 37.39 -15.50 15.34 20.25 26.25 [rand] [f=57] o=32 v=-0.393819: -1.00 3.59 2.09 -0.02 0.83 0.39 [grid] [f=83] o=33 v=-0.068675: -36.31 23.02 -16.35 15.32 7.69 35.47 [rand] [f=52] o=34 v=-0.071099: -35.98 42.46 -19.28 42.33 27.79 41.70 [rand] [f=53] *o=35 v=-0.437659: -1.34 4.78 1.97 -0.57 2.15 1.00 [grid] [f=68] o=36 v=-0.061721: -4.68 42.29 -22.73 -32.38 41.70 -16.89 [rand] [f=32] o=37 v=-0.087556: -18.91 34.13 -9.21 0.29 19.60 18.09 [rand] [f=83] o=38 v=-0.079304: 17.70 -0.87 6.83 14.41 -4.88 -8.66 [rand] [f=56] o=39 v=-0.437507: -1.38 4.81 1.97 -0.61 2.19 1.00 [grid] [f=83] o=40 v=-0.433891: -1.18 4.52 2.02 -0.26 2.07 0.87 [rand] [f=83] o=41 v=-0.074072: -4.88 35.98 -9.04 16.09 21.22 8.45 [rand] [f=53] o=42 v=-0.065205: -1.74 6.46 16.33 -10.80 -3.21 -6.07 [rand] [f=54] o=43 v=-0.064492: -36.52 24.32 5.17 -39.67 8.77 -1.30 [rand] [f=33] o=44 v=-0.057700: -25.31 -1.13 0.27 -8.26 -6.42 28.52 [grid] [f=62] o=45 v=-0.104340: 4.50 17.68 -1.61 6.12 8.73 -1.44 [rand] [f=83] o=46 v=-0.068916: -6.25 0.79 7.77 -29.83 -4.71 -5.76 [grid] [f=83] o=47 v=-0.068205: -16.06 12.46 6.25 17.15 -1.66 13.44 [rand] [f=74] o=48 v=-0.436766: -1.31 4.75 1.95 -0.62 2.01 0.99 [rand] [f=83] o=49 v=-0.060272: 22.70 -26.21 -15.45 25.89 -39.88 -32.78 [rand] [f=43] o=50 v=-0.060599: -24.45 -11.40 -2.73 32.38 -19.77 21.59 [rand] [f=69] o=51 v=-0.059952: 11.65 -24.85 -12.44 6.00 -31.48 -24.84 [rand] [f=73] o=52 v=-0.054898: 26.62 -20.56 0.70 -7.00 -6.54 -29.86 [grid] [f=45] o=53 v=-0.057850: -36.19 42.61 -18.95 -7.59 -28.52 -17.81 [rand] [f=47] o=54 v=-0.070345: 23.44 39.24 -28.22 44.82 22.12 -29.81 [rand] [f=50] o=55 v=-0.064893: -33.72 35.60 -17.18 21.47 18.31 35.52 [rand] [f=54] o=56 v=-0.065744: -34.60 30.88 -19.20 -32.26 9.81 38.20 [rand] [f=60] o=57 v=-0.061123: 16.26 -10.76 -2.87 28.40 -17.85 -22.69 [rand] [f=54] o=58 v=-0.072984: 27.79 -6.58 -0.77 4.05 -10.50 -33.65 [rand] [f=64] o=59 v=-0.072898: -1.66 8.79 14.98 -4.49 -2.18 -4.45 [rand] [f=47] o=60 v=-0.065764: -37.25 40.94 -28.25 -13.02 38.31 -5.70 [rand] [f=50] o=61 v=-0.069547: -27.34 39.30 -15.46 -33.57 27.13 19.68 [rand] [f=83] o=62 v=-0.069859: -22.74 40.99 -19.09 12.63 24.33 21.31 [rand] [f=47] o=63 v=-0.070867: 29.59 12.71 -6.58 7.94 -4.07 -32.75 [grid] [f=83] o=64 v=-0.102330: -9.07 -6.61 5.89 -1.92 -8.37 11.60 [rand] [f=83] o=65 v=-0.061683: 5.35 -21.59 -0.01 13.99 -32.60 -6.48 [grid] [f=66] o=66 v=-0.437092: -1.40 4.87 1.94 -0.69 2.26 1.06 [rand] [f=83] o=67 v=-0.107835: -8.87 26.69 -5.35 -9.01 13.23 4.77 [rand] [f=83] o=68 v=-0.053996: -34.62 39.83 14.31 -18.62 -36.34 -7.84 [rand] [f=41] o=69 v=-0.057358: -2.43 19.47 1.29 1.23 -4.06 8.96 [rand] [f=50] o=70 v=-0.057856: 19.96 -28.71 14.56 20.16 -27.01 -10.98 [rand] [f=83] o=71 v=-0.091047: -0.38 -18.15 8.69 1.96 -18.36 1.35 [grid] [f=77] o=72 v=-0.053401: 11.67 -23.42 9.83 -31.67 -18.76 -21.07 [rand] [f=48] o=73 v=-0.065696: -6.75 9.64 -1.09 27.54 -3.25 3.60 [grid] [f=55] o=74 v=-0.080271: 37.77 20.98 -9.63 7.62 8.11 -36.70 [rand] [f=58] o=75 v=-0.057847: 8.98 14.16 11.82 -12.25 3.83 -15.08 [rand] [f=71] o=76 v=-0.116384: -2.10 35.78 -12.13 -3.06 21.87 -0.39 [grid] [f=83] o=77 v=-0.059814: 8.25 37.40 -16.64 -32.19 22.03 -11.36 [rand] [f=72] o=78 v=-0.056388: -6.35 41.05 0.67 30.95 20.87 11.25 [rand] [f=64] o=79 v=-0.057833: -3.93 -21.03 -2.40 31.67 -31.78 8.49 [grid] [f=48] o=80 v=-0.058826: -34.75 -6.28 27.87 -40.69 -29.77 -3.51 [rand] [f=53] o=81 v=-0.088490: 11.85 11.23 0.95 -10.47 3.29 -7.12 [rand] [f=70] o=82 v=-0.064660: 27.26 10.95 -9.85 34.74 -4.54 -28.65 [grid] [f=55] o=83 v=-0.076531: -18.13 -15.20 8.58 -9.70 -16.84 13.15 [rand] [f=74] o=84 v=-0.057806: -30.24 30.81 -22.86 15.73 16.32 33.77 [rand] [f=62] o=85 v=-0.219138: -0.94 1.82 4.14 -0.96 -0.91 -1.37 [rand] [f=83] o=86 v=-0.076534: -23.73 -4.65 6.86 -32.99 -7.77 7.60 [grid] [f=62] o=87 v=-0.063956: -4.23 33.95 -5.83 25.61 22.54 11.58 [rand] [f=47] + - saving #35 for use with twobest + - skip # 0 for twobest: too close to set #35 + - skip #39 for twobest: too close to set #35 + - skip # 3 for twobest: too close to set #35 + - skip # 1 for twobest: too close to set #35 + - skip # 5 for twobest: too close to set #35 + - skip #66 for twobest: too close to set #35 + - skip #21 for twobest: too close to set #35 + - skip #48 for twobest: too close to set #35 + - skip # 8 for twobest: too close to set #35 + - skip # 6 for twobest: too close to set #35 + - skip #40 for twobest: too close to set #35 + - skip #32 for twobest: too close to set #35 + - skip #23 for twobest: too close to set #35 + - skip # 2 for twobest: too close to set #35 + - skip #85 for twobest: too close to set #35 + - skip # 4 for twobest: too close to set #32 + - saving #14 for use with twobest + - saving #76 for use with twobest + - skip #28 for twobest: too close to set #76 + - saving #30 for use with twobest + - saving #10 for use with twobest + - skip #67 for twobest: too close to set #30 + - saving #45 for use with twobest + - saving #64 for use with twobest + - saving #13 for use with twobest + - saving #71 for use with twobest + - saving #27 for use with twobest + - saving #19 for use with twobest + - skip #81 for twobest: too close to set #19 + - saving #15 for use with twobest + - saving #37 for use with twobest + - saving #26 for use with twobest + - saving #16 for use with twobest + - saving #20 for use with twobest + - saving #22 for use with twobest + - saving #74 for use with twobest + - saving # 9 for use with twobest + - saving #38 for use with twobest + - saving #12 for use with twobest + - saving # 7 for use with twobest + - saving #86 for use with twobest + - saving #83 for use with twobest + - saving #41 for use with twobest + - saving #58 for use with twobest + - saving #59 for use with twobest + - saving #24 for use with twobest + - saving #29 for use with twobest + - Coarse startup search net CPU time = 0.0 s ++ Start refinement #1 on 30 coarse parameter sets + * Enter alignment setup routine + - Smoothing base; radius=1.94 + - Smoothing source; radius=1.94 + !source mask fill: ubot=112.297 usiz=488.908 + - retaining old weight image + - using 79514 points from base image [use_all=2] + * Exit alignment setup routine + 68715 total points stored in 136 'TOHD(13.0877)' bloks (0 duplicates) *[#22156=-0.453765] *[#22187=-0.453952] *[#22189=-0.453992] *[#22196=-0.454158] *[#22198=-0.454219] *[#22201=-0.454302] *[#22202=-0.454532] *[#22203=-0.454566] *[#22204=-0.454736] *[#22205=-0.454909] *[#22208=-0.45498] *[#22209=-0.454988] *[#22211=-0.45503] *[#22212=-0.455081] *[#22213=-0.455147] *[#22214=-0.455268] *[#22215=-0.455358] *[#22216=-0.455573] *[#22219=-0.455726] *[#22220=-0.455833] *[#22223=-0.455991] *[#22225=-0.456031] *[#22228=-0.45617] *[#22229=-0.456336] *[#22231=-0.45647] *[#22233=-0.456597] *[#22234=-0.456669] *[#22237=-0.456758] *[#22238=-0.456834] *[#22239=-0.457034] *[#22240=-0.457113] *[#22242=-0.457181] *[#22243=-0.457181] *[#22245=-0.45745] *[#22246=-0.457463] *[#22247=-0.457642] *[#22248=-0.45768] *[#22252=-0.457695] *[#22253=-0.457751] *[#22254=-0.457998] + - param set #1 has cost=-0.457998 [o=35 t=0] + -- Parameters = -1.1333 4.5622 1.9050 -0.4349 1.9157 0.7413 1.0015 0.9967 1.0012 0.0002 0.0015 -0.0053 *[#22332=-0.458771] *[#22343=-0.459429] *[#22346=-0.45947] *[#22347=-0.459662] *[#22350=-0.45992] *[#22353=-0.460228] *[#22354=-0.460277] + - param set #2 has cost=-0.460277 [o=14 t=1] + -- Parameters = -0.9735 4.3473 1.7913 -0.4498 1.5708 0.4245 0.9961 0.9931 0.9980 -0.0006 0.0130 -0.0128 + - param set #3 has cost=-0.105345 [o=76 t=2] + -- Parameters = -1.6628 35.4633 -12.0856 -2.9916 21.7933 -0.3471 0.9986 0.9932 1.0030 -0.0002 -0.0018 -0.0000 + - param set #4 has cost=-0.102444 [o=30 t=3] + -- Parameters = -6.3299 30.2512 -8.0414 -8.0225 17.3057 2.8960 1.0118 0.9954 1.0032 0.0107 -0.0005 0.0008 + - param set #5 has cost=-0.389857 [o=10 t=4] + -- Parameters = -0.2894 5.7495 3.1831 0.1642 3.1116 -0.2403 1.0403 1.0294 1.0227 0.0242 0.0193 0.0265 + - param set #6 has cost=-0.200047 [o=45 t=5] + -- Parameters = -0.1510 11.5132 -0.9610 0.5680 4.6999 0.1893 1.0243 1.1103 0.9380 -0.0004 -0.0200 0.0064 + - param set #7 has cost=-0.116422 [o=64 t=6] + -- Parameters = -8.3334 -4.2981 5.1672 -2.5085 -7.3779 10.1070 1.0179 1.0408 1.0066 0.0021 -0.0019 -0.0067 + - param set #8 has cost=-0.112753 [o=13 t=7] + -- Parameters = -12.7059 7.5386 4.3427 -11.3067 -0.2939 6.7280 1.0438 1.0233 1.0158 0.0114 0.0328 -0.0108 + - param set #9 has cost=-0.098436 [o=71 t=8] + -- Parameters = -0.8598 -17.4257 9.8111 0.1990 -18.4779 1.1238 1.0684 1.0101 1.0112 0.0027 -0.0045 -0.0051 + - param set #10 has cost=-0.090147 [o=27 t=9] + -- Parameters = -19.0365 12.8885 1.0083 -20.0909 4.7023 8.1171 1.0142 1.0157 1.0088 0.0026 -0.0052 -0.0066 + - param set #11 has cost=-0.080887 [o=19 t=10] + -- Parameters = 10.5108 10.7851 1.1170 -8.2234 4.4151 -6.0218 1.0057 1.0397 1.0055 -0.0008 -0.0004 -0.0002 + - param set #12 has cost=-0.080809 [o=15 t=11] + -- Parameters = 3.6820 17.5936 3.8144 -0.6683 5.2278 -9.9206 1.0137 1.0402 0.9929 0.0015 -0.0003 -0.0015 + - param set #13 has cost=-0.080150 [o=37 t=12] + -- Parameters = -19.0638 34.7184 -9.4944 0.4763 19.9822 17.5713 0.9986 0.9911 1.0422 -0.0032 0.0005 0.0036 + - param set #14 has cost=-0.080872 [o=26 t=13] + -- Parameters = -15.7393 36.7170 -10.6411 0.2478 21.3085 11.8213 1.0073 1.0033 1.0035 0.0021 0.0019 -0.0006 + - param set #15 has cost=-0.080191 [o=16 t=14] + -- Parameters = -8.1431 14.4617 -0.6699 -25.7139 4.0744 -3.0795 1.0113 0.9960 1.0058 0.0026 0.0027 -0.0047 + - param set #16 has cost=-0.083424 [o=20 t=15] + -- Parameters = 16.1833 41.5221 -19.2208 15.3322 26.9033 -14.3943 0.9992 1.0129 0.9908 -0.0015 0.0046 0.0008 + - param set #17 has cost=-0.082284 [o=22 t=16] + -- Parameters = 17.8615 12.3604 5.0197 12.7276 3.2033 -11.5883 0.9486 1.0012 0.9918 0.0116 0.0067 -0.0086 + - param set #18 has cost=-0.071387 [o=74 t=17] + -- Parameters = 37.9301 21.6170 -9.6120 7.6578 8.4395 -36.7973 1.0078 1.0341 1.0006 0.0002 -0.0020 0.0017 + - param set #19 has cost=-0.073912 [o=9 t=18] + -- Parameters = 28.2405 32.4896 -15.1500 22.5558 16.2411 -26.4534 1.0697 1.0108 0.9797 -0.0033 -0.0025 -0.0008 + - param set #20 has cost=-0.080758 [o=38 t=19] + -- Parameters = 16.1802 -1.1908 5.5826 13.2260 -3.9234 -8.2839 0.9973 1.0390 1.0028 0.0017 0.0044 0.0039 + - param set #21 has cost=-0.079601 [o=12 t=20] + -- Parameters = 11.0145 9.2534 6.4919 12.6437 -3.4753 -9.0684 1.0149 0.9985 0.9428 0.0016 -0.0101 -0.0125 + - param set #22 has cost=-0.079647 [o=7 t=21] + -- Parameters = -27.6918 33.1757 -13.6036 -13.6877 21.2409 25.1745 1.0733 1.0065 1.0197 0.0022 0.0023 0.0024 + - param set #23 has cost=-0.076681 [o=86 t=22] + -- Parameters = -23.8057 1.8641 6.0355 -33.5297 -5.4608 7.8221 0.9920 0.9969 1.0122 0.0049 0.0016 -0.0077 + - param set #24 has cost=-0.094539 [o=83 t=23] + -- Parameters = -11.4848 -10.9982 8.4956 -4.0186 -12.4320 9.4436 1.0935 0.9895 0.9975 -0.0051 0.0001 0.0146 + - param set #25 has cost=-0.066671 [o=41 t=24] + -- Parameters = -4.7313 36.0131 -9.0148 16.1328 21.2584 8.3856 0.9981 0.9993 0.9971 0.0001 0.0016 0.0010 + - param set #26 has cost=-0.079326 [o=58 t=25] + -- Parameters = 28.5206 -4.3089 0.2487 6.1260 -9.7494 -29.2504 1.0385 1.0976 1.0112 -0.0017 -0.0127 0.0071 + - param set #27 has cost=-0.435936 [o=59 t=26] + -- Parameters = -1.0382 4.9008 2.5904 -0.4508 2.4094 0.7114 1.0203 1.0051 1.0149 0.0037 0.0025 0.0056 + - param set #28 has cost=-0.065198 [o=24 t=27] + -- Parameters = 26.4371 -32.0389 -6.0281 43.0458 -39.3623 -19.9939 0.9989 1.0019 0.9944 -0.0015 -0.0036 -0.0016 + - param set #29 has cost=-0.063427 [o=29 t=28] + -- Parameters = -2.8984 34.4447 -9.7092 -29.4308 24.3405 -12.4366 0.9972 1.0066 1.0011 0.0116 -0.0009 -0.0003 + - param set #30 has cost=-0.444357 [o=-1 t=-1] + -- Parameters = -1.2155 4.5896 2.8155 -0.4407 1.7860 1.0249 1.0024 0.9956 1.0219 0.0009 0.0000 -0.0000 + - sorting parameter sets by cost + - scanning for distances from #1 + --- dist(#2,#1) = 0.0515 + --- dist(#3,#1) = 0.0581 + --- dist(#4,#1) = 0.0828 + --- dist(#5,#1) = 0.177 + --- dist(#6,#1) = 0.169 + --- dist(#7,#1) = 0.108 + --- dist(#8,#1) = 0.147 + --- dist(#9,#1) = 0.389 + --- dist(#10,#1) = 0.324 + --- dist(#11,#1) = 0.272 + --- dist(#12,#1) = 0.192 + --- dist(#13,#1) = 0.226 + --- dist(#14,#1) = 0.465 + --- dist(#15,#1) = 0.235 + --- dist(#16,#1) = 0.144 + --- dist(#17,#1) = 0.405 + --- dist(#18,#1) = 0.166 + --- dist(#19,#1) = 0.214 + --- dist(#20,#1) = 0.281 + --- dist(#21,#1) = 0.38 + --- dist(#22,#1) = 0.36 + --- dist(#23,#1) = 0.15 + --- dist(#24,#1) = 0.369 + --- dist(#25,#1) = 0.368 + --- dist(#26,#1) = 0.365 + --- dist(#27,#1) = 0.486 + --- dist(#28,#1) = 0.396 + --- dist(#29,#1) = 0.483 + --- dist(#30,#1) = 0.376 ++ Start refinement #2 on 30 coarse parameter sets + * Enter alignment setup routine + - Smoothing base; radius=1.51 + - Smoothing source; radius=1.51 + !source mask fill: ubot=112.297 usiz=488.908 + - retaining old weight image + - using 79514 points from base image [use_all=2] + * Exit alignment setup routine + 68727 total points stored in 138 'TOHD(13.0305)' bloks (0 duplicates) *[#25156=-0.467165] *[#25187=-0.468324] *[#25191=-0.468389] *[#25196=-0.468925] *[#25197=-0.469275] *[#25212=-0.469409] *[#25215=-0.469648] *[#25221=-0.469721] *[#25222=-0.46973] *[#25224=-0.469767] *[#25226=-0.469784] *[#25227=-0.469835] *[#25229=-0.469895] *[#25230=-0.46995] *[#25231=-0.470049] *[#25232=-0.470203] *[#25233=-0.470325] *[#25240=-0.470369] *[#25245=-0.4704] *[#25247=-0.47052] *[#25248=-0.470556] *[#25249=-0.470589] *[#25250=-0.47068] *[#25251=-0.470783] *[#25252=-0.470832] *[#25255=-0.471021] *[#25256=-0.47113] *[#25257=-0.471181] *[#25259=-0.471215] *[#25260=-0.471314] *[#25262=-0.471337] *[#25265=-0.471384] + - param set #1 has cost=-0.471384 [o=14 t=1] + -- Parameters = -1.0293 4.2232 1.7741 -0.4048 1.5794 0.5984 1.0023 0.9896 0.9986 0.0001 0.0078 -0.0148 + - param set #2 has cost=-0.470775 [o=35 t=0] + -- Parameters = -1.0599 4.3202 1.7810 -0.4654 1.6754 0.7233 1.0009 0.9922 0.9993 -0.0009 0.0025 -0.0123 + - param set #3 has cost=-0.465842 [o=-1 t=-1] + -- Parameters = -1.1762 4.5294 1.8562 -0.5441 1.9893 0.8072 1.0041 0.9955 0.9991 -0.0023 0.0039 -0.0041 + - param set #4 has cost=-0.458273 [o=59 t=26] + -- Parameters = -1.1177 4.8397 2.0705 -0.4371 2.4043 0.7050 1.0006 0.9983 1.0043 0.0021 0.0028 0.0057 + - param set #5 has cost=-0.438640 [o=10 t=4] + -- Parameters = -0.6458 4.7913 2.7534 0.0419 2.4815 0.0775 1.0064 0.9914 1.0148 0.0189 0.0177 0.0096 + - param set #6 has cost=-0.406657 [o=45 t=5] + -- Parameters = -1.6815 5.0602 0.4425 -0.6885 2.8437 1.3127 0.9983 1.0035 0.9627 -0.0020 -0.0110 0.0129 + - param set #7 has cost=-0.271353 [o=64 t=6] + -- Parameters = -3.0325 2.3415 3.3859 -0.8857 -1.1241 3.5410 1.0728 1.0648 1.0303 0.0314 -0.0461 -0.0334 + - param set #8 has cost=-0.234686 [o=13 t=7] + -- Parameters = -1.8754 4.8532 3.0900 -1.1903 -1.7322 1.8042 1.0499 1.0867 0.9989 0.0265 0.0022 -0.0254 + - param set #9 has cost=-0.093319 [o=76 t=2] + -- Parameters = -1.6128 35.3205 -11.9386 -3.2489 21.6615 0.0111 1.0059 0.9916 1.0051 -0.0027 -0.0036 -0.0017 + - param set #10 has cost=-0.092174 [o=30 t=3] + -- Parameters = -5.5873 30.2600 -7.8262 -7.3577 17.1974 2.5768 1.0264 0.9900 1.0107 0.0095 -0.0009 0.0015 + - param set #11 has cost=-0.089805 [o=71 t=8] + -- Parameters = -0.9870 -17.6486 9.6006 0.1620 -18.6452 1.3412 1.0721 1.0194 1.0058 0.0114 -0.0044 -0.0063 + - param set #12 has cost=-0.099813 [o=83 t=23] + -- Parameters = -10.3369 -8.7042 6.5171 -2.6674 -10.9364 10.0830 1.0500 1.0228 0.9917 -0.0015 0.0027 0.0001 + - param set #13 has cost=-0.087796 [o=27 t=9] + -- Parameters = -18.3068 15.9121 0.7166 -18.5538 5.3401 7.7584 1.0253 1.0141 1.0047 0.0028 -0.0018 -0.0089 + - param set #14 has cost=-0.076416 [o=20 t=15] + -- Parameters = 15.5843 42.2599 -19.9427 14.8331 27.7632 -13.8490 1.0004 1.0148 0.9785 -0.0045 0.0060 -0.0017 + - param set #15 has cost=-0.079520 [o=22 t=16] + -- Parameters = 18.0062 11.8177 5.2315 12.5774 2.9933 -11.4500 0.9360 0.9950 0.9944 0.0198 0.0037 -0.0105 + - param set #16 has cost=-0.077871 [o=19 t=10] + -- Parameters = 10.1117 9.9313 0.9570 -7.6783 3.7609 -5.8750 1.0096 1.0425 1.0163 -0.0022 -0.0024 -0.0019 + - param set #17 has cost=-0.074069 [o=26 t=13] + -- Parameters = -15.7105 36.5317 -10.6429 0.2508 21.2415 11.7527 1.0063 1.0038 1.0036 0.0013 0.0027 -0.0004 + - param set #18 has cost=-0.197255 [o=15 t=11] + -- Parameters = -1.8495 9.2513 -0.0800 -2.8562 3.1537 0.3154 1.0995 1.0906 0.9690 0.0069 0.0054 -0.0044 + - param set #19 has cost=-0.076171 [o=38 t=19] + -- Parameters = 16.0203 -0.9838 5.2075 12.9115 -3.6952 -7.7027 0.9912 1.0394 1.0050 -0.0033 0.0047 0.0120 + - param set #20 has cost=-0.073070 [o=16 t=14] + -- Parameters = -8.1352 14.3834 -0.7546 -25.7577 4.0122 -3.0882 1.0091 0.9947 1.0064 0.0032 0.0042 -0.0061 + - param set #21 has cost=-0.075672 [o=37 t=12] + -- Parameters = -19.3890 34.2360 -9.5276 0.0785 19.5644 17.5923 1.0056 0.9836 1.0489 -0.0037 0.0004 0.0037 + - param set #22 has cost=-0.072336 [o=7 t=21] + -- Parameters = -27.7405 33.2227 -13.6916 -13.3070 21.3135 25.0811 1.0740 1.0053 1.0167 0.0112 0.0019 0.0023 + - param set #23 has cost=-0.221190 [o=12 t=20] + -- Parameters = 3.0354 2.8127 0.8172 0.8129 0.3053 -4.0476 1.0472 1.0268 0.9781 0.0068 0.0108 -0.0080 + - param set #24 has cost=-0.073064 [o=58 t=25] + -- Parameters = 28.9910 -4.9476 -0.0312 6.0048 -9.8465 -29.7911 1.0407 1.0897 1.0068 -0.0024 -0.0147 0.0149 + - param set #25 has cost=-0.070116 [o=86 t=22] + -- Parameters = -22.3081 2.2864 5.8561 -32.4471 -4.5642 6.2117 0.9812 1.0039 1.0179 0.0208 0.0007 -0.0104 + - param set #26 has cost=-0.069655 [o=9 t=18] + -- Parameters = 28.5054 32.7630 -14.6715 22.1924 16.2250 -25.5240 1.0821 1.0099 0.9854 -0.0024 -0.0025 -0.0014 + - param set #27 has cost=-0.061165 [o=74 t=17] + -- Parameters = 37.5583 22.1500 -9.3939 7.6445 8.5726 -36.5929 1.0043 1.0429 1.0071 -0.0024 -0.0036 0.0052 + - param set #28 has cost=-0.063725 [o=41 t=24] + -- Parameters = -4.7373 35.6931 -8.9274 16.2007 21.0727 8.3361 0.9979 0.9919 1.0014 -0.0008 0.0024 0.0007 + - param set #29 has cost=-0.057688 [o=24 t=27] + -- Parameters = 26.4263 -31.8486 -6.0736 42.9220 -39.6906 -20.0196 0.9934 0.9975 0.9949 -0.0027 -0.0036 -0.0034 + - param set #30 has cost=-0.063660 [o=29 t=28] + -- Parameters = -1.9580 34.6972 -10.4985 -29.2312 24.2389 -9.5355 0.9667 1.0220 1.0158 0.0328 -0.0000 0.0059 + - sorting parameter sets by cost + - scanning for distances from #1 + --- dist(#2,#1) = 0.0241 + --- dist(#3,#1) = 0.0481 + --- dist(#4,#1) = 0.0925 + --- dist(#5,#1) = 0.11 + --- dist(#6,#1) = 0.125 + --- dist(#7,#1) = 0.243 + --- dist(#8,#1) = 0.14 + --- dist(#9,#1) = 0.0646 + --- dist(#10,#1) = 0.145 + --- dist(#11,#1) = 0.162 + --- dist(#12,#1) = 0.389 + --- dist(#13,#1) = 0.325 + --- dist(#14,#1) = 0.273 + --- dist(#15,#1) = 0.216 + --- dist(#16,#1) = 0.238 + --- dist(#17,#1) = 0.139 + --- dist(#18,#1) = 0.475 + --- dist(#19,#1) = 0.213 + --- dist(#20,#1) = 0.375 + --- dist(#21,#1) = 0.404 + --- dist(#22,#1) = 0.282 + --- dist(#23,#1) = 0.375 + --- dist(#24,#1) = 0.362 + --- dist(#25,#1) = 0.356 + --- dist(#26,#1) = 0.369 + --- dist(#27,#1) = 0.393 + --- dist(#28,#1) = 0.381 + --- dist(#29,#1) = 0.482 + --- dist(#30,#1) = 0.481 ++ Start refinement #3 on 30 coarse parameter sets + * Enter alignment setup routine + - Smoothing base; radius=1.18 + - Smoothing source; radius=1.18 + !source mask fill: ubot=112.297 usiz=488.908 + - retaining old weight image + - using 79514 points from base image [use_all=2] + * Exit alignment setup routine + 68161 total points stored in 136 'TOHD(12.9958)' bloks (0 duplicates) *[#28486=-0.473685] *[#28514=-0.473846] *[#28526=-0.473929] *[#28528=-0.474096] *[#28531=-0.474123] *[#28534=-0.474144] *[#28535=-0.474178] *[#28537=-0.474216] *[#28538=-0.474221] *[#28539=-0.474234] *[#28540=-0.474266] *[#28541=-0.474279] *[#28542=-0.474292] *[#28545=-0.474386] *[#28547=-0.474405] *[#28549=-0.474435] *[#28550=-0.474448] *[#28552=-0.474463] *[#28555=-0.474483] *[#28556=-0.474509] *[#28557=-0.474537] *[#28560=-0.474544] *[#28562=-0.474578] *[#28563=-0.474597] *[#28564=-0.474619] *[#28565=-0.474639] *[#28566=-0.474658] *[#28567=-0.474676] *[#28569=-0.474696] *[#28570=-0.474715] *[#28571=-0.47473] *[#28574=-0.474759] *[#28575=-0.474768] *[#28576=-0.474785] *[#28577=-0.474788] *[#28579=-0.474851] *[#28580=-0.474893] *[#28581=-0.474905] *[#28584=-0.474937] *[#28585=-0.474942] *[#28586=-0.474963] *[#28587=-0.474972] *[#28588=-0.474988] *[#28589=-0.475005] *[#28592=-0.475006] *[#28595=-0.475015] *[#28596=-0.475034] *[#28597=-0.475049] *[#28598=-0.47506] *[#28601=-0.475072] *[#28602=-0.475102] *[#28603=-0.475126] *[#28604=-0.475138] *[#28606=-0.475169] + - param set #1 has cost=-0.475169 [o=14 t=1] + -- Parameters = -1.0198 4.1484 1.6319 -0.4246 1.4965 0.6126 1.0039 0.9907 0.9954 0.0009 0.0048 -0.0171 + - param set #2 has cost=-0.475017 [o=35 t=0] + -- Parameters = -1.1588 4.1731 1.6291 -0.4881 1.5117 0.8350 1.0021 0.9911 0.9961 -0.0012 0.0012 -0.0166 + - param set #3 has cost=-0.472387 [o=-1 t=-1] + -- Parameters = -1.1103 4.2316 1.6838 -0.5199 1.6273 0.7970 0.9993 0.9889 0.9969 0.0011 -0.0026 -0.0127 + - param set #4 has cost=-0.466286 [o=59 t=26] + -- Parameters = -1.1289 4.5090 1.7201 -0.5241 2.0585 0.7386 1.0050 0.9951 0.9960 -0.0012 -0.0023 -0.0029 + - param set #5 has cost=-0.462084 [o=10 t=4] + -- Parameters = -0.7385 4.6031 1.7552 -0.3927 2.0694 0.1311 1.0054 0.9943 0.9970 0.0052 0.0190 -0.0043 + - param set #6 has cost=-0.464845 [o=45 t=5] + -- Parameters = -1.3555 4.4627 1.6585 -0.3667 1.8958 1.1329 1.0012 0.9939 0.9951 0.0069 -0.0116 -0.0065 + - param set #7 has cost=-0.434886 [o=64 t=6] + -- Parameters = -1.8012 3.7271 2.0049 -0.3560 0.7662 1.9359 1.0241 0.9910 1.0031 0.0064 -0.0353 -0.0227 + - param set #8 has cost=-0.455481 [o=13 t=7] + -- Parameters = -1.4215 4.1661 1.7612 -0.3286 1.0793 1.2422 1.0031 0.9834 0.9994 0.0198 -0.0154 -0.0237 + - param set #9 has cost=-0.457729 [o=12 t=20] + -- Parameters = -0.4412 3.5840 1.6364 -0.3732 0.5856 -0.2696 1.0202 0.9853 0.9942 0.0039 0.0285 -0.0411 + - param set #10 has cost=-0.467596 [o=15 t=11] + -- Parameters = -0.9201 4.3463 1.4253 -0.3839 1.7444 0.4497 1.0055 0.9881 0.9908 0.0016 0.0090 -0.0112 + - param set #11 has cost=-0.102042 [o=83 t=23] + -- Parameters = -9.5948 -7.0954 5.9528 -3.1518 -9.8297 8.9539 1.0558 1.0195 0.9892 0.0019 -0.0011 -0.0152 + - param set #12 has cost=-0.087802 [o=76 t=2] + -- Parameters = -1.6628 35.2397 -12.0111 -3.2706 21.6122 -0.0030 1.0126 0.9880 1.0046 -0.0027 -0.0042 -0.0017 + - param set #13 has cost=-0.088903 [o=30 t=3] + -- Parameters = -4.5025 29.9523 -8.5785 -6.4197 17.7051 2.2821 1.0252 0.9846 1.0081 0.0190 -0.0014 -0.0002 + - param set #14 has cost=-0.086254 [o=71 t=8] + -- Parameters = -1.0021 -17.8041 9.5973 0.3150 -18.8558 1.3796 1.0727 1.0232 1.0057 0.0181 -0.0052 -0.0069 + - param set #15 has cost=-0.083531 [o=27 t=9] + -- Parameters = -18.0716 16.0634 0.5836 -18.4959 5.4113 7.4360 1.0289 1.0148 1.0074 0.0095 -0.0017 -0.0089 + - param set #16 has cost=-0.075036 [o=22 t=16] + -- Parameters = 18.3235 11.4693 5.4786 12.6858 2.7435 -11.5776 0.9129 0.9930 0.9961 0.0202 0.0032 -0.0100 + - param set #17 has cost=-0.090346 [o=19 t=10] + -- Parameters = 5.1838 9.1011 0.3104 -7.7238 3.1521 -3.2037 1.0420 1.0729 1.0296 -0.0083 0.0105 -0.0058 + - param set #18 has cost=-0.074458 [o=20 t=15] + -- Parameters = 15.5409 44.9334 -19.9243 13.6296 28.6799 -13.1253 1.0018 1.0119 0.9750 -0.0105 0.0052 -0.0009 + - param set #19 has cost=-0.076926 [o=38 t=19] + -- Parameters = 14.9816 1.4623 2.5998 12.5205 -1.5932 -7.2348 0.9908 1.0614 1.0112 -0.0107 0.0051 0.0063 + - param set #20 has cost=-0.069629 [o=37 t=12] + -- Parameters = -19.2896 34.2683 -9.2439 0.4672 19.2806 17.4588 1.0034 0.9826 1.0545 0.0017 -0.0016 0.0037 + - param set #21 has cost=-0.068765 [o=26 t=13] + -- Parameters = -15.2866 36.5380 -10.0723 0.3700 20.5521 11.8859 1.0208 0.9979 1.0042 -0.0010 0.0025 -0.0051 + - param set #22 has cost=-0.072510 [o=16 t=14] + -- Parameters = -8.3556 14.5643 -0.8265 -25.9663 4.1328 -2.9202 1.0012 0.9951 1.0028 0.0035 0.0086 -0.0062 + - param set #23 has cost=-0.070961 [o=58 t=25] + -- Parameters = 29.1622 -5.0752 -0.1369 6.0137 -10.0410 -29.8970 1.0553 1.0868 1.0058 -0.0028 -0.0160 0.0131 + - param set #24 has cost=-0.069941 [o=7 t=21] + -- Parameters = -28.8573 34.0029 -14.8591 -12.6490 20.8524 24.5089 1.0868 0.9934 0.9987 0.0060 0.0020 -0.0008 + - param set #25 has cost=-0.067313 [o=86 t=22] + -- Parameters = -22.0967 2.2993 5.4371 -32.1879 -4.4287 6.1499 0.9829 1.0057 1.0157 0.0262 0.0023 -0.0104 + - param set #26 has cost=-0.068284 [o=9 t=18] + -- Parameters = 28.3746 32.8131 -13.9486 21.8130 16.6306 -24.3993 1.0871 1.0199 0.9894 -0.0085 -0.0033 -0.0051 + - param set #27 has cost=-0.060664 [o=41 t=24] + -- Parameters = -4.7413 35.6610 -8.7886 16.2420 21.0273 8.3383 0.9980 0.9923 1.0025 -0.0007 0.0028 0.0005 + - param set #28 has cost=-0.060352 [o=29 t=28] + -- Parameters = -1.9518 34.1935 -10.2278 -29.1746 24.0936 -9.6500 0.9666 1.0154 1.0315 0.0331 -0.0009 0.0070 + - param set #29 has cost=-0.056313 [o=74 t=17] + -- Parameters = 37.9900 22.5946 -9.3982 7.3523 8.4903 -36.7845 1.0248 1.0467 1.0075 -0.0039 -0.0060 0.0050 + - param set #30 has cost=-0.055626 [o=24 t=27] + -- Parameters = 26.3884 -31.9311 -6.2358 42.9017 -39.7717 -19.9823 0.9927 0.9976 0.9875 -0.0045 -0.0043 -0.0047 + - sorting parameter sets by cost + - scanning for distances from #1 + --- dist(#2,#1) = 0.0161 XXX + --- dist(#3,#1) = 0.0267 + --- dist(#4,#1) = 0.0641 + --- dist(#5,#1) = 0.0737 + --- dist(#6,#1) = 0.0643 + --- dist(#7,#1) = 0.108 + --- dist(#8,#1) = 0.0906 + --- dist(#9,#1) = 0.18 + --- dist(#10,#1) = 0.141 + --- dist(#11,#1) = 0.118 + --- dist(#12,#1) = 0.323 + --- dist(#13,#1) = 0.389 + --- dist(#14,#1) = 0.274 + --- dist(#15,#1) = 0.213 + --- dist(#16,#1) = 0.2 + --- dist(#17,#1) = 0.242 + --- dist(#18,#1) = 0.51 + --- dist(#19,#1) = 0.284 + --- dist(#20,#1) = 0.377 + --- dist(#21,#1) = 0.373 + --- dist(#22,#1) = 0.376 + --- dist(#23,#1) = 0.405 + --- dist(#24,#1) = 0.367 + --- dist(#25,#1) = 0.353 + --- dist(#26,#1) = 0.394 + --- dist(#27,#1) = 0.376 + --- dist(#28,#1) = 0.488 + --- dist(#29,#1) = 0.481 + - cast out 1 parameter set for being too close to best set + - Total coarse refinement net CPU time = 0.0 s; 9900 funcs ++ *** Fine pass begins *** + * Enter alignment setup routine + - Smoothing base; radius=1.00 + - Smoothing source; radius=1.00 + !source mask fill: ubot=112.297 usiz=488.908 + - retaining old weight image + * Exit alignment setup routine ++ Picking best parameter set out of 30 cases + 68054 total points stored in 136 'TOHD(12.9811)' bloks (0 duplicates) + - cost(#1)=-0.471478 * [o=14 t=1] + -- Parameters = -1.0198 4.1484 1.6319 -0.4246 1.4965 0.6126 1.0039 0.9907 0.9954 0.0009 0.0048 -0.0171 + - cost(#2)=-0.468681 [o=-1 t=-1] + -- Parameters = -1.1103 4.2316 1.6838 -0.5199 1.6273 0.7970 0.9993 0.9889 0.9969 0.0011 -0.0026 -0.0127 + - cost(#3)=-0.463711 [o=15 t=11] + -- Parameters = -0.9201 4.3463 1.4253 -0.3839 1.7444 0.4497 1.0055 0.9881 0.9908 0.0016 0.0090 -0.0112 + - cost(#4)=-0.462498 [o=59 t=26] + -- Parameters = -1.1289 4.5090 1.7201 -0.5241 2.0585 0.7386 1.0050 0.9951 0.9960 -0.0012 -0.0023 -0.0029 + - cost(#5)=-0.461067 [o=45 t=5] + -- Parameters = -1.3555 4.4627 1.6585 -0.3667 1.8958 1.1329 1.0012 0.9939 0.9951 0.0069 -0.0116 -0.0065 + - cost(#6)=-0.458004 [o=10 t=4] + -- Parameters = -0.7385 4.6031 1.7552 -0.3927 2.0694 0.1311 1.0054 0.9943 0.9970 0.0052 0.0190 -0.0043 + - cost(#7)=-0.453518 [o=12 t=20] + -- Parameters = -0.4412 3.5840 1.6364 -0.3732 0.5856 -0.2696 1.0202 0.9853 0.9942 0.0039 0.0285 -0.0411 + - cost(#8)=-0.451778 [o=13 t=7] + -- Parameters = -1.4215 4.1661 1.7612 -0.3286 1.0793 1.2422 1.0031 0.9834 0.9994 0.0198 -0.0154 -0.0237 + - cost(#9)=-0.431025 [o=64 t=6] + -- Parameters = -1.8012 3.7271 2.0049 -0.3560 0.7662 1.9359 1.0241 0.9910 1.0031 0.0064 -0.0353 -0.0227 + - cost(#10)=-0.100616 [o=83 t=23] + -- Parameters = -9.5948 -7.0954 5.9528 -3.1518 -9.8297 8.9539 1.0558 1.0195 0.9892 0.0019 -0.0011 -0.0152 + - cost(#11)=-0.088258 [o=19 t=10] + -- Parameters = 5.1838 9.1011 0.3104 -7.7238 3.1521 -3.2037 1.0420 1.0729 1.0296 -0.0083 0.0105 -0.0058 + - cost(#12)=-0.087405 [o=30 t=3] + -- Parameters = -4.5025 29.9523 -8.5785 -6.4197 17.7051 2.2821 1.0252 0.9846 1.0081 0.0190 -0.0014 -0.0002 + - cost(#13)=-0.085856 [o=76 t=2] + -- Parameters = -1.6628 35.2397 -12.0111 -3.2706 21.6122 -0.0030 1.0126 0.9880 1.0046 -0.0027 -0.0042 -0.0017 + - cost(#14)=-0.084523 [o=71 t=8] + -- Parameters = -1.0021 -17.8041 9.5973 0.3150 -18.8558 1.3796 1.0727 1.0232 1.0057 0.0181 -0.0052 -0.0069 + - cost(#15)=-0.082191 [o=27 t=9] + -- Parameters = -18.0716 16.0634 0.5836 -18.4959 5.4113 7.4360 1.0289 1.0148 1.0074 0.0095 -0.0017 -0.0089 + - cost(#16)=-0.075171 [o=38 t=19] + -- Parameters = 14.9816 1.4623 2.5998 12.5205 -1.5932 -7.2348 0.9908 1.0614 1.0112 -0.0107 0.0051 0.0063 + - cost(#17)=-0.073591 [o=22 t=16] + -- Parameters = 18.3235 11.4693 5.4786 12.6858 2.7435 -11.5776 0.9129 0.9930 0.9961 0.0202 0.0032 -0.0100 + - cost(#18)=-0.072897 [o=20 t=15] + -- Parameters = 15.5409 44.9334 -19.9243 13.6296 28.6799 -13.1253 1.0018 1.0119 0.9750 -0.0105 0.0052 -0.0009 + - cost(#19)=-0.071141 [o=16 t=14] + -- Parameters = -8.3556 14.5643 -0.8265 -25.9663 4.1328 -2.9202 1.0012 0.9951 1.0028 0.0035 0.0086 -0.0062 + - cost(#20)=-0.069182 [o=58 t=25] + -- Parameters = 29.1622 -5.0752 -0.1369 6.0137 -10.0410 -29.8970 1.0553 1.0868 1.0058 -0.0028 -0.0160 0.0131 + - cost(#21)=-0.068434 [o=7 t=21] + -- Parameters = -28.8573 34.0029 -14.8591 -12.6490 20.8524 24.5089 1.0868 0.9934 0.9987 0.0060 0.0020 -0.0008 + - cost(#22)=-0.067791 [o=37 t=12] + -- Parameters = -19.2896 34.2683 -9.2439 0.4672 19.2806 17.4588 1.0034 0.9826 1.0545 0.0017 -0.0016 0.0037 + - cost(#23)=-0.067300 [o=26 t=13] + -- Parameters = -15.2866 36.5380 -10.0723 0.3700 20.5521 11.8859 1.0208 0.9979 1.0042 -0.0010 0.0025 -0.0051 + - cost(#24)=-0.066885 [o=9 t=18] + -- Parameters = 28.3746 32.8131 -13.9486 21.8130 16.6306 -24.3993 1.0871 1.0199 0.9894 -0.0085 -0.0033 -0.0051 + - cost(#25)=-0.065651 [o=86 t=22] + -- Parameters = -22.0967 2.2993 5.4371 -32.1879 -4.4287 6.1499 0.9829 1.0057 1.0157 0.0262 0.0023 -0.0104 + - cost(#26)=-0.059028 [o=41 t=24] + -- Parameters = -4.7413 35.6610 -8.7886 16.2420 21.0273 8.3383 0.9980 0.9923 1.0025 -0.0007 0.0028 0.0005 + - cost(#27)=-0.059123 [o=29 t=28] + -- Parameters = -1.9518 34.1935 -10.2278 -29.1746 24.0936 -9.6500 0.9666 1.0154 1.0315 0.0331 -0.0009 0.0070 + - cost(#28)=-0.054794 [o=74 t=17] + -- Parameters = 37.9900 22.5946 -9.3982 7.3523 8.4903 -36.7845 1.0248 1.0467 1.0075 -0.0039 -0.0060 0.0050 + - cost(#29)=-0.053459 [o=24 t=27] + -- Parameters = 26.3884 -31.9311 -6.2358 42.9017 -39.7717 -19.9823 0.9927 0.9976 0.9875 -0.0045 -0.0043 -0.0047 + - cost(#30)=-0.022224 [o=-2 t=-2] + -- Parameters = 0.2258 5.1650 -5.7636 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 + -num_rtb 99 ==> refine all 30 cases + - cost(#1)=-0.472088 * [o=14 t=1] + -- Parameters = -1.0620 4.1379 1.6822 -0.4448 1.4358 0.6854 1.0016 0.9889 0.9968 0.0010 0.0031 -0.0189 + - cost(#2)=-0.471070 [o=-1 t=-1] + -- Parameters = -1.0972 4.1849 1.6736 -0.4210 1.5555 0.7395 1.0034 0.9909 0.9962 0.0007 0.0011 -0.0152 + - cost(#3)=-0.470946 [o=15 t=11] + -- Parameters = -0.9878 4.1819 1.6591 -0.4514 1.4856 0.4892 1.0034 0.9914 0.9972 -0.0001 0.0076 -0.0172 + - cost(#4)=-0.469397 [o=59 t=26] + -- Parameters = -1.0848 4.2551 1.7608 -0.4823 1.6380 0.7284 1.0048 0.9932 0.9974 -0.0003 0.0019 -0.0120 + - cost(#5)=-0.466175 [o=45 t=5] + -- Parameters = -1.3094 4.3676 1.7285 -0.6060 1.7770 0.9930 1.0022 0.9928 0.9980 -0.0006 -0.0093 -0.0111 + - cost(#6)=-0.465396 [o=10 t=4] + -- Parameters = -0.9790 4.4174 1.8118 -0.3539 1.7701 0.4465 1.0034 0.9940 0.9983 0.0049 0.0142 -0.0117 + - cost(#7)=-0.466979 [o=12 t=20] + -- Parameters = -0.7716 3.7372 1.6652 -0.3675 0.6004 0.2272 1.0024 0.9830 0.9965 0.0024 0.0190 -0.0373 + - cost(#8)=-0.468799 [o=13 t=7] + -- Parameters = -1.2916 3.9679 1.6970 -0.3747 0.9458 1.0801 1.0043 0.9884 0.9988 0.0050 -0.0105 -0.0263 + - cost(#9)=-0.457037 [o=64 t=6] + -- Parameters = -1.7540 4.0110 1.6095 -0.5694 1.1112 1.8696 1.0031 0.9849 0.9960 0.0043 -0.0258 -0.0265 + - cost(#10)=-0.214639 [o=83 t=23] + -- Parameters = -3.8960 -0.2690 2.2340 0.1574 -3.5684 5.5748 1.0617 1.0604 1.0003 0.0419 -0.0883 -0.0788 + - cost(#11)=-0.294205 [o=19 t=10] + -- Parameters = -3.4626 6.6135 1.6864 -2.1563 3.1356 2.6479 1.0476 1.0576 1.0050 -0.0295 -0.0329 0.0182 + - cost(#12)=-0.088089 [o=30 t=3] + -- Parameters = -4.2603 30.0837 -8.7500 -6.1371 17.7417 1.9491 1.0262 0.9833 1.0051 0.0275 -0.0021 -0.0009 + - cost(#13)=-0.086031 [o=76 t=2] + -- Parameters = -1.7132 35.2499 -11.9454 -3.2701 21.5303 0.1552 1.0167 0.9865 1.0047 -0.0010 -0.0053 -0.0018 + - cost(#14)=-0.085691 [o=71 t=8] + -- Parameters = -0.9164 -17.6279 9.6316 0.7559 -18.9047 1.6121 1.0776 1.0236 1.0090 0.0298 -0.0092 -0.0095 + - cost(#15)=-0.082954 [o=27 t=9] + -- Parameters = -17.7304 16.3017 0.3328 -18.3872 5.6171 7.1126 1.0299 1.0073 1.0038 0.0185 -0.0007 -0.0072 + - cost(#16)=-0.197311 [o=38 t=19] + -- Parameters = -0.8140 3.3480 1.2959 -0.6874 -1.8590 -1.2975 1.1370 1.0169 1.0053 -0.0969 0.0661 -0.0603 + - cost(#17)=-0.073644 [o=22 t=16] + -- Parameters = 18.2681 11.4898 5.5466 12.6297 2.7201 -11.5065 0.9138 0.9924 0.9967 0.0210 0.0034 -0.0102 + - cost(#18)=-0.073672 [o=20 t=15] + -- Parameters = 15.3468 44.8110 -19.8631 13.2606 28.8154 -12.9296 0.9992 1.0053 0.9750 -0.0167 0.0028 0.0001 + - cost(#19)=-0.072141 [o=16 t=14] + -- Parameters = -8.4497 14.4740 -0.7297 -26.0044 4.2919 -2.6346 1.0044 0.9676 1.0077 0.0053 0.0091 -0.0081 + - cost(#20)=-0.069831 [o=58 t=25] + -- Parameters = 28.9783 -5.2461 -0.2415 5.9238 -9.8640 -29.7768 1.0563 1.0841 1.0056 -0.0146 -0.0149 0.0134 + - cost(#21)=-0.072342 [o=7 t=21] + -- Parameters = -29.8786 34.9791 -15.5752 -13.0628 20.9857 23.8904 1.1166 0.9806 0.9900 0.0069 0.0136 -0.0070 + - cost(#22)=-0.067802 [o=37 t=12] + -- Parameters = -19.2984 34.2707 -9.2529 0.4718 19.2797 17.4592 1.0034 0.9822 1.0543 0.0023 -0.0019 0.0036 + - cost(#23)=-0.070552 [o=26 t=13] + -- Parameters = -14.6794 35.9681 -10.2047 -0.2051 20.8112 12.1473 1.0445 0.9915 1.0133 -0.0023 0.0228 -0.0065 + - cost(#24)=-0.067873 [o=9 t=18] + -- Parameters = 28.1434 32.7796 -13.9559 21.6185 16.6699 -24.1653 1.0842 1.0345 0.9928 -0.0085 -0.0057 -0.0058 + - cost(#25)=-0.067574 [o=86 t=22] + -- Parameters = -20.9651 1.9367 5.6749 -31.6098 -4.0166 5.1625 0.9856 0.9976 1.0396 0.0267 0.0016 -0.0167 + - cost(#26)=-0.059054 [o=41 t=24] + -- Parameters = -4.7093 35.6573 -8.7367 16.2360 21.0015 8.3051 0.9981 0.9920 1.0031 -0.0010 0.0036 0.0005 + - cost(#27)=-0.059222 [o=29 t=28] + -- Parameters = -1.9972 34.1880 -10.2400 -29.1816 24.0725 -9.6208 0.9674 1.0139 1.0308 0.0347 -0.0016 0.0069 + - cost(#28)=-0.055553 [o=74 t=17] + -- Parameters = 37.8499 22.5336 -9.4541 7.2032 8.6063 -36.5146 1.0245 1.0457 1.0066 -0.0038 -0.0127 0.0054 + - cost(#29)=-0.054232 [o=24 t=27] + -- Parameters = 26.2206 -32.0906 -6.4187 42.8026 -39.8845 -19.6833 0.9928 0.9989 0.9858 -0.0038 -0.0135 -0.0054 + - cost(#30)=-0.461343 [o=-2 t=-2] + -- Parameters = -1.1249 4.4928 1.8227 -0.6066 2.0588 0.7522 1.0043 0.9943 0.9991 -0.0068 -0.0006 -0.0017 + - case #1 [o=14 t=1] is now the best + - Initial cost = -0.472088 + - Initial fine Parameters = -1.0620 4.1379 1.6822 -0.4448 1.4358 0.6854 1.0016 0.9889 0.9968 0.0010 0.0031 -0.0189 + - Finalish cost = -0.473261 ; 590 funcs + - ini Finalish Parameters = -1.0860 3.9381 1.5974 -0.4848 1.0386 0.7066 1.0018 0.9878 0.9951 0.0004 0.0025 -0.0275 + - Final cost = -0.473261 ; 264 funcs + Final fine fit Parameters: x-shift= -1.0864 y-shift= 3.9380 z-shift= 1.5971 ... enorm= 4.3862 mm z-angle= -0.4846 x-angle= 1.0388 y-angle= 0.7063 ... total= 1.3441 deg x-scale= 1.0018 y-scale= 0.9878 z-scale= 0.9951 ... vol3D= 0.9847=(0.9949)^3 [base about same as source] y/x-shear= 0.0004 z/x-shear= 0.0025 z/y-shear= -0.0275 + - Fine net CPU time = 0.0 s ++ Computing output image ++ image warp: parameters = -1.0864 3.9380 1.5971 -0.4846 1.0388 0.7063 1.0018 0.9878 0.9951 0.0004 0.0025 -0.0275 ++ Unloading unneeded data ++ Output dataset ./__tt_anatSS.T1W_ob_temp_al_junk+orig.BRIK ++ Wrote -1Dmatrix_save ./anatSS.T1W_al_junk_e2a_only_mat.aff12.1D ++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 30.9 ++ ########################################################### ++ # PLEASE check results VISUALLY for alignment quality # ++ ########################################################### #Script is running (command trimmed): cat_matvec -ONELINE ./anatSS.T1W_al_junk_e2a_only_mat.aff12.1D ./__tt_anatSS.T1W_obla2e_mat.1D -I > ./anatSS.T1W_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_ns+orig -1Dmatrix_apply ./anatSS.T1W_al_junk_mat.aff12.1D -prefix ./anatSS.T1W_al_junk -input ./__tt_anatSS.T1W+orig -master BASE -mast_dxyz 0.937513 -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_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./__tt_vr_base_min_outlier_ts_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_vr_base_min_outlier_ts_ns+orig.BRIK is 7.042221 degrees from plumb. ++ Source dataset: ./__tt_anatSS.T1W+orig.HEAD ++ Base dataset: ./__tt_vr_base_min_outlier_ts_ns+orig.HEAD ++ Loading datasets into memory ++ largeness ==> set -twobest 29 ++ NOTE: base and source coordinate systems have different handedness + Orientations: base=Right handed (RAI); source=Left handed (ASR) + - It is nothing to worry about: 3dAllineate aligns based on coordinates. + - But it is always important to check the alignment visually to be sure. ++ base center of mass = 44.637 49.116 33.059 (index) + source center of mass = 146.927 104.031 84.548 (index) + source-target CM = -1.005 -3.457 8.550 (xyz) + -cmass x y z shifts = -1.005 -3.457 8.550 + shift search range is +/- = 69.817 69.817 47.348 + 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] = -10.000000 .. 10.000000 center = 0.000000 + Range param#2 [y-shift] = -10.000000 .. 10.000000 center = 0.000000 + Range param#3 [z-shift] = -10.000000 .. 10.000000 center = 0.000000 + 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] = -40.000000 .. 40.000000 center = 0.000000 + Range param#2 [y-shift] = -40.000000 .. 40.000000 center = 0.000000 + Range param#3 [z-shift] = -40.000000 .. 40.000000 center = 0.000000 ++ Final parameter search ranges: + x-shift = -40.000 .. 40.000 + y-shift = -40.000 .. 40.000 + z-shift = -40.000 .. 40.000 + 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 0.9375 mm ++ OpenMP thread count = 15 ++ ========== 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 = 0.0221 0.9855 -0.1034 20.1907 -0.0092 -0.0753 -0.9892 194.9344 0.9988 -0.0227 -0.0046 -32.5083 ++ Unloading unneeded data ++ Output dataset ./anatSS.T1W_al_junk+orig.BRIK ++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.6 ++ ########################################################### #++ Creating final output: anat data aligned to epi # copy is not necessary #++ Saving history #Script is running (command trimmed): 3dNotes -h "align_epi_anat.py -anat2epi -anat anatSS.T1W+orig -suffix \ _al_junk -epi vr_base_min_outlier+orig -epi_base 0 -epi_strip 3dAutomask \ -anat_has_skull no -giant_move -volreg off -tshift off" \ ./anatSS.T1W_al_junk+orig #++ Removing all the temporary files #Script is running: \rm -f ./__tt_vr_base_min_outlier* #Script is running: \rm -f ./__tt_anatSS.T1W* # Finished alignment successfully if ( ! -f anatQQ.T1W+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.e02 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb02.SM327_all4runs.r01.e02.tshift+orig ++ 3dvolreg: AFNI version=AFNI_23.0.01 (Jan 18 2023) [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 7.042221 degrees from plumb. ++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK ++ Oblique dataset:./pb02.SM327_all4runs.r01.e02.tshift+orig.BRIK is 7.042221 degrees from plumb. ++ Reading input dataset ./pb02.SM327_all4runs.r01.e02.tshift+orig.BRIK ++ Edging: x=4 y=4 z=3 ++ Creating mask for -maxdisp + Automask has 85394 voxels + 10790 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 466 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..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237..238..239..240..241..242..243..244..245..246..247..248..249..250..251..252..253..254..255..256..257..258..259..260..261..262..263..264..265..266..267..268..269..270..271..272..273..274..275..276..277..278..279..280..281..282..283..284..285..286..287..288..289..290..291..292..293..294..295..296..297..298..299..300..301..302..303..304..305..306..307..308..309..310..311..312..313..314..315..316..317..318..319..320..321..322..323..324..325..326..327..328..329..330..331..332..333..334..335..336..337..338..339..340..341..342..343..344..345..346..347..348..349..350..351..352..353..354..355..356..357..358..359..360..361..362..363..364..365..366..367..368..369..370..371..372..373..374..375..376..377..378..379..380..381..382..383..384..385..386..387..388..389..390..391..392..393..394..395..396..397..398..399..400..401..402..403..404..405..406..407..408..409..410..411..412..413..414..415..416..417..418..419..420..421..422..423..424..425..426..427..428..429..430..431..432..433..434..435..436..437..438..439..440..441..442..443..444..445..446..447..448..449..450..451..452..453..454..455..456..457..458..459..460..461..462..463..464..465.. ++ CPU time for realignment=0 s [=0 s/sub-brick] ++ Min : roll=-0.332 pitch=-0.316 yaw=-0.192 dS=-0.532 dL=-0.386 dP=-0.412 ++ Mean: roll=-0.160 pitch=+0.272 yaw=-0.060 dS=+0.199 dL=-0.180 dP=-0.044 ++ Max : roll=+0.004 pitch=+0.887 yaw=+0.134 dS=+0.703 dL=+0.179 dP=+0.280 ++ Max displacements (mm) for each sub-brick: 0.85(0.00) 0.96(0.18) 1.01(0.17) 0.96(0.27) 1.03(0.10) 1.05(0.12) 0.92(0.16) 1.07(0.18) 0.90(0.26) 0.83(0.10) 0.93(0.21) 0.93(0.28) 0.99(0.15) 0.89(0.19) 0.94(0.18) 0.88(0.13) 0.95(0.15) 0.84(0.17) 0.78(0.10) 0.91(0.13) 0.74(0.19) 0.81(0.07) 0.72(0.17) 0.74(0.09) 0.73(0.05) 0.66(0.09) 0.83(0.22) 0.71(0.12) 0.80(0.10) 0.71(0.27) 0.66(0.06) 0.76(0.13) 0.65(0.19) 0.71(0.17) 0.60(0.12) 0.77(0.52) 1.05(0.29) 0.69(0.43) 0.63(0.30) 0.67(0.11) 0.63(0.07) 0.69(0.09) 0.54(0.29) 0.66(0.18) 0.60(0.08) 0.62(0.11) 0.74(0.40) 0.63(0.15) 0.76(0.30) 0.58(0.26) 0.62(0.23) 0.59(0.04) 0.54(0.21) 0.63(0.14) 0.61(0.17) 0.68(0.16) 0.55(0.14) 0.54(0.03) 0.58(0.08) 0.47(0.13) 0.60(0.19) 0.46(0.25) 0.54(0.11) 0.49(0.07) 0.36(0.16) 0.42(0.07) 0.43(0.17) 0.49(0.54) 0.40(0.16) 0.47(0.17) 0.43(0.11) 0.42(0.04) 0.48(0.11) 0.40(0.16) 0.47(0.15) 0.50(0.26) 0.47(0.04) 0.45(0.05) 0.47(0.08) 0.45(0.43) 0.40(0.12) 0.31(0.10) 0.38(0.07) 0.28(0.11) 0.42(0.14) 0.29(0.16) 0.31(0.19) 0.44(0.22) 0.24(0.26) 0.34(0.12) 0.23(0.19) 0.22(0.04) 0.27(0.09) 0.24(0.13) 0.21(0.18) 0.20(0.16) 0.23(0.09) 0.25(0.12) 0.18(0.14) 0.23(0.13) 0.15(0.11) 0.21(0.17) 0.15(0.13) 0.13(0.13) 0.27(0.15) 0.18(0.16) 0.20(0.10) 0.17(0.08) 0.00(0.17) 0.14(0.14) 0.06(0.15) 0.28(0.29) 0.14(0.22) 0.15(0.07) 0.21(0.12) 0.27(0.28) 0.40(0.18) 0.60(0.33) 0.69(0.11) 0.49(0.21) 0.43(0.07) 0.39(0.05) 0.44(0.05) 0.35(0.10) 0.41(0.08) 0.33(0.13) 0.60(0.29) 0.43(0.19) 0.47(0.06) 0.52(0.09) 0.41(0.11) 0.34(0.07) 0.23(0.15) 0.37(0.18) 0.41(0.04) 0.40(0.08) 0.39(0.04) 0.44(0.14) 0.28(0.19) 0.46(0.22) 0.43(0.08) 0.37(0.12) 0.50(0.18) 0.33(0.22) 0.46(0.16) 0.45(0.08) 0.34(0.16) 0.48(0.21) 0.39(0.15) 0.53(0.17) 0.48(0.08) 0.54(0.09) 0.41(0.19) 0.45(0.07) 0.50(0.08) 0.40(0.16) 0.54(0.20) 0.47(0.15) 0.53(0.11) 0.64(0.15) 0.50(0.19) 0.59(0.16) 0.52(0.15) 0.58(0.09) 0.47(0.16) 0.47(0.02) 0.48(0.07) 0.47(0.06) 0.54(0.16) 0.42(0.18) 0.53(0.17) 0.48(0.15) 0.46(0.07) 0.48(0.07) 0.47(0.12) 0.54(0.14) 0.62(0.26) 0.59(0.31) 0.60(0.17) 0.58(0.03) 0.58(0.11) 0.55(0.13) 0.58(0.23) 0.55(0.25) 0.57(0.22) 0.61(0.47) 0.47(0.31) 0.48(0.34) 0.69(0.36) 0.79(0.13) 0.62(0.20) 0.66(0.06) 0.71(0.12) 0.62(0.20) 0.54(0.18) 0.63(0.16) 0.62(0.12) 0.61(0.02) 0.68(0.09) 0.65(0.21) 0.67(0.16) 0.68(0.13) 0.67(0.10) 0.73(0.10) 0.74(0.18) 0.75(0.10) 0.74(0.13) 0.73(0.18) 0.71(0.17) 0.69(0.02) 0.78(0.12) 0.73(0.14) 0.72(0.17) 0.73(0.04) 0.74(0.06) 0.79(0.09) 0.78(0.20) 0.86(0.29) 0.81(0.13) 0.87(0.14) 0.88(0.05) 0.85(0.19) 0.87(0.26) 0.77(0.25) 0.81(0.10) 0.76(0.17) 0.78(0.09) 0.75(0.05) 0.72(0.12) 0.72(0.11) 0.72(0.15) 0.76(0.21) 0.73(0.23) 0.75(0.10) 0.71(0.11) 0.64(0.30) 0.52(0.55) 0.63(0.29) 0.77(0.32) 0.82(0.22) 0.85(0.08) 0.80(0.09) 0.77(0.14) 0.84(0.26) 0.79(0.21) 0.75(0.07) 0.78(0.08) 0.78(0.13) 0.79(0.16) 0.79(0.31) 0.77(0.22) 0.80(0.04) 0.80(0.20) 0.80(0.20) 0.85(0.15) 0.82(0.12) 0.86(0.10) 0.83(0.04) 0.85(0.10) 0.87(0.12) 0.82(0.16) 0.87(0.20) 0.81(0.14) 0.84(0.06) 0.99(0.19) 0.94(0.19) 0.91(0.19) 0.89(0.12) 0.92(0.09) 0.98(0.07) 0.98(0.05) 0.89(0.11) 0.90(0.14) 0.95(0.27) 0.88(0.14) 0.91(0.09) 0.91(0.04) 0.90(0.14) 0.93(0.21) 0.88(0.21) 0.93(0.19) 0.94(0.05) 0.92(0.12) 0.97(0.16) 0.92(0.15) 0.97(0.19) 0.93(0.18) 0.95(0.04) 0.98(0.12) 0.92(0.16) 1.01(0.12) 0.93(0.24) 0.89(0.28) 0.91(0.18) 1.09(0.18) 0.99(0.15) 0.98(0.16) 1.00(0.10) 1.00(0.13) 1.01(0.20) 0.97(0.12) 1.00(0.07) 1.02(0.04) 1.00(0.11) 1.05(0.26) 1.01(0.19) 1.05(0.07) 1.08(0.10) 1.01(0.19) 1.13(0.19) 1.07(0.24) 1.13(0.27) 1.13(0.08) 1.14(0.05) 1.27(0.16) 1.19(0.15) 1.19(0.27) 1.15(0.17) 1.16(0.04) 1.21(0.10) 1.15(0.18) 1.27(0.31) 1.20(0.24) 1.22(0.07) 1.30(0.12) 1.35(0.14) 1.23(0.14) 1.24(0.08) 1.23(0.06) 1.22(0.15) 1.25(0.06) 1.18(0.09) 1.31(0.26) 1.25(0.25) 1.13(0.13) 1.19(0.07) 1.23(0.14) 1.27(0.19) 1.23(0.08) 1.16(0.23) 1.07(0.33) 1.02(0.10) 1.01(0.15) 1.16(0.22) 1.06(0.16) 1.16(0.22) 1.13(0.11) 1.16(0.05) 1.23(0.12) 1.22(0.17) 1.29(0.14) 1.16(0.16) 1.28(0.22) 1.25(0.09) 1.28(0.04) 1.28(0.03) 1.22(0.08) 1.34(0.17) 1.24(0.22) 1.29(0.17) 1.28(0.15) 1.28(0.03) 1.41(0.24) 1.28(0.16) 1.42(0.14) 1.37(0.07) 1.36(0.18) 1.38(0.10) 1.30(0.11) 1.40(0.13) 1.36(0.28) 1.41(0.15) 1.37(0.18) 1.41(0.08) 1.48(0.31) 1.44(0.15) 1.54(0.16) 1.48(0.15) 1.48(0.09) 1.52(0.08) 1.46(0.28) 1.56(0.12) 1.47(0.15) 1.51(0.29) 1.43(0.17) 1.46(0.12) 1.53(0.09) 1.46(0.11) 1.61(0.25) 1.58(0.17) 1.52(0.08) 1.59(0.34) 1.59(0.73) 1.62(0.19) 1.62(0.12) 1.66(0.16) 1.76(0.19) 1.51(0.28) 1.58(0.22) 1.54(0.31) 1.57(0.08) 1.56(0.14) 1.34(0.26) 1.43(0.26) 1.58(0.19) 1.48(0.19) 1.56(0.19) 1.56(0.03) 1.58(0.31) 1.64(0.17) 1.54(0.12) 1.62(0.21) 1.57(0.15) 1.57(0.04) 1.74(0.19) 1.65(0.20) 1.66(0.23) 1.65(0.08) 1.72(0.11) 1.74(0.07) 1.68(0.15) 1.79(0.22) 1.71(0.16) 1.78(0.09) 1.71(0.20) 1.76(0.16) 1.73(0.16) 1.49(0.41) 1.52(0.11) 1.62(0.11) 1.70(0.17) 1.67(0.10) 1.78(0.15) 1.71(0.19) 1.74(0.18) 1.71(0.07) 1.56(0.25) 1.60(0.15) 1.77(0.23) 1.68(0.30) 1.81(0.14) 1.75(0.07) 1.76(0.13) 1.79(0.06) 1.76(0.05) 1.84(0.24) 1.73(0.13) 1.82(0.15) 1.74(0.09) 1.86(0.15) 1.88(0.03) 1.79(0.09) 1.88(0.22) 1.79(0.19) 1.86(0.16) 1.80(0.14) 1.85(0.11) 1.87(0.12) 1.75(0.20) 1.81(0.12) 1.77(0.29) 1.54(0.39) 1.42(0.23) 1.44(0.12) 1.52(0.20) 1.59(0.11) ++ Max displacement in automask = 1.88 (mm) at sub-brick 452 ++ Max delta displ in automask = 0.73 (mm) at sub-brick 392 ++ Wrote dataset to disk in ./rm.epi.volreg.r01.e02+orig.BRIK 3dcalc -overwrite -a pb02.SM327_all4runs.r01.e02.tshift+orig -expr 1 -prefix rm.epi.all1 ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands *+ WARNING: input 'a' is not used in the expression cat_matvec -ONELINE anatQQ.T1W.aff12.1D anatSS.T1W_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D foreach eind ( 01 02 03 04 05 06 07 08 09 10 11 12 ) 3dNwarpApply -master anatQQ.T1W+tlrc -dxyz 2.5 -source pb02.SM327_all4runs.r01.e01.tshift+orig -nwarp anatQQ.T1W_WARP.nii mat.r01.warp.aff12.1D -prefix rm.epi.nomask.r01.e01 ++ 3dNwarpApply: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.T1W+tlrc' ++ output grid size = 2.5 mm *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb02.SM327_all4runs.r01.e01.tshift+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb02.SM327_all4runs.r01.e01.tshift+orig.BRIK is 7.042221 degrees from plumb. ++ opened source dataset 'pb02.SM327_all4runs.r01.e01.tshift+orig' ++ Processing -nwarp ++ Warping:...............................................Z ++ Output dataset ./rm.epi.nomask.r01.e01+tlrc.BRIK ++ total Elapsed time = 819.9 sec end 3dNwarpApply -master anatQQ.T1W+tlrc -dxyz 2.5 -source pb02.SM327_all4runs.r01.e02.tshift+orig -nwarp anatQQ.T1W_WARP.nii mat.r01.warp.aff12.1D -prefix rm.epi.nomask.r01.e02 ++ 3dNwarpApply: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.T1W+tlrc' ++ output grid size = 2.5 mm *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb02.SM327_all4runs.r01.e02.tshift+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb02.SM327_all4runs.r01.e02.tshift+orig.BRIK is 7.042221 degrees from plumb. ++ opened source dataset 'pb02.SM327_all4runs.r01.e02.tshift+orig' ++ Processing -nwarp ++ Warping:...............................................Z ++ Output dataset ./rm.epi.nomask.r01.e02+tlrc.BRIK ++ total Elapsed time = 809.9 sec end 3dNwarpApply -master anatQQ.T1W+tlrc -dxyz 2.5 -source pb02.SM327_all4runs.r01.e03.tshift+orig -nwarp anatQQ.T1W_WARP.nii mat.r01.warp.aff12.1D -prefix rm.epi.nomask.r01.e03 ++ 3dNwarpApply: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.T1W+tlrc' ++ output grid size = 2.5 mm *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb02.SM327_all4runs.r01.e03.tshift+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb02.SM327_all4runs.r01.e03.tshift+orig.BRIK is 7.042221 degrees from plumb. ++ opened source dataset 'pb02.SM327_all4runs.r01.e03.tshift+orig' ++ Processing -nwarp ++ Warping:...............................................Z ++ Output dataset ./rm.epi.nomask.r01.e03+tlrc.BRIK ++ total Elapsed time = 787.5 sec end 3dNwarpApply -master anatQQ.T1W+tlrc -dxyz 2.5 -source pb02.SM327_all4runs.r01.e04.tshift+orig -nwarp anatQQ.T1W_WARP.nii mat.r01.warp.aff12.1D -prefix rm.epi.nomask.r01.e04 ++ 3dNwarpApply: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.T1W+tlrc' ++ output grid size = 2.5 mm *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb02.SM327_all4runs.r01.e04.tshift+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb02.SM327_all4runs.r01.e04.tshift+orig.BRIK is 7.042221 degrees from plumb. ++ opened source dataset 'pb02.SM327_all4runs.r01.e04.tshift+orig' ++ Processing -nwarp ++ Warping:...............................................Z ++ Output dataset ./rm.epi.nomask.r01.e04+tlrc.BRIK ++ total Elapsed time = 804.4 sec end 3dNwarpApply -master anatQQ.T1W+tlrc -dxyz 2.5 -source pb02.SM327_all4runs.r01.e05.tshift+orig -nwarp anatQQ.T1W_WARP.nii mat.r01.warp.aff12.1D -prefix rm.epi.nomask.r01.e05 ++ 3dNwarpApply: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.T1W+tlrc' ++ output grid size = 2.5 mm *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb02.SM327_all4runs.r01.e05.tshift+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb02.SM327_all4runs.r01.e05.tshift+orig.BRIK is 7.042221 degrees from plumb. ++ opened source dataset 'pb02.SM327_all4runs.r01.e05.tshift+orig' ++ Processing -nwarp ++ Warping:...............................................Z ++ Output dataset ./rm.epi.nomask.r01.e05+tlrc.BRIK ++ total Elapsed time = 768.6 sec end 3dNwarpApply -master anatQQ.T1W+tlrc -dxyz 2.5 -source pb02.SM327_all4runs.r01.e06.tshift+orig -nwarp anatQQ.T1W_WARP.nii mat.r01.warp.aff12.1D -prefix rm.epi.nomask.r01.e06 ++ 3dNwarpApply: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.T1W+tlrc' ++ output grid size = 2.5 mm *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb02.SM327_all4runs.r01.e06.tshift+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb02.SM327_all4runs.r01.e06.tshift+orig.BRIK is 7.042221 degrees from plumb. ++ opened source dataset 'pb02.SM327_all4runs.r01.e06.tshift+orig' ++ Processing -nwarp ++ Warping:...............................................Z ++ Output dataset ./rm.epi.nomask.r01.e06+tlrc.BRIK ++ total Elapsed time = 761.4 sec end 3dNwarpApply -master anatQQ.T1W+tlrc -dxyz 2.5 -source pb02.SM327_all4runs.r01.e07.tshift+orig -nwarp anatQQ.T1W_WARP.nii mat.r01.warp.aff12.1D -prefix rm.epi.nomask.r01.e07 ++ 3dNwarpApply: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.T1W+tlrc' ++ output grid size = 2.5 mm *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb02.SM327_all4runs.r01.e07.tshift+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb02.SM327_all4runs.r01.e07.tshift+orig.BRIK is 7.042221 degrees from plumb. ++ opened source dataset 'pb02.SM327_all4runs.r01.e07.tshift+orig' ++ Processing -nwarp ++ Warping:...............................................Z ++ Output dataset ./rm.epi.nomask.r01.e07+tlrc.BRIK ++ total Elapsed time = 750.4 sec end 3dNwarpApply -master anatQQ.T1W+tlrc -dxyz 2.5 -source pb02.SM327_all4runs.r01.e08.tshift+orig -nwarp anatQQ.T1W_WARP.nii mat.r01.warp.aff12.1D -prefix rm.epi.nomask.r01.e08 ++ 3dNwarpApply: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.T1W+tlrc' ++ output grid size = 2.5 mm *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb02.SM327_all4runs.r01.e08.tshift+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb02.SM327_all4runs.r01.e08.tshift+orig.BRIK is 7.042221 degrees from plumb. ++ opened source dataset 'pb02.SM327_all4runs.r01.e08.tshift+orig' ++ Processing -nwarp ++ Warping:...............................................Z ++ Output dataset ./rm.epi.nomask.r01.e08+tlrc.BRIK ++ total Elapsed time = 753.5 sec end 3dNwarpApply -master anatQQ.T1W+tlrc -dxyz 2.5 -source pb02.SM327_all4runs.r01.e09.tshift+orig -nwarp anatQQ.T1W_WARP.nii mat.r01.warp.aff12.1D -prefix rm.epi.nomask.r01.e09 ++ 3dNwarpApply: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.T1W+tlrc' ++ output grid size = 2.5 mm *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb02.SM327_all4runs.r01.e09.tshift+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb02.SM327_all4runs.r01.e09.tshift+orig.BRIK is 7.042221 degrees from plumb. ++ opened source dataset 'pb02.SM327_all4runs.r01.e09.tshift+orig' ++ Processing -nwarp ++ Warping:...............................................Z ++ Output dataset ./rm.epi.nomask.r01.e09+tlrc.BRIK ++ total Elapsed time = 754.2 sec end 3dNwarpApply -master anatQQ.T1W+tlrc -dxyz 2.5 -source pb02.SM327_all4runs.r01.e10.tshift+orig -nwarp anatQQ.T1W_WARP.nii mat.r01.warp.aff12.1D -prefix rm.epi.nomask.r01.e10 ++ 3dNwarpApply: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.T1W+tlrc' ++ output grid size = 2.5 mm *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb02.SM327_all4runs.r01.e10.tshift+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb02.SM327_all4runs.r01.e10.tshift+orig.BRIK is 7.042221 degrees from plumb. ++ opened source dataset 'pb02.SM327_all4runs.r01.e10.tshift+orig' ++ Processing -nwarp ++ Warping:...............................................Z ++ Output dataset ./rm.epi.nomask.r01.e10+tlrc.BRIK ++ total Elapsed time = 764.3 sec end 3dNwarpApply -master anatQQ.T1W+tlrc -dxyz 2.5 -source pb02.SM327_all4runs.r01.e11.tshift+orig -nwarp anatQQ.T1W_WARP.nii mat.r01.warp.aff12.1D -prefix rm.epi.nomask.r01.e11 ++ 3dNwarpApply: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.T1W+tlrc' ++ output grid size = 2.5 mm *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb02.SM327_all4runs.r01.e11.tshift+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb02.SM327_all4runs.r01.e11.tshift+orig.BRIK is 7.042221 degrees from plumb. ++ opened source dataset 'pb02.SM327_all4runs.r01.e11.tshift+orig' ++ Processing -nwarp ++ Warping:...............................................Z ++ Output dataset ./rm.epi.nomask.r01.e11+tlrc.BRIK ++ total Elapsed time = 858.1 sec end 3dNwarpApply -master anatQQ.T1W+tlrc -dxyz 2.5 -source pb02.SM327_all4runs.r01.e12.tshift+orig -nwarp anatQQ.T1W_WARP.nii mat.r01.warp.aff12.1D -prefix rm.epi.nomask.r01.e12 ++ 3dNwarpApply: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.T1W+tlrc' ++ output grid size = 2.5 mm *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb02.SM327_all4runs.r01.e12.tshift+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb02.SM327_all4runs.r01.e12.tshift+orig.BRIK is 7.042221 degrees from plumb. ++ opened source dataset 'pb02.SM327_all4runs.r01.e12.tshift+orig' ++ Processing -nwarp ++ Warping:...............................................Z ++ Output dataset ./rm.epi.nomask.r01.e12+tlrc.BRIK ++ total Elapsed time = 849.0 sec end 3dNwarpApply -master anatQQ.T1W+tlrc -dxyz 2.5 -source rm.epi.all1+orig -nwarp anatQQ.T1W_WARP.nii mat.r01.warp.aff12.1D -interp cubic -ainterp NN -quiet -prefix rm.epi.1.r01 ++ 3dNwarpApply: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.T1W+tlrc' ++ output grid size = 2.5 mm *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./rm.epi.all1+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:./rm.epi.all1+orig.BRIK is 7.042221 degrees from plumb. ++ opened source dataset 'rm.epi.all1+orig' 3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc ++ 3dTstat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: KR Hammett & RW Cox end cat dfile.r01.1D 3dcopy rm.epi.min.r01+tlrc mask_epi_extents ++ 3dcopy: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] foreach run ( 01 ) foreach eind ( 01 02 03 04 05 06 07 08 09 10 11 12 ) 3dcalc -a rm.epi.nomask.r01.e01+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb03.SM327_all4runs.r01.e01.volreg ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb03.SM327_all4runs.r01.e01.volreg+tlrc.BRIK end 3dcalc -a rm.epi.nomask.r01.e02+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb03.SM327_all4runs.r01.e02.volreg ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb03.SM327_all4runs.r01.e02.volreg+tlrc.BRIK end 3dcalc -a rm.epi.nomask.r01.e03+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb03.SM327_all4runs.r01.e03.volreg ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb03.SM327_all4runs.r01.e03.volreg+tlrc.BRIK end 3dcalc -a rm.epi.nomask.r01.e04+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb03.SM327_all4runs.r01.e04.volreg ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb03.SM327_all4runs.r01.e04.volreg+tlrc.BRIK end 3dcalc -a rm.epi.nomask.r01.e05+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb03.SM327_all4runs.r01.e05.volreg ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb03.SM327_all4runs.r01.e05.volreg+tlrc.BRIK end 3dcalc -a rm.epi.nomask.r01.e06+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb03.SM327_all4runs.r01.e06.volreg ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb03.SM327_all4runs.r01.e06.volreg+tlrc.BRIK end 3dcalc -a rm.epi.nomask.r01.e07+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb03.SM327_all4runs.r01.e07.volreg ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb03.SM327_all4runs.r01.e07.volreg+tlrc.BRIK end 3dcalc -a rm.epi.nomask.r01.e08+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb03.SM327_all4runs.r01.e08.volreg ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb03.SM327_all4runs.r01.e08.volreg+tlrc.BRIK end 3dcalc -a rm.epi.nomask.r01.e09+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb03.SM327_all4runs.r01.e09.volreg ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb03.SM327_all4runs.r01.e09.volreg+tlrc.BRIK end 3dcalc -a rm.epi.nomask.r01.e10+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb03.SM327_all4runs.r01.e10.volreg ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb03.SM327_all4runs.r01.e10.volreg+tlrc.BRIK end 3dcalc -a rm.epi.nomask.r01.e11+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb03.SM327_all4runs.r01.e11.volreg ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb03.SM327_all4runs.r01.e11.volreg+tlrc.BRIK end 3dcalc -a rm.epi.nomask.r01.e12+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb03.SM327_all4runs.r01.e12.volreg ++ 3dcalc: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./pb03.SM327_all4runs.r01.e12.volreg+tlrc.BRIK end end cat_matvec -ONELINE anatQQ.T1W.aff12.1D anatSS.T1W_al_junk_mat.aff12.1D -I 3dNwarpApply -master anatQQ.T1W+tlrc -dxyz 2.5 -source vr_base_min_outlier+orig -nwarp anatQQ.T1W_WARP.nii mat.basewarp.aff12.1D -prefix final_epi_vr_base_min_outlier ++ 3dNwarpApply: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.T1W+tlrc' ++ output grid size = 2.5 mm *+ 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 7.042221 degrees from plumb. ++ opened source dataset 'vr_base_min_outlier+orig' ++ Processing -nwarp ++ Warping:.Z ++ Output dataset ./final_epi_vr_base_min_outlier+tlrc.BRIK ++ total Elapsed time = 4.0 sec 3dcopy anatQQ.T1W+tlrc anat_final.SM327_all4runs ++ 3dcopy: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] 3dAllineate -base final_epi_vr_base_min_outlier+tlrc -allcostX -input anat_final.SM327_all4runs+tlrc tee out.allcostX.txt ++ 3dAllineate: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Zhark the Registrator ++ Source dataset: ./anat_final.SM327_all4runs+tlrc.HEAD ++ Base dataset: ./final_epi_vr_base_min_outlier+tlrc.HEAD ++ Loading datasets into memory ++ Local correlation: blok type = 'TOHD(12.9425)' + -cmass x y z shifts = 0.674 4.244 -3.531 + shift search range is +/- = 75.435 85.868 72.225 *+ 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 = 0.196381 sp = 0.33994 mi = 2.67395 crM = 0.0466262 nmi = 0.845186 je = 2.67395 hel = -0.095533 crA = 0.215944 crU = 0.21358 lss = 0.803619 lpc = 0.230832 lpa = 0.769168 lpc+ = 0.386997 lpa+ = 0.925332 ++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 1.9 ++ ########################################################### @radial_correlate -nfirst 0 -polort 4 -do_clean yes -rdir radcor.pb03.volreg pb03.SM327_all4runs.r01.e02.volreg+tlrc.HEAD ++ 3dTcat: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ elapsed time = 2.3 s ++ 3dAutomask: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Emperor Zhark -- detrend -polort 4, new eset = det.r01 ++ 3dTproject: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Cox the Algebraic (Linear) ++ Setting up regressors ++ 1 Blocks * 5 polynomials -- 5 polort regressors ++ 466 retained time points MINUS 5 regressors ==> 461 D.O.F. left ++ no -mask option ==> processing all 545468 voxels in dataset ++ THD_dset_to_vectim: allocated 1016752352 bytes *+ WARNING: 3dTproject input data :: 103786 vectors are constant -- running correlation on dataset pb03.SM327_all4runs.r01.e02.volreg+tlrc.HEAD ... ++ merge blur: rad 20, FWHM 40 ++ 3dmerge: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ default -1dindex = 0 ++ default -1tindex = 1 Program 3dmerge 3dmerge: edit and combine 3D datasets, by RW Cox ++ editing input dataset in memory (969.7 MB) .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. -- Wrote edited dataset: ./sphere.mean.20.r01+tlrc.BRIK ++ 3dTcorrelate: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Wrote dataset: ./radcor.20.r01.corr+tlrc.BRIK ++ 3dbucket: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ---- done ++ have do_clean, cleaning up... foreach run ( 01 ) 3dAutomask -prefix rm.mask_r01 pb03.SM327_all4runs.r01.e02.volreg+tlrc ++ 3dAutomask: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] ++ Authored by: Emperor Zhark ++ Loading dataset pb03.SM327_all4runs.r01.e02.volreg+tlrc ++ Forming automask + Fixed clip level = 2003.187866 + Used gradual clip level = 1804.521362 .. 2127.928467 + Number voxels above clip level = 121425 + Clustering voxels ... + Largest cluster has 119945 voxels + Clustering voxels ... + Largest cluster has 114794 voxels + Filled 1164 voxels in small holes; now have 115958 voxels + Filled 24 voxels in large holes; now have 115982 voxels + Clustering voxels ... + Largest cluster has 115954 voxels + Clustering non-brain voxels ... + Clustering voxels ... + Largest cluster has 429261 voxels + Mask now has 116207 voxels ++ 116207 voxels in the mask [out of 545468: 21.30%] ++ first 10 x-planes are zero [from L] ++ last 6 x-planes are zero [from R] ++ first 10 y-planes are zero [from P] ++ last 7 y-planes are zero [from A] ++ first 1 z-planes are zero [from I] ++ last 10 z-planes are zero [from S] ++ CPU time = 0.000000 sec end 3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.SM327_all4runs ++ 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, 116207 survived, 429261 were zero ++ writing result full_mask.SM327_all4runs... 3dresample -master full_mask.SM327_all4runs+tlrc -input anatQQ.T1W+tlrc -prefix rm.resam.anat 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.SM327_all4runs ++ 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, 129565 survived, 415903 were zero ++ filled 0 holes (0 voxels) ++ writing result mask_anat.SM327_all4runs... 3dmask_tool -input full_mask.SM327_all4runs+tlrc mask_anat.SM327_all4runs+tlrc -inter -prefix mask_epi_anat.SM327_all4runs ++ 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: 19942 clipped, 112915 survived, 412611 were zero ++ writing result mask_epi_anat.SM327_all4runs... 3dABoverlap -no_automask full_mask.SM327_all4runs+tlrc mask_anat.SM327_all4runs+tlrc tee out.mask_ae_overlap.txt ++ 3dABoverlap: AFNI version=AFNI_23.0.01 (Jan 18 2023) [64-bit] #A=./full_mask.SM327_all4runs+tlrc.BRIK B=./mask_anat.SM327_all4runs+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) 116207 129565 132857 112915 3292 16650 2.8329 12.8507 1.0483 0.9831 1.0722 3ddot -dodice full_mask.SM327_all4runs+tlrc mask_anat.SM327_all4runs+tlrc tee out.mask_ae_dice.txt 0.91886 3dresample -master full_mask.SM327_all4runs+tlrc -prefix ./rm.resam.group -input /home/taliw/abin/MNI152_2009_template_SSW.nii.gz[0] 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, 122282 survived, 423186 were zero ++ filled 0 holes (0 voxels) ++ writing result mask_group... 3ddot -dodice mask_anat.SM327_all4runs+tlrc mask_group+tlrc tee out.mask_at_dice.txt 0.97082 tedana --version tee out.tedana_version.txt tedana v0.0.12 foreach run ( 01 ) tedana -d pb03.SM327_all4runs.r01.e01.volreg+tlrc.HEAD pb03.SM327_all4runs.r01.e02.volreg+tlrc.HEAD pb03.SM327_all4runs.r01.e03.volreg+tlrc.HEAD pb03.SM327_all4runs.r01.e04.volreg+tlrc.HEAD pb03.SM327_all4runs.r01.e05.volreg+tlrc.HEAD pb03.SM327_all4runs.r01.e06.volreg+tlrc.HEAD pb03.SM327_all4runs.r01.e07.volreg+tlrc.HEAD pb03.SM327_all4runs.r01.e08.volreg+tlrc.HEAD pb03.SM327_all4runs.r01.e09.volreg+tlrc.HEAD pb03.SM327_all4runs.r01.e10.volreg+tlrc.HEAD pb03.SM327_all4runs.r01.e11.volreg+tlrc.HEAD pb03.SM327_all4runs.r01.e12.volreg+tlrc.HEAD -e 12.0 31.7 51.4 --mask mask_anat.SM327_all4runs+tlrc.HEAD --out-dir tedana_r01 --convention orig Exception ignored on calling ctypes callback function: .match_module_callback at 0x7f248d84f040> Traceback (most recent call last): File "/home/taliw/.local/lib/python3.8/site-packages/threadpoolctl.py", line 400, in match_module_callback self._make_module_from_path(filepath) File "/home/taliw/.local/lib/python3.8/site-packages/threadpoolctl.py", line 515, in _make_module_from_path module = module_class(filepath, prefix, user_api, internal_api) File "/home/taliw/.local/lib/python3.8/site-packages/threadpoolctl.py", line 606, in __init__ self.version = self.get_version() File "/home/taliw/.local/lib/python3.8/site-packages/threadpoolctl.py", line 646, in get_version config = get_config().split() AttributeError: 'NoneType' object has no attribute 'split' INFO tedana:tedana_workflow:466 Using output directory: /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/tedana_r01 INFO tedana:tedana_workflow:479 Loading input data: ['pb03.SM327_all4runs.r01.e01.volreg+tlrc.HEAD', 'pb03.SM327_all4runs.r01.e02.volreg+tlrc.HEAD', 'pb03.SM327_all4runs.r01.e03.volreg+tlrc.HEAD', 'pb03.SM327_all4runs.r01.e04.volreg+tlrc.HEAD', 'pb03.SM327_all4runs.r01.e05.volreg+tlrc.HEAD', 'pb03.SM327_all4runs.r01.e06.volreg+tlrc.HEAD', 'pb03.SM327_all4runs.r01.e07.volreg+tlrc.HEAD', 'pb03.SM327_all4runs.r01.e08.volreg+tlrc.HEAD', 'pb03.SM327_all4runs.r01.e09.volreg+tlrc.HEAD', 'pb03.SM327_all4runs.r01.e10.volreg+tlrc.HEAD', 'pb03.SM327_all4runs.r01.e11.volreg+tlrc.HEAD', 'pb03.SM327_all4runs.r01.e12.volreg+tlrc.HEAD'] INFO io:__init__:106 Generating figures directory: /home/taliw/data/Candies/SM327/afni/SM327_all4runs.results/tedana_r01/figures INFO tedana:tedana_workflow:561 Using user-defined mask WARNING utils:make_adaptive_mask:108 10 voxels in user-defined mask do not have good signal. Removing voxels from mask. INFO tedana:tedana_workflow:609 Computing T2* map Traceback (most recent call last): File "/home/taliw/.local/bin/tedana", line 8, in sys.exit(_main()) File "/home/taliw/.local/lib/python3.8/site-packages/tedana/workflows/tedana.py", line 933, in _main tedana_workflow(**kwargs) File "/home/taliw/.local/lib/python3.8/site-packages/tedana/workflows/tedana.py", line 610, in tedana_workflow t2s_limited, s0_limited, t2s_full, s0_full = decay.fit_decay( File "/home/taliw/.local/lib/python3.8/site-packages/tedana/decay.py", line 356, in fit_decay raise ValueError( ValueError: Second dimension of data (12) does not match number of echoes provided (tes; 3)