echo auto-generated by afni_proc.py, Fri Oct 9 17:02:41 2026 auto-generated by afni_proc.py, Fri Oct 9 17:02:41 2026 echo (version 8.10, October 6, 2026) (version 8.10, October 6, 2026) echo execution started: `date` date execution started: Fri Oct 9 17:02:46 EDT 2026 afni -ver Precompiled binary linux_rocky_8: Oct 8 2026 (Version AFNI_26.3.01 'Philip the Arab') afni_history -check_date 7 Jan 2026 -- is current: afni_history as new as: 07 Jan 2026 most recent entry is: 06 Oct 2026 if ( 0 ) then if ( 0 > 0 ) then set subj = sub-10871 endif set output_dir = sub-10871.results if ( -d sub-10871.results ) then set runs = ( `count_afni -digits 2 1 1` ) count_afni -digits 2 1 1 mkdir -p sub-10871.results mkdir sub-10871.results/stimuli cp /data/NIMH_SSCC/p001_ap_pamenc/data_15_timing/sub-10871/timing_pamenc/times.CONTROL.txt /data/NIMH_SSCC/p001_ap_pamenc/data_15_timing/sub-10871/timing_pamenc/times.TASK.txt sub-10871.results/stimuli 3dcopy /data/NIMH_SSCC/p001_ap_pamenc/data_13_ssw/sub-10871/anatSS.sub-10871.nii sub-10871.results/anatSS.sub-10871 ++ 3dcopy: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] 3dcopy /data/NIMH_SSCC/ptaylor/REF_TEMPLATES/MNI152_2009_template_SSW.nii.gz sub-10871.results/MNI152_2009_template_SSW.nii.gz ++ 3dcopy: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] 3dcopy /data/NIMH_SSCC/gaia/UCLA_phenomics/data_clean/sub-10871/anat/sub-10871_T1w.nii.gz sub-10871.results/copy_af_anat_w_skull ++ 3dcopy: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] 3dcopy /data/NIMH_SSCC/ptaylor/REF_TEMPLATES/APQC_atlas_MNI_2009c_asym.nii.gz sub-10871.results/ROI_import_MNI_2009c_asym ++ 3dcopy: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] 3dcopy /data/NIMH_SSCC/p001_ap_pamenc/data_13_ssw/sub-10871/anatQQ.sub-10871.nii sub-10871.results/anatQQ.sub-10871 ++ 3dcopy: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] 3dcopy /data/NIMH_SSCC/p001_ap_pamenc/data_13_ssw/sub-10871/anatQQ.sub-10871.aff12.1D sub-10871.results/anatQQ.sub-10871.aff12.1D ++ 3dcopy: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] 3dcopy /data/NIMH_SSCC/p001_ap_pamenc/data_13_ssw/sub-10871/anatQQ.sub-10871_WARP.nii sub-10871.results/anatQQ.sub-10871_WARP.nii ++ 3dcopy: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] 3dTcat -prefix sub-10871.results/pb00.sub-10871.r01.tcat /data/NIMH_SSCC/gaia/UCLA_phenomics/data_clean/sub-10871/func/sub-10871_task-pamenc_bold.nii.gz[0..$] ++ 3dTcat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ elapsed time = 2.8 s set tr_counts = ( 242 ) cd sub-10871.results gtkyd_check.py -infiles pb00.sub-10871.r01.tcat+orig.HEAD -outdir gtkyd ++ Have 1 dsets to check ++ Making new output directory: gtkyd ++ Now starting to Get To Know Your Data... ++ --------------------------- ++ DONE. See the outputs: group summary table : gtkyd.xls group detailed values : gtkyd/rep_gtkyd_detail_*.dat group unique values : gtkyd/rep_gtkyd_unique_*.dat individual value lists : gtkyd/dset_*.txt tee out.gtkyd.outliers.txt gen_ss_review_table.py -infiles gtkyd/dset_gtkyd_pb00.sub-10871.r01.tcat.txt -outlier_sep space -report_outliers datum VARY -report_outliers orient VARY -report_outliers av_space VARY -- no outlier subjects to list @radial_correlate -nfirst 0 -polort 4 -do_clean yes -rdir radcor.pb00.tcat pb00.sub-10871.r01.tcat+orig.HEAD ++ 3dTcat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ elapsed time = 3.3 s ++ 3dAutomask: AFNI version=AFNI_26.3.01 (Oct 8 2026) [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 35.420746 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 35.420746 degrees from plumb. -- radcor: detrend -polort 4, new eset = det.r01 input : epi.r01+orig ++ 3dTproject: AFNI version=AFNI_26.3.01 (Oct 8 2026) [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 35.420746 degrees from plumb. ++ Setting up regressors ++ 1 Blocks * 5 polynomials -- 5 polort regressors ++ 242 retained time points MINUS 5 regressors ==> 237 D.O.F. left ++ no -mask option ==> processing all 139264 voxels in dataset ++ 3dTproject input data :: 2176 vectors are constant -- radcor: running correlation on dataset pb00.sub-10871.r01.tcat+orig.HEAD ... ++ radcor: merge blur: rad 20, FWHM 40 ++ 3dmerge: AFNI version=AFNI_26.3.01 (Oct 8 2026) [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 35.420746 degrees from plumb. ++ default -1dindex = 0 ++ default -1tindex = 1 ++ Oblique dataset:./det.r01+orig.BRIK is 35.420746 degrees from plumb. Program 3dmerge 3dmerge: edit and combine 3D datasets, by RW Cox ++ editing input dataset in memory (128.6 MB) ++ edt_blur: sigx 16.9864, dx 3, fwhm 40, sfac 2.5, firx 15 .................................................................................................................................................................................................................................................. -- Wrote edited dataset: ./sphere.mean.20.r01+orig.BRIK ++ 3dTcorrelate: AFNI version=AFNI_26.3.01 (Oct 8 2026) [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 35.420746 degrees from plumb. ++ Oblique dataset:./det.r01+orig.BRIK is 35.420746 degrees from plumb. ++ Wrote dataset: ./radcor.20.r01.corr+orig.BRIK ++ 3dbucket: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ---- radcor: done ++ have do_clean, cleaning up... find_variance_lines.tcsh -polort 4 -rdir vlines.pb00.tcat pb00.sub-10871.r01.tcat+orig.HEAD tee out.vlines.pb00.tcat.txt ++ have nslices : 34 ++ params: min_cvox 7, nerode 0, perc 90, polort 4, ignore_edges 1, sdpower 2, thresh 0.90, num_pc 0, do_pc_3dD 1, do_pc_vstat 1 ++ copying pb00.sub-10871.r01.tcat+orig.HEAD[0..$] to ts.0.orig.r01.nii.gz ++ 3dTcat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ elapsed time = 6.5 s ++ creating automask from first dset ++ 3dAutomask: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Emperor Zhark *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /lscratch/32397853/sub-10871/sub-10871.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/ts.0.orig.r01.nii.gz is 35.420746 degrees from plumb. ++ Loading dataset ts.0.orig.r01.nii.gz ++ Forming automask + Fixed clip level = 406.393860 + Used gradual clip level = 350.576538 .. 464.348511 + Number voxels above clip level = 38201 + Clustering voxels ... + Largest cluster has 37819 voxels + Clustering voxels ... + Largest cluster has 37437 voxels + Filled 417 voxels in small holes; now have 37854 voxels + Clustering voxels ... + Largest cluster has 37853 voxels + Clustering non-brain voxels ... + Clustering voxels ... + Largest cluster has 101411 voxels + Mask now has 37853 voxels ++ 37853 voxels in the mask [out of 139264: 27.18%] ++ first 11 x-planes are zero [from R] ++ last 9 x-planes are zero [from L] ++ first 2 y-planes are zero [from P] ++ last 6 y-planes are zero [from A] ++ first 0 z-planes are zero [from I] ++ last 1 z-planes are zero [from S] ++ Output dataset ./mask.nii.gz ++ CPU time = 0.000000 sec -- will apply mask mask.nii.gz ++ requiring 7 voxels in mask columns ++ 3dLocalstat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Emperor Zhark *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /lscratch/32397853/sub-10871/sub-10871.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/mask.nii.gz is 35.420746 degrees from plumb. ++ Number of voxels in mask = 37853 ++ Oblique dataset:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/mask.nii.gz is 35.420746 degrees from plumb. ++ Neighborhood comprises 69 voxels ++ Start sub-brick [0] ++ Output dataset ./tmp.mask.col.count.nii.gz ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./mask.nii.gz ++ 3dLocalstat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Emperor Zhark *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /lscratch/32397853/sub-10871/sub-10871.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/mask.nii.gz is 35.420746 degrees from plumb. ++ Neighborhood comprises 69 voxels ++ Start sub-brick [0] ++ Output dataset ./tmp.edge.nii.gz ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./tmp.e2.nii.gz ++ processing 1 input dataset(s), NN=2... ++ padding all datasets by 1 (for dilations) *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/tmp.e2.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/tmp.e2.nii.gz is 35.420746 degrees from plumb. ++ have 1 volume of input, no combining ++ frac 0 over 1 volumes gives min count 0 ++ voxel limits: 0 clipped, 83300 survived, 55964 were zero ++ writing result tmp.edge.nii.gz... ++ Output dataset ./tmp.edge.nii.gz ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./mask_edge.nii.gz -- detrend -polort 4, new eset = ts.1.det.r01.nii.gz ++ 3dTproject: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Cox the Algebraic (Linear) *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /lscratch/32397853/sub-10871/sub-10871.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/ts.0.orig.r01.nii.gz is 35.420746 degrees from plumb. ++ Setting up regressors ++ 1 Blocks * 5 polynomials -- 5 polort regressors ++ 242 retained time points MINUS 5 regressors ==> 237 D.O.F. left ++ no -mask option ==> processing all 139264 voxels in dataset ++ 3dTproject input data :: 2176 vectors are constant ++ 3dTstat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: KR Hammett & RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /lscratch/32397853/sub-10871/sub-10871.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/ts.1.det.r01.nii.gz is 35.420746 degrees from plumb. ++ Output dataset ./tmp.stdev.nii.gz ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [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 /lscratch/32397853/sub-10871/sub-10871.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/mask.nii.gz is 35.420746 degrees from plumb. ++ Oblique dataset:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/var.0.orig.r01.nii.gz is 35.420746 degrees from plumb. ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./var.1.scale.r01.nii.gz ++ 3dLocalstat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Emperor Zhark *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /lscratch/32397853/sub-10871/sub-10871.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/mask.nii.gz is 35.420746 degrees from plumb. ++ Number of voxels in mask = 37301 ++ Oblique dataset:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 35.420746 degrees from plumb. ++ Neighborhood comprises 69 voxels ++ Start sub-brick [0] ++ Output dataset ./proj.r01.nii.gz 3dClusterize -ithr 0 -idat 0 -NN 2 -2sided -1 0.90 -inset proj.r01.nii.gz -pref_map clustset.r01.nii.gz -outvol_if_no_clust ++ Neighborhood definition (NN=2) accepted ++ User input stat threshold: -1 ++ User input stat threshold: 0.90 *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /lscratch/32397853/sub-10871/sub-10871.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/proj.r01.nii.gz is 35.420746 degrees from plumb. ++ 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,-1,0.90,NN2 ++ 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. ++ Writing out map of cluster ROIs. ++ Output dataset ./clustset.r01.nii.gz # # Cluster report #[ Dataset prefix = proj.r01.nii.gz ] #[ Threshold vol = [0] 'MEAN' ] #[ Supplement dat vol = [0] 'MEAN' ] #[ Option summary = 2sided,-1,0.90,NN2 ] #[ Threshold value(s) = left-tail thr=-1.000000; right-tail thr=0.900000 ] #[ Aux. stat. info. = not a stat! ] #[ Nvoxel threshold = 0; Volume threshold = 0.000 ] #[ Single voxel volume = 36.000 (microliters) ] #[ Neighbor type, NN = 2 ] #[ Voxel datum type = float ] #[ Voxel dimensions = 3.000 mm X 3.000 mm X 4.000 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 #------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ------- ------- ------- ----- ----- ----- 22 -26.6 -72.3 -8.4 -26.6 -26.6 -72.3 -72.3 -50.4 33.6 0.9015 2.1e-05 0.9015 -26.6 -72.3 -50.4 22 -54.9 -79.6 -20.4 -56.6 -53.6 -81.3 -78.3 -42.4 1.6 0.9463 0.0058 0.9704 -53.6 -78.3 -42.4 16 51.4 -79.6 -26.4 51.4 51.4 -81.3 -78.3 -42.4 -10.4 0.9234 9.3e-04 0.9275 51.4 -81.3 -38.4 7 33.4 -117.3 -46.4 33.4 33.4 -117.3 -117.3 -58.4 -34.4 0.9113 0 0.9113 33.4 -117.3 -58.4 7 18.4 -126.3 -42.4 18.4 18.4 -126.3 -126.3 -54.4 -30.4 0.9102 3.5e-05 0.9102 18.4 -126.3 -54.4 1 -53.6 -78.3 -54.4 -53.6 -53.6 -78.3 -78.3 -54.4 -54.4 0.9704 0 0.9704 -53.6 -78.3 -54.4 #------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ------- ------- ------- ----- ----- ----- # 75 -9.1 -85.3 -23.1 0.922 0.0027 -26.60 -72.30 -12.38 -53.60 -78.30 -12.38 51.40 -81.30 -12.38 33.40 -117.30 -12.38 18.40 -126.30 -12.38 -53.60 -78.30 -12.38 -- check for edge clusters to remove (OK to make brick of 0s)... ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./clustset.edge.r01.nii.gz *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/clustset.edge.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/clustset.edge.r01.nii.gz is 35.420746 degrees from plumb. ++ have 6 clusters but 4 are at edges -- creating inner clusterset clustset.inner.r01.nii.gz (2 clusters) ++ 3dbucket: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] -- keeping clusters : 1 6 removing clusters: 2 3 4 5 ++ updated inner coord list: -26.60 -72.30 -12.38 -53.60 -78.30 -12.38 -- evaluating intersection (across clustset.inner.r*.nii.gz) ... ++ 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 /lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/clustset.inner.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/clustset.inner.r01.nii.gz is 35.420746 degrees from plumb. ++ have 1 volume of input, no combining ++ frac 1 over 1 volumes gives min count 1 ++ voxel limits: 0 clipped, 23 survived, 139241 were zero ++ writing result clust.inter.nii.gz... ++ Output dataset ./clust.inter.nii.gz ++ Neighborhood definition (NN=2) accepted *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/clust.inter.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/clust.inter.nii.gz is 35.420746 degrees from plumb. ++ User input stat threshold: 0 ++ User input stat threshold: 0.9 ++ Data volume: [0] '2sided,-1,0.90,NN2' ++ Threshold volume: [0] '2sided,-1,0.90,NN2' ++ 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,0,0.9,NN2 ++ 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. ++ Writing out map of cluster ROIs. ++ Output dataset ./clust.inter.enum.nii.gz # # Cluster report #[ Dataset prefix = clust.inter.nii.gz ] #[ Threshold vol = [0] '2sided,-1,0.90,NN2' ] #[ Supplement dat vol = [0] '2sided,-1,0.90,NN2' ] #[ Option summary = 2sided,0,0.9,NN2 ] #[ Threshold value(s) = left-tail thr=0.000000; right-tail thr=0.900000 ] #[ Aux. stat. info. = not a stat! ] #[ Nvoxel threshold = 0; Volume threshold = 0.000 ] #[ Single voxel volume = 36.000 (microliters) ] #[ Neighbor type, NN = 2 ] #[ Voxel datum type = byte ] #[ Voxel dimensions = 3.000 mm X 3.000 mm X 4.000 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 #------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ------- ------- ------- ----- ----- ----- 22 -26.6 -72.3 -8.4 -26.6 -26.6 -72.3 -72.3 -50.4 33.6 1 0 1 -26.6 -72.3 -50.4 1 -53.6 -78.3 -54.4 -53.6 -53.6 -78.3 -78.3 -54.4 -54.4 1 0 1 -53.6 -78.3 -54.4 #------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ------- ------- ------- ----- ----- ----- # 23 -27.7 -72.6 -10.4 1 0 -26.60 -72.30 -12.38 -53.60 -78.30 -12.38 ++ Check about making images ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands ++ 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 -26.60 -72.30 -12.38 -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_26.3.01 ++ chauffeur ver : 7.3 ------------------ 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_SEKKKUUpJeh ++ 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 /lscratch/32397853/sub-10871/sub-10871.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 35.420746 degrees from plumb. *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /lscratch/32397853/sub-10871/sub-10871.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 35.420746 degrees from plumb. ++ Ulay to be visualized within user range: [0%, 98%] -> [0.000000, 1.000000] ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_SEKKKUUpJeh/tmp_ulay.nii ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_SEKKKUUpJeh/tmp_olay.nii ++ User-entered function range value value (1) ++ Dimensions (xyzt): 64 64 34 1 ++ (initial) Slice spacing ordered (x,y,z) is: 64 64 34 ++ Will have user's chosen: SET_DICOM_XYZ -26.60 -72.30 -12.38 ------------------- end of optionizing ------------------- -- trying to start Xvfb :826 [1] 2384294 +/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/__tmp_chauf_SEKKKUUpJeh++ Writing one 256x180 image to filter '/usr/bin/pnmtopng -compression 9 > ./img_r01_01.sag.png' AFNI QUITTs! +++ Command Echo: afni -q -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=1x1:64:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=1x1:64:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=1x1:34:0: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 -26.60 -72.30 -12.38 -com SAVE_PNG sagittalimage ./img_r01_01.sag blowup=4 -com QUITT ./__tmp_chauf_SEKKKUUpJeh +* Removing temporary image directory './__tmp_chauf_SEKKKUUpJeh'. [1] Done Xvfb :826 -screen 0 1024x768x24 >& "${log_xvfb}" ++ DONE (good exit) see: ./img_r01_01* ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands ++ 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 -53.60 -78.30 -12.38 -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_26.3.01 ++ chauffeur ver : 7.3 ------------------ 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_TqIhBk4Vup8 ++ 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 /lscratch/32397853/sub-10871/sub-10871.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 35.420746 degrees from plumb. *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /lscratch/32397853/sub-10871/sub-10871.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:/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 35.420746 degrees from plumb. ++ Ulay to be visualized within user range: [0%, 98%] -> [0.000000, 1.000000] ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_TqIhBk4Vup8/tmp_ulay.nii ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_TqIhBk4Vup8/tmp_olay.nii ++ User-entered function range value value (1) ++ Dimensions (xyzt): 64 64 34 1 ++ (initial) Slice spacing ordered (x,y,z) is: 64 64 34 ++ Will have user's chosen: SET_DICOM_XYZ -53.60 -78.30 -12.38 ------------------- end of optionizing ------------------- -- trying to start Xvfb :371 [1] 2384846 +/lscratch/32397853/sub-10871/sub-10871.results/vlines.pb00.tcat/__tmp_chauf_TqIhBk4Vup8++ Writing one 256x180 image to filter '/usr/bin/pnmtopng -compression 9 > ./img_r01_02.sag.png' AFNI QUITTs! +++ Command Echo: afni -q -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=1x1:64:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=1x1:64:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=1x1:34:0: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 -53.60 -78.30 -12.38 -com SAVE_PNG sagittalimage ./img_r01_02.sag blowup=4 -com QUITT ./__tmp_chauf_TqIhBk4Vup8 +* Removing temporary image directory './__tmp_chauf_TqIhBk4Vup8'. [1] Done Xvfb :371 -screen 0 1024x768x24 >& "${log_xvfb}" ++ DONE (good exit) see: ./img_r01_02* +++ Have 2 images. Will wrap to fill 7x1 matrix +++ Transforming all input to rgb for a good reason +++ Writing image to QC_var_lines.jpg +++ Arranging 2 images (each 256x180) 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: 2 found questionable intersected regions : 2 =============== bad_coords.full.r01.txt =============== -26.60 -72.30 -12.38 -53.60 -78.30 -12.38 51.40 -81.30 -12.38 33.40 -117.30 -12.38 18.40 -126.30 -12.38 -53.60 -78.30 -12.38 =============== bad_coords.inter.txt =============== -26.60 -72.30 -12.38 -53.60 -78.30 -12.38 =============== bad_coords.r01.txt =============== -26.60 -72.30 -12.38 -53.60 -78.30 -12.38 touch out.pre_ss_warn.txt foreach run ( 01 ) 3dToutcount -automask -fraction -polort 4 -legendre pb00.sub-10871.r01.tcat+orig ++ 3dToutcount: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.sub-10871.r01.tcat+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb00.sub-10871.r01.tcat+orig.BRIK is 35.420746 degrees from plumb. ++ 37853 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 foreach run ( 01 ) 3dTto1D -method 4095_warn -input pb00.sub-10871.r01.tcat+orig tee -a out.4095_all.txt *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.sub-10871.r01.tcat+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb00.sub-10871.r01.tcat+orig.BRIK is 35.420746 degrees from plumb. ++ computing 4095_warn, nvox = 139264, nmask = 139264, nt = 242 ++ global max = 1931.000000, global 4095 count = 0 ++ max of 1931 is okay, clearing results... end awk /warning/ {print} out.4095_all.txt tee out.4095_warn.txt set minindex = `3dTstat -argmin -prefix - outcount_rall.1D\'` 3dTstat -argmin -prefix - outcount_rall.1D' ++ 3dTstat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: KR Hammett & RW Cox set ovals = ( `1d_tool.py -set_run_lengths $tr_counts -index_to_run_tr $minindex` ) 1d_tool.py -set_run_lengths 242 -index_to_run_tr 30 set minoutrun = 01 set minouttr = 30 echo min outlier: run 01, TR 30 tee out.min_outlier.txt min outlier: run 01, TR 30 foreach run ( 01 ) 3dTshift -tzero 0 -quintic -prefix pb01.sub-10871.r01.tshift -tpattern alt+z2 pb00.sub-10871.r01.tcat+orig ++ 3dTshift: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb00.sub-10871.r01.tcat+orig.BRIK, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:./pb00.sub-10871.r01.tcat+orig.BRIK is 35.420746 degrees from plumb. ++ updating time offset to 0 end 3dbucket -prefix vr_base_min_outlier pb01.sub-10871.r01.tshift+orig[30] ++ 3dbucket: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] 3dLocalUnifize -input vr_base_min_outlier+orig -prefix vr_base_min_outlier_unif ++ Start 3dLocalUnifize work ++ Making working directory: ./__wdir_LocalUni_GB85MTYvy7v ++ 3dTcat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ elapsed time = 0.1 s ++ 3dAutomask: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Emperor Zhark *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /lscratch/32397853/sub-10871/sub-10871.results/__wdir_LocalUni_GB85MTYvy7v/dset_00_cp.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:/lscratch/32397853/sub-10871/sub-10871.results/__wdir_LocalUni_GB85MTYvy7v/dset_00_cp.nii.gz is 35.420746 degrees from plumb. ++ Loading dataset dset_00_cp.nii.gz ++ Forming automask + Fixed clip level = 406.958099 + Used gradual clip level = 351.019196 .. 464.608612 + Number voxels above clip level = 38155 + Clustering voxels ... + Largest cluster has 37851 voxels + Clustering voxels ... + Largest cluster has 37379 voxels + Filled 400 voxels in small holes; now have 37779 voxels + Filled 2 voxels in large holes; now have 37781 voxels + Clustering voxels ... + Largest cluster has 37781 voxels + Clustering non-brain voxels ... + Clustering voxels ... + Largest cluster has 101483 voxels + Mask now has 37781 voxels ++ 37781 voxels in the mask [out of 139264: 27.13%] ++ first 11 x-planes are zero [from R] ++ last 9 x-planes are zero [from L] ++ first 2 y-planes are zero [from P] ++ last 6 y-planes are zero [from A] ++ first 0 z-planes are zero [from I] ++ last 1 z-planes are zero [from S] ++ Output dataset ./dset_00_mask.nii.gz ++ CPU time = 0.000000 sec ++ 3dLocalstat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Emperor Zhark *+ WARNING: If you are performing spatial transformations on an oblique dset, such as /lscratch/32397853/sub-10871/sub-10871.results/__wdir_LocalUni_GB85MTYvy7v/dset_00_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:/lscratch/32397853/sub-10871/sub-10871.results/__wdir_LocalUni_GB85MTYvy7v/dset_00_mask.nii.gz is 35.420746 degrees from plumb. ++ Number of voxels in mask = 37781 ++ Oblique dataset:/lscratch/32397853/sub-10871/sub-10871.results/__wdir_LocalUni_GB85MTYvy7v/dset_00_cp.nii.gz is 35.420746 degrees from plumb. ++ Neighborhood comprises 123 voxels ++ Start sub-brick [0] ++ Output dataset ./dset_01_lu.nii.gz ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./dset_02_rat.nii.gz ++ Apply filter threshold to scaled image: 1.5 ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./dset_04_filt.nii.gz ++ 3dcopy: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] +* Removing the working dir: '__wdir_LocalUni_GB85MTYvy7v' ++ DONE! View the finished, locally-unifized product: /lscratch/32397853/sub-10871/sub-10871.results/vr_base_min_outlier_unif align_epi_anat.py -anat2epi -anat anatSS.sub-10871+orig -suffix _al_junk -epi vr_base_min_outlier_unif+orig -epi_base 0 -epi_strip 3dAutomask -anat_has_skull no -giant_move -cost lpc+ZZ -check_flip -volreg off -tshift off #++ align_epi_anat version: 1.65 #++ turning off volume registration #Script is running (command trimmed): 3dAttribute DELTA ./vr_base_min_outlier_unif+orig #Script is running (command trimmed): 3dAttribute DELTA ./vr_base_min_outlier_unif+orig #Script is running (command trimmed): 3dAttribute DELTA ./anatSS.sub-10871+orig #++ Multi-cost is lpc+ZZ #++ Removing all the temporary files #Script is running: \rm -f ./__tt_vr_base_min_outlier_unif* #Script is running: \rm -f ./__tt_anatSS.sub-10871* #Script is running (command trimmed): 3dcopy ./anatSS.sub-10871+orig ./anatSS.sub-10871_unflipped+orig ++ 3dcopy: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] #Script is running (command trimmed): 3dinfo ./anatSS.sub-10871_unflipped+orig | \grep 'Data Axes Tilt:'| \grep 'Oblique' #++ Dataset /lscratch/32397853/sub-10871/sub-10871.results/anatSS.sub-10871_unflipped+orig is not oblique #Script is running (command trimmed): 3dinfo ./vr_base_min_outlier_unif+orig | \grep 'Data Axes Tilt:'| \grep 'Oblique' #++ Dataset /lscratch/32397853/sub-10871/sub-10871.results/vr_base_min_outlier_unif+orig is ***oblique**** #Script is running (command trimmed): 3dAttribute DELTA ./anatSS.sub-10871_unflipped+orig #++ Spacing for anat to oblique epi alignment is 1.000000 #++ Matching obliquity of anat to epi #Script is running (command trimmed): 3dWarp -verb -card2oblique ./vr_base_min_outlier_unif+orig -prefix ./anatSS.sub-10871_unflipped_ob -newgrid 1.000000 ./anatSS.sub-10871_unflipped+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > ./anatSS.sub-10871_unflipped_obla2e_mat.1D ++ 3dWarp: AFNI version=AFNI_26.3.01 (Oct 8 2026) [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_unif_ts ./vr_base_min_outlier_unif+orig'[0]' ++ 3dbucket: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] #++ removing skull or area outside brain #Script is running (command trimmed): 3dAutomask -apply_prefix ./vr_base_min_outlier_unif_ts_ns ./__tt_vr_base_min_outlier_unif_ts+orig ++ 3dAutomask: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Emperor Zhark *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./__tt_vr_base_min_outlier_unif_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_unif_ts+orig.BRIK is 35.420746 degrees from plumb. ++ Loading dataset ./__tt_vr_base_min_outlier_unif_ts+orig ++ Forming automask + Fixed clip level = 0.500100 + Used gradual clip level = 0.498900 .. 0.501150 + Number voxels above clip level = 37229 + Clustering voxels ... + Largest cluster has 37228 voxels + Clustering voxels ... + Largest cluster has 37197 voxels + Filled 299 voxels in small holes; now have 37496 voxels + Filled 3 voxels in large holes; now have 37499 voxels + Clustering voxels ... + Largest cluster has 37499 voxels + Clustering non-brain voxels ... + Clustering voxels ... + Largest cluster has 101765 voxels + Mask now has 37499 voxels ++ 37499 voxels in the mask [out of 139264: 26.93%] ++ first 11 x-planes are zero [from R] ++ last 9 x-planes are zero [from L] ++ first 2 y-planes are zero [from P] ++ last 6 y-planes are zero [from A] ++ first 0 z-planes are zero [from I] ++ last 1 z-planes are zero [from S] ++ applying mask to original data ++ Writing masked data ++ CPU time = 0.000000 sec #++ Computing weight mask #Script is running (command trimmed): 3dBrickStat -automask -percentile 90.000000 1 90.000000 ./vr_base_min_outlier_unif_ts_ns+orig #++ Applying threshold of 1.149901 on /lscratch/32397853/sub-10871/sub-10871.results/vr_base_min_outlier_unif_ts_ns+orig #Script is running (command trimmed): 3dcalc -datum float -prefix ./vr_base_min_outlier_unif_ts_ns_wt -a ./vr_base_min_outlier_unif_ts_ns+orig -expr 'min(1,(a/1.149901))' ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands #++ Aligning anat data to epi data #Script is running (command trimmed): 3dAllineate -lpc+ZZ -wtprefix ./anatSS.sub-10871_unflipped_ob_al_junk_wtal -weight ./vr_base_min_outlier_unif_ts_ns_wt+orig -source ./anatSS.sub-10871_unflipped_ob+orig -prefix ./anatSS.sub-10871_unflipped_ob_temp_al_junk -base ./vr_base_min_outlier_unif_ts_ns+orig -cmass -1Dmatrix_save ./anatSS.sub-10871_al_junk_e2a_only_mat.aff12.1D -master BASE -mast_dxyz 1.000000 -weight_frac 1.0 -maxrot 6 -maxshf 10 -warp aff -source_automask+4 -twobest 11 -twopass -maxrot 45 -maxshf 40 -fineblur 1 -source_automask+2 ++ 3dAllineate: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Zhark the Registrator ++ lpc+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./vr_base_min_outlier_unif_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:./vr_base_min_outlier_unif_ts_ns_wt+orig.BRIK is 35.420746 degrees from plumb. ++ Oblique dataset:./vr_base_min_outlier_unif_ts_ns+orig.BRIK is 35.420746 degrees from plumb. ++ Option '-cmass' enables center-of-mass code = 7 = +xyz ++ Source dataset: ./anatSS.sub-10871_unflipped_ob+orig.HEAD ++ Base dataset: ./vr_base_min_outlier_unif_ts_ns+orig.HEAD ++ Loading datasets into memory ++ NOTE: base and source coordinate systems have different handedness + Orientations: base=Left handed (RPI); source=Right handed (RAI) + - It is nothing to worry about: 3dAllineate aligns based on coordinates. + - But it is always important to check the alignment visually to be sure. ++ Local correlation: blok type = 'TOHD(17.0941)' ++ lpc+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration] ++ changing output grid spacing to 1.0000 mm ++ OpenMP thread count = 8 ++ ======= Allineation of 1 sub-bricks using Local Pearson Signed + Others ======= ++ *** Coarse pass begins *** ++ *** Fine pass begins *** + Final fine fit Parameters: x-shift= -0.0038 y-shift= 0.5132 z-shift= -0.0819 ... enorm= 0.5197 mm z-angle= -0.3517 x-angle= 1.8566 y-angle= 0.1601 ... total= 1.8958 deg x-scale= 0.9972 y-scale= 1.0063 z-scale= 1.0089 ... vol3D= 1.0125=(1.0041)^3 [base about same as source] y/x-shear= 0.0018 z/x-shear= 0.0042 z/y-shear= -0.0008 ++ Wrote -1Dmatrix_save ./anatSS.sub-10871_al_junk_e2a_only_mat.aff12.1D ++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 76.5 ++ ########################################################### ++ # PLEASE check results VISUALLY for alignment quality # ++ ########################################################### #Script is running (command trimmed): 3dLRflip -prefix ./__tt_anatSS.sub-10871_lr_al_junk -overwrite ./anatSS.sub-10871_unflipped_ob+orig ++ processing ./anatSS.sub-10871_unflipped_ob+orig ... #Script is running (command trimmed): 3dAllineate -lpc+ZZ -weight ./vr_base_min_outlier_unif_ts_ns_wt+orig -source ./__tt_anatSS.sub-10871_lr_al_junk+orig -prefix ./anatSS.sub-10871_flip_al_junk -base ./vr_base_min_outlier_unif_ts_ns+orig -cmass -1Dmatrix_save ./anatSS.sub-10871_flip__al_junk_mat.aff12.1D -master BASE -mast_dxyz 1.000000 -weight_frac 1.0 -maxrot 6 -maxshf 10 -warp aff -source_automask+4 -twobest 11 -twopass -maxrot 45 -maxshf 40 -fineblur 1 -source_automask+2 ++ 3dAllineate: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Zhark the Registrator ++ lpc+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration] *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./vr_base_min_outlier_unif_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:./vr_base_min_outlier_unif_ts_ns_wt+orig.BRIK is 35.420746 degrees from plumb. ++ Oblique dataset:./vr_base_min_outlier_unif_ts_ns+orig.BRIK is 35.420746 degrees from plumb. ++ Option '-cmass' enables center-of-mass code = 7 = +xyz ++ Source dataset: ./__tt_anatSS.sub-10871_lr_al_junk+orig.HEAD ++ Base dataset: ./vr_base_min_outlier_unif_ts_ns+orig.HEAD ++ Loading datasets into memory ++ NOTE: base and source coordinate systems have different handedness + Orientations: base=Left handed (RPI); source=Right handed (RAI) + - It is nothing to worry about: 3dAllineate aligns based on coordinates. + - But it is always important to check the alignment visually to be sure. ++ Local correlation: blok type = 'TOHD(17.0941)' ++ lpc+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration] ++ changing output grid spacing to 1.0000 mm ++ OpenMP thread count = 8 ++ ======= Allineation of 1 sub-bricks using Local Pearson Signed + Others ======= ++ *** Coarse pass begins *** ++ *** Fine pass begins *** + Final fine fit Parameters: x-shift= -3.3493 y-shift= 2.6075 z-shift= 0.6106 ... enorm= 4.2884 mm z-angle= -5.1005 x-angle= -0.1139 y-angle= 5.0540 ... total= 7.1837 deg x-scale= 0.9864 y-scale= 1.0550 z-scale= 0.9671 ... vol3D= 1.0064=(1.0021)^3 [base about same as source] y/x-shear= -0.0869 z/x-shear= 0.0154 z/y-shear= 0.0020 ++ Wrote -1Dmatrix_save ./anatSS.sub-10871_flip__al_junk_mat.aff12.1D ++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 74.7 ++ ########################################################### ++ # PLEASE check results VISUALLY for alignment quality # ++ ########################################################### #Script is running (command trimmed): 3dAllineate -allcostX1D IDENTITY __tt_lr_noflipcosts.1D -weight ./vr_base_min_outlier_unif_ts_ns_wt+orig -source ./anatSS.sub-10871_unflipped_ob_temp_al_junk+orig -base ./vr_base_min_outlier_unif_ts_ns+orig -cmass -master BASE -mast_dxyz 1.000000 -weight_frac 1.0 -maxrot 6 -maxshf 10 -warp aff -source_automask+4 -twobest 11 -twopass -maxrot 45 -maxshf 40 -fineblur 1 -source_automask+2 ++ 3dAllineate: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./vr_base_min_outlier_unif_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:./vr_base_min_outlier_unif_ts_ns_wt+orig.BRIK is 35.420746 degrees from plumb. ++ Oblique dataset:./vr_base_min_outlier_unif_ts_ns+orig.BRIK is 35.420746 degrees from plumb. ++ Option '-cmass' enables center-of-mass code = 7 = +xyz ++ Source dataset: ./anatSS.sub-10871_unflipped_ob_temp_al_junk+orig.HEAD ++ Base dataset: ./vr_base_min_outlier_unif_ts_ns+orig.HEAD ++ Loading datasets into memory ++ Local correlation: blok type = 'TOHD(17.0941)' ++ OpenMP thread count = 8 ++ Writing -allcostX1D results to '__tt_lr_noflipcosts.1D' ++ -allcostX1D finished #Script is running (command trimmed): 3dAllineate -allcostX1D IDENTITY __tt_lr_flipcosts.1D -weight ./vr_base_min_outlier_unif_ts_ns_wt+orig -source ./anatSS.sub-10871_flip_al_junk+orig -base ./vr_base_min_outlier_unif_ts_ns+orig -cmass -master BASE -mast_dxyz 1.000000 -weight_frac 1.0 -maxrot 6 -maxshf 10 -warp aff -source_automask+4 -twobest 11 -twopass -maxrot 45 -maxshf 40 -fineblur 1 -source_automask+2 ++ 3dAllineate: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./vr_base_min_outlier_unif_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:./vr_base_min_outlier_unif_ts_ns_wt+orig.BRIK is 35.420746 degrees from plumb. ++ Oblique dataset:./vr_base_min_outlier_unif_ts_ns+orig.BRIK is 35.420746 degrees from plumb. ++ Option '-cmass' enables center-of-mass code = 7 = +xyz ++ Source dataset: ./anatSS.sub-10871_flip_al_junk+orig.HEAD ++ Base dataset: ./vr_base_min_outlier_unif_ts_ns+orig.HEAD ++ Loading datasets into memory ++ Local correlation: blok type = 'TOHD(17.0941)' ++ OpenMP thread count = 8 ++ Writing -allcostX1D results to '__tt_lr_flipcosts.1D' ++ -allcostX1D finished No flip cost is -0.250023 for lpc+ZZ cost function Flip cost is -0.080651 for lpc+ZZ cost function Data does not need flipping #Script is running (command trimmed): cat_matvec -ONELINE ./anatSS.sub-10871_al_junk_e2a_only_mat.aff12.1D ./anatSS.sub-10871_unflipped_obla2e_mat.1D -I > ./anatSS.sub-10871_al_junk_mat.aff12.1D #++ Combining anat to epi and oblique transformations #Script is running (command trimmed): 3dAllineate -base ./vr_base_min_outlier_unif_ts_ns+orig -1Dmatrix_apply ./anatSS.sub-10871_al_junk_mat.aff12.1D -prefix ./anatSS.sub-10871_al_junk -input ./anatSS.sub-10871_unflipped+orig -master BASE -mast_dxyz 1.000000 -weight_frac 1.0 -maxrot 6 -maxshf 10 -warp aff -source_automask+4 -twobest 11 -twopass -maxrot 45 -maxshf 40 -fineblur 1 -source_automask+2 ++ 3dAllineate: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Zhark the Registrator *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./vr_base_min_outlier_unif_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:./vr_base_min_outlier_unif_ts_ns+orig.BRIK is 35.420746 degrees from plumb. ++ Source dataset: ./anatSS.sub-10871_unflipped+orig.HEAD ++ Base dataset: ./vr_base_min_outlier_unif_ts_ns+orig.HEAD ++ Loading datasets into memory ++ NOTE: base and source coordinate systems have different handedness + Orientations: base=Left handed (RPI); source=Right handed (LPI) + - It is nothing to worry about: 3dAllineate aligns based on coordinates. + - But it is always important to check the alignment visually to be sure. + -cmass x y z shifts = 1.433 52.893 30.402 + shift search range is +/- = 60.669 60.669 42.372 + 2.4% 87.2% 71.8% ++ changing output grid spacing to 1.0000 mm ++ OpenMP thread count = 8 ++ ========== Applying transformation to 1 sub-bricks ========== ++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 1.1 ++ ########################################################### #++ 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.sub-10871+orig -suffix \ _al_junk -epi vr_base_min_outlier_unif+orig -epi_base 0 -epi_strip \ 3dAutomask -anat_has_skull no -giant_move -cost lpc+ZZ -check_flip \ -volreg off -tshift off" \ ./anatSS.sub-10871_al_junk+orig #++ Removing all the temporary files #Script is running: \rm -f ./__tt_vr_base_min_outlier_unif* #Script is running: \rm -f ./__tt_anatSS.sub-10871* # Finished alignment successfully if ( ! -f anatQQ.sub-10871+tlrc.HEAD ) then foreach run ( 01 ) 3dvolreg -verbose -zpad 1 -base vr_base_min_outlier+orig -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb01.sub-10871.r01.tshift+orig ++ 3dvolreg: AFNI version=AFNI_26.3.01 (Oct 8 2026) [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 35.420746 degrees from plumb. ++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK ++ Oblique dataset:./pb01.sub-10871.r01.tshift+orig.BRIK is 35.420746 degrees from plumb. ++ Reading input dataset ./pb01.sub-10871.r01.tshift+orig.BRIK ++ Edging: x=3 y=3 z=2 ++ Creating mask for -maxdisp + Automask has 39861 voxels + 5699 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ edt_blur: sigx 9, dx 3, fwhm 21.1934, sfac 2.5, firx 8 ++ Starting final pass on 242 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.. ++ CPU time for realignment=0 s [=0 s/sub-brick] ++ Min : roll=-0.239 pitch=-0.119 yaw=-0.010 dS=-0.185 dL=-0.319 dP=-0.348 ++ Mean: roll=-0.074 pitch=+0.215 yaw=+0.093 dS=+0.030 dL=-0.121 dP=-0.167 ++ Max : roll=+0.056 pitch=+0.701 yaw=+0.219 dS=+0.135 dL=+0.064 dP=+0.112 ++ Max displacements (mm) for each sub-brick: 0.20(0.00) 0.29(0.12) 0.30(0.05) 0.28(0.03) 0.26(0.03) 0.26(0.05) 0.20(0.06) 0.19(0.04) 0.20(0.04) 0.20(0.11) 0.19(0.09) 0.18(0.03) 0.21(0.04) 0.20(0.03) 0.18(0.05) 0.18(0.03) 0.22(0.06) 0.18(0.12) 0.22(0.09) 0.20(0.06) 0.21(0.03) 0.23(0.03) 0.20(0.04) 0.19(0.02) 0.23(0.06) 0.19(0.07) 0.18(0.06) 0.12(0.06) 0.19(0.08) 0.09(0.11) 0.00(0.09) 0.08(0.08) 0.06(0.04) 0.06(0.02) 0.06(0.03) 0.10(0.04) 0.07(0.05) 0.07(0.03) 0.10(0.05) 0.09(0.03) 0.06(0.05) 0.11(0.06) 0.09(0.04) 0.10(0.03) 0.10(0.03) 0.08(0.07) 0.16(0.12) 0.25(0.14) 0.18(0.17) 0.18(0.08) 0.15(0.05) 0.16(0.04) 0.14(0.04) 0.15(0.04) 0.16(0.03) 0.15(0.03) 0.16(0.02) 0.19(0.04) 0.19(0.01) 0.18(0.02) 0.18(0.03) 0.18(0.02) 0.16(0.04) 0.18(0.06) 0.16(0.03) 0.16(0.02) 0.17(0.03) 0.16(0.04) 0.18(0.03) 0.20(0.04) 0.21(0.03) 0.21(0.03) 0.26(0.06) 0.30(0.13) 0.22(0.14) 0.23(0.04) 0.22(0.03) 0.21(0.06) 0.22(0.02) 0.24(0.03) 0.24(0.02) 0.24(0.02) 0.26(0.03) 0.24(0.03) 0.26(0.02) 0.28(0.04) 0.27(0.03) 0.27(0.06) 0.26(0.09) 0.25(0.06) 0.26(0.02) 0.26(0.02) 0.25(0.04) 0.30(0.05) 0.30(0.05) 0.31(0.13) 0.30(0.15) 0.31(0.08) 0.33(0.05) 0.31(0.04) 0.34(0.04) 0.38(0.04) 0.34(0.05) 0.34(0.09) 0.42(0.12) 0.35(0.13) 0.37(0.03) 0.38(0.03) 0.37(0.03) 0.39(0.03) 0.38(0.03) 0.36(0.03) 0.36(0.02) 0.39(0.06) 0.40(0.04) 0.39(0.04) 0.42(0.04) 0.41(0.03) 0.40(0.01) 0.41(0.03) 0.39(0.06) 0.38(0.03) 0.43(0.04) 0.43(0.04) 0.51(0.10) 0.75(0.31) 0.63(0.26) 0.59(0.07) 0.55(0.05) 0.56(0.05) 0.54(0.04) 0.57(0.04) 0.57(0.09) 0.57(0.08) 0.61(0.07) 0.57(0.09) 0.60(0.08) 0.56(0.07) 0.58(0.03) 0.56(0.04) 0.56(0.02) 0.58(0.05) 0.58(0.03) 0.61(0.07) 0.57(0.05) 0.66(0.11) 0.68(0.05) 0.59(0.14) 0.62(0.04) 0.63(0.04) 0.62(0.06) 0.62(0.03) 0.62(0.04) 0.61(0.03) 0.61(0.02) 0.62(0.03) 0.63(0.04) 0.64(0.04) 0.64(0.02) 0.66(0.02) 0.68(0.03) 0.67(0.04) 0.69(0.05) 0.69(0.03) 0.68(0.03) 0.69(0.03) 0.72(0.05) 0.71(0.06) 0.67(0.09) 0.69(0.06) 0.68(0.02) 0.72(0.05) 0.80(0.10) 0.77(0.07) 0.74(0.06) 0.73(0.04) 0.74(0.04) 0.74(0.02) 0.78(0.08) 0.74(0.18) 0.75(0.16) 0.74(0.07) 0.79(0.06) 0.78(0.03) 0.79(0.04) 0.79(0.02) 0.79(0.03) 0.81(0.03) 0.81(0.02) 0.81(0.02) 0.84(0.03) 0.87(0.06) 0.86(0.03) 0.86(0.05) 0.87(0.06) 0.85(0.03) 0.87(0.03) 0.88(0.03) 0.90(0.05) 0.90(0.07) 0.92(0.06) 0.90(0.04) 0.92(0.06) 0.93(0.02) 0.90(0.04) 0.91(0.05) 0.96(0.08) 0.94(0.03) 0.94(0.03) 0.96(0.03) 0.96(0.03) 0.97(0.05) 0.97(0.03) 0.96(0.04) 0.94(0.08) 0.91(0.05) 1.01(0.22) 1.45(0.55) 1.53(0.11) 1.31(0.32) 1.30(0.04) 1.29(0.03) 1.27(0.05) 1.28(0.05) 1.28(0.03) 1.30(0.04) 1.33(0.07) 1.32(0.05) 1.33(0.03) 1.32(0.04) 1.29(0.04) 1.29(0.04) 1.29(0.05) 1.28(0.03) 1.27(0.06) 1.29(0.05) 1.30(0.01) 1.33(0.04) 1.32(0.04) 1.29(0.05) 1.34(0.06) 1.37(0.08) ++ Max displacement in automask = 1.53 (mm) at sub-brick 218 ++ Max delta displ in automask = 0.55 (mm) at sub-brick 217 ++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK 3dcalc -overwrite -a pb01.sub-10871.r01.tshift+orig -expr 1 -prefix rm.epi.all1 ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands cat_matvec -ONELINE anatQQ.sub-10871.aff12.1D anatSS.sub-10871_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D 3dNwarpApply -master anatQQ.sub-10871+tlrc -dxyz 3 -source pb01.sub-10871.r01.tshift+orig -nwarp anatQQ.sub-10871_WARP.nii mat.r01.warp.aff12.1D -prefix rm.epi.nomask.r01 ++ 3dNwarpApply: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.sub-10871+tlrc' ++ output grid size = 3 mm *+ WARNING: If you are performing spatial transformations on an oblique dset, such as ./pb01.sub-10871.r01.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:./pb01.sub-10871.r01.tshift+orig.BRIK is 35.420746 degrees from plumb. ++ opened source dataset 'pb01.sub-10871.r01.tshift+orig' ++ Processing -nwarp ++ Warping:.................................................Z ++ total Elapsed time = 599.4 sec 3dNwarpApply -master anatQQ.sub-10871+tlrc -dxyz 3 -source rm.epi.all1+orig -nwarp anatQQ.sub-10871_WARP.nii mat.r01.warp.aff12.1D -interp cubic -ainterp NN -quiet -prefix rm.epi.1.r01 ++ 3dNwarpApply: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.sub-10871+tlrc' ++ output grid size = 3 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 35.420746 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_26.3.01 (Oct 8 2026) [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_26.3.01 (Oct 8 2026) [64-bit] foreach run ( 01 ) 3dcalc -a rm.epi.nomask.r01+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.sub-10871.r01.volreg ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands end cat_matvec -ONELINE anatQQ.sub-10871.aff12.1D anatSS.sub-10871_al_junk_mat.aff12.1D -I 3dNwarpApply -master anatQQ.sub-10871+tlrc -dxyz 3 -source vr_base_min_outlier+orig -nwarp anatQQ.sub-10871_WARP.nii mat.basewarp.aff12.1D -prefix final_epi_vr_base_min_outlier ++ 3dNwarpApply: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Zhark the Warped ++ -master dataset is 'anatQQ.sub-10871+tlrc' ++ output grid size = 3 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 35.420746 degrees from plumb. ++ opened source dataset 'vr_base_min_outlier+orig' ++ Processing -nwarp ++ Warping:.Z ++ total Elapsed time = 7.5 sec 3dcopy anatQQ.sub-10871+tlrc anat_final.sub-10871 ++ 3dcopy: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] 3dAllineate -base final_epi_vr_base_min_outlier+tlrc -allcostX -input anat_final.sub-10871+tlrc tee out.allcostX.txt ++ 3dAllineate: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Zhark the Registrator ++ Source dataset: ./anat_final.sub-10871+tlrc.HEAD ++ Base dataset: ./final_epi_vr_base_min_outlier+tlrc.HEAD ++ Loading datasets into memory ++ Local correlation: blok type = 'TOHD(15.531)' + -cmass x y z shifts = 1.092 0.360 -8.322 + shift search range is +/- = 69.336 79.929 71.262 ++ OpenMP thread count = 8 + 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 = 0.176304 sp = 0.322846 mi = 2.50554 crM = 0.0852462 nmi = 0.840338 je = 2.50554 hel = -0.0892069 crA = 0.292573 crU = 0.273793 lss = 0.823696 lpc = 0.329866 lpa = 0.670134 lpc+ = 0.499433 lpa+ = 0.8397 ++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 2.2 ++ ########################################################### 3dNwarpApply -source copy_af_anat_w_skull+orig -master anat_final.sub-10871+tlrc -ainterp wsinc5 -nwarp anatQQ.sub-10871_WARP.nii anatQQ.sub-10871.aff12.1D -prefix follow_anat_anat_w_skull ++ 3dNwarpApply: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Zhark the Warped ++ opened source dataset 'copy_af_anat_w_skull+orig' ++ -master dataset is 'anat_final.sub-10871+tlrc' ++ Processing -nwarp ++ Warping:.Z ++ total Elapsed time = 7.8 sec @radial_correlate -nfirst 0 -polort 4 -do_clean yes -rdir radcor.pb02.volreg pb02.sub-10871.r01.volreg+tlrc.HEAD ++ 3dTcat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ elapsed time = 10.3 s ++ 3dAutomask: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Emperor Zhark -- radcor: detrend -polort 4, new eset = det.r01 input : epi.r01+tlrc ++ 3dTproject: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Cox the Algebraic (Linear) ++ Setting up regressors ++ 1 Blocks * 5 polynomials -- 5 polort regressors ++ 242 retained time points MINUS 5 regressors ==> 237 D.O.F. left ++ no -mask option ==> processing all 311296 voxels in dataset ++ 3dTproject input data :: 92713 vectors are constant -- radcor: running correlation on dataset pb02.sub-10871.r01.volreg+tlrc.HEAD ... ++ radcor: merge blur: rad 20, FWHM 40 ++ 3dmerge: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ default -1dindex = 0 ++ default -1tindex = 1 Program 3dmerge 3dmerge: edit and combine 3D datasets, by RW Cox ++ editing input dataset in memory (287.4 MB) ++ edt_blur: sigx 16.9864, dx 3, fwhm 40, sfac 2.5, firx 15 .................................................................................................................................................................................................................................................. -- Wrote edited dataset: ./sphere.mean.20.r01+tlrc.BRIK ++ 3dTcorrelate: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Wrote dataset: ./radcor.20.r01.corr+tlrc.BRIK ++ 3dbucket: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ---- radcor: done ++ have do_clean, cleaning up... foreach run ( 01 ) 3dAutomask -prefix rm.mask_r01 pb02.sub-10871.r01.volreg+tlrc ++ 3dAutomask: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: Emperor Zhark ++ Loading dataset pb02.sub-10871.r01.volreg+tlrc ++ Forming automask + Fixed clip level = 402.399078 + Used gradual clip level = 365.468201 .. 465.998352 + Number voxels above clip level = 66938 + Clustering voxels ... + Largest cluster has 66415 voxels + Clustering voxels ... + Largest cluster has 65888 voxels + Filled 485 voxels in small holes; now have 66373 voxels + Filled 1 voxels in large holes; now have 66374 voxels + Clustering voxels ... + Largest cluster has 66371 voxels + Clustering non-brain voxels ... + Clustering voxels ... + Largest cluster has 244925 voxels + Mask now has 66371 voxels ++ 66371 voxels in the mask [out of 311296: 21.32%] ++ first 8 x-planes are zero [from L] ++ last 8 x-planes are zero [from R] ++ first 8 y-planes are zero [from P] ++ last 6 y-planes are zero [from A] ++ first 0 z-planes are zero [from I] ++ last 8 z-planes are zero [from S] ++ CPU time = 0.000000 sec end 3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub-10871 ++ processing 1 input dataset(s), NN=2... ++ padding all datasets by 0 (for dilations) ++ have 1 volume of input, no combining ++ frac 0 over 1 volumes gives min count 0 ++ voxel limits: 0 clipped, 66371 survived, 244925 were zero ++ writing result full_mask.sub-10871... 3dresample -master full_mask.sub-10871+tlrc -input anatQQ.sub-10871+tlrc -prefix rm.resam.anat 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub-10871 ++ processing 1 input dataset(s), NN=2... ++ padding all datasets by 5 (for dilations) ++ have 1 volume of input, no combining ++ frac 0 over 1 volumes gives min count 0 ++ voxel limits: 0 clipped, 73800 survived, 237496 were zero ++ filled 0 holes (0 voxels) ++ writing result mask_anat.sub-10871... 3dmask_tool -input full_mask.sub-10871+tlrc mask_anat.sub-10871+tlrc -inter -prefix mask_epi_anat.sub-10871 ++ processing 2 input dataset(s), NN=2... ++ padding all datasets by 0 (for dilations) ++ have 2 volumes of input to combine ++ frac 1 over 2 volumes gives min count 2 ++ voxel limits: 12713 clipped, 63729 survived, 234854 were zero ++ writing result mask_epi_anat.sub-10871... 3dABoverlap -no_automask full_mask.sub-10871+tlrc mask_anat.sub-10871+tlrc tee out.mask_ae_overlap.txt ++ 3dABoverlap: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] #A=./full_mask.sub-10871+tlrc.BRIK B=./mask_anat.sub-10871+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) 66371 73800 76442 63729 2642 10071 3.9807 13.6463 1.0975 0.9453 1.0583 3ddot -dodice full_mask.sub-10871+tlrc mask_anat.sub-10871+tlrc tee out.mask_ae_dice.txt 0.909304 3dresample -master mask_epi_anat.sub-10871+tlrc -prefix ./rm.resam.group -input /data/NIMH_SSCC/ptaylor/REF_TEMPLATES/MNI152_2009_template_SSW.nii.gz[0] 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group ++ processing 1 input dataset(s), NN=2... ++ padding all datasets by 5 (for dilations) ++ have 1 volume of input, no combining ++ frac 0 over 1 volumes gives min count 0 ++ voxel limits: 0 clipped, 71053 survived, 240243 were zero ++ filled 0 holes (0 voxels) ++ writing result mask_group... 3ddot -dodice mask_anat.sub-10871+tlrc mask_group+tlrc tee out.mask_at_dice.txt 0.979462 foreach run ( 01 ) 3dBlurInMask -preserve -FWHM 6.0 -Mmask mask_epi_anat.sub-10871+tlrc -prefix pb03.sub-10871.r01.blur pb02.sub-10871.r01.volreg+tlrc ++ 3dBlurInMask: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: RW Cox ++ 1 unique nonzero values in -Mmask; 63729 nonzero voxels ++ forcing output to be stored in float format ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 + voxels in Mmask[1] = 63729 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 ++ mri_blur3D: #iter=6 fx=0.03006 fy=0.03006 fz=0.03006 end foreach run ( 01 ) 3dTstat -prefix rm.mean_r01 pb03.sub-10871.r01.blur+tlrc ++ 3dTstat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: KR Hammett & RW Cox 3dcalc -a pb03.sub-10871.r01.blur+tlrc -b rm.mean_r01+tlrc -c mask_epi_extents+tlrc -expr c * min(200, a/b*100)*step(a)*step(b) -prefix pb04.sub-10871.r01.scale ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands end 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D 1d_tool.py -infile motion_demean.1D -set_nruns 1 -split_into_pad_runs mot_demean 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_sub-10871 total number of censored TRs (simple form) = 2 1deval -a motion_sub-10871_censor.1D -b outcount_sub-10871_censor.1D -expr a*b 3dresample -master final_epi_vr_base_min_outlier+tlrc -rmode NN -input ROI_import_MNI_2009c_asym+tlrc -prefix ROI_import_MNI_2009c_asym_resam 3drefit -copytables ROI_import_MNI_2009c_asym+tlrc ROI_import_MNI_2009c_asym_resam+tlrc ++ 3drefit: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset ROI_import_MNI_2009c_asym_resam+tlrc + copy tabledata ++ 3drefit processed 1 datasets 3drefit -cmap INT_CMAP ROI_import_MNI_2009c_asym_resam+tlrc ++ 3drefit: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset ROI_import_MNI_2009c_asym_resam+tlrc ++ 3drefit processed 1 datasets 1d_tool.py -infile censor_sub-10871_combined_2.1D -show_trs_uncensored space set ktrs = 1dcat out.keep_trs_rall.txt 3dDeconvolve -input pb04.sub-10871.r01.scale+tlrc.HEAD -censor censor_sub-10871_combined_2.1D -ortvec mot_demean.r01.1D mot_demean_r01 -polort 4 -num_stimts 2 -stim_times_AM1 1 stimuli/times.CONTROL.txt dmBLOCK -stim_label 1 CONTROL -stim_times_AM1 2 stimuli/times.TASK.txt dmBLOCK -stim_label 2 TASK -jobs 8 -gltsym SYM: TASK -CONTROL -glt_label 1 T-C -gltsym SYM: 0.5*TASK +0.5*CONTROL -glt_label 2 meanTC -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -errts errts.sub-10871 -x1D_stop -bucket stats.sub-10871 ++ '-stim_times_AM1 1 stimuli/times.CONTROL.txt' has 1 auxiliary values per time point ++ '-stim_times_AM1 1': basis function model 'dmBLOCK' uses 1 parameters, out of the 1 found in timing file 'stimuli/times.CONTROL.txt' ++ '-stim_times_AM1 2 stimuli/times.TASK.txt' has 1 auxiliary values per time point ++ '-stim_times_AM1 2': basis function model 'dmBLOCK' uses 1 parameters, out of the 1 found in timing file 'stimuli/times.TASK.txt' ++ 3dDeconvolve extending num_stimts from 2 to 8 due to -ortvec ++ 3dDeconvolve: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: B. Douglas Ward, et al. ++ STAT automask has 263131 voxels (out of 311296 = 84.5%) ++ Skipping check for initial transients ++ Input polort=4; Longest run=484.0 s; Recommended minimum polort=4 ++ OK ++ ++ -stim_times using TR=2 s for stimulus timing conversion ++ -stim_times using TR=2 s for any -iresp output datasets ++ [you can alter the -iresp TR via the -TR_times option] ++ ** -stim_times NOTE ** guessing GLOBAL times if 1 time per line; LOCAL otherwise ++ ** GUESSED ** -stim_times_AM1 1 using LOCAL times ++ ** GUESSED ** -stim_times_AM1 2 using LOCAL times ------------------------------------------------------------ GLT matrix from 'SYM: TASK -CONTROL': 0 0 0 0 0 -1 1 0 0 0 0 0 0 ------------------------------------------------------------ GLT matrix from 'SYM: 0.5*TASK +0.5*CONTROL': 0 0 0 0 0 0.5 0.5 0 0 0 0 0 0 ++ Number of time points: 242 (before censor) ; 240 (after) + Number of parameters: 13 [11 baseline ; 2 signal] ++ total shared memory needed = 11,206,656 bytes (about 11 million) ++ mmap() memory allocated: 11,206,656 bytes (about 11 million) ++ Memory required for output bricks = 11,206,656 bytes (about 11 million) ++ Wrote matrix image to file X.jpg ++ Wrote matrix values to file X.xmat.1D ++ ========= Things you can do with the matrix file ========= ++ (a) Linear regression with ARMA(1,1) modeling of serial correlation: 3dREMLfit -matrix X.xmat.1D -input pb04.sub-10871.r01.scale+tlrc.HEAD \ -tout -Rbuck stats.sub-10871_REML -Rvar stats.sub-10871_REMLvar \ -Rerrts errts.sub-10871_REML -verb ++ N.B.: 3dREMLfit command above written to file stats.REML_cmd ++ (b) Visualization/analysis of the matrix via ExamineXmat.R ++ (c) Synthesis of sub-model datasets using 3dSynthesize ++ ========================================================== ++ Wrote matrix values to file X.nocensor.xmat.1D ++ ----- Signal+Baseline matrix condition [X] (240x13): 6.46803 ++ VERY GOOD ++ ++ ----- Signal-only matrix condition [X] (240x2): 1.09035 ++ VERY GOOD ++ ++ ----- Baseline-only matrix condition [X] (240x11): 6.23901 ++ VERY GOOD ++ ++ ----- stim_base-only matrix condition [X] (240x6): 4.96208 ++ VERY GOOD ++ ++ ----- polort-only matrix condition [X] (240x5): 1.01961 ++ VERY GOOD ++ ++ 3dDeconvolve exits: -x1D_stop option was invoked if ( 0 != 0 ) then 1d_tool.py -show_cormat_warnings -infile X.xmat.1D tee out.cormat_warn.txt Warnings regarding Correlation Matrix: X.xmat.1D severity correlation cosine regressor pair -------- ----------- ------ ---------------------------------------- medium: -0.412 0.171 ( 5 vs. 6) CONTROL#0 vs. TASK#0 1d_tool.py -show_xmat_warnings -infile X.xmat.1D tee out.xmat_warn.txt 1d_tool.py -show_df_info -infile X.xmat.1D tee out.df_info.txt initial DF : 242 : 100.0% DF used for regs of interest : 2 : 0.8% DF used for censoring : 2 : 0.8% DF used for polort : 5 : 2.1% DF used for motion : 6 : 2.5% total DF used : 15 : 6.2% final DF : 227 : 93.8% tcsh -x stats.REML_cmd 3dREMLfit -matrix X.xmat.1D -input pb04.sub-10871.r01.scale+tlrc.HEAD -tout -Rbuck stats.sub-10871_REML -Rvar stats.sub-10871_REMLvar -Rerrts errts.sub-10871_REML -verb ++ 3dREMLfit: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: RWCox ++ Number of OpenMP threads = 8 ++ No mask ==> computing for all 311296 voxels ++ FDR automask has 263131 voxels (out of 311296 = 84.5%) ++ ----- matrix condition (240x13): 6.46803 ++ VERY GOOD ++ + masked off 92719 voxels for being all zero; 218577 left in mask ++ Converting input dataset to vector image + dataset = 301 million bytes + vectim = 212 million bytes ++ starting REML setup calculations; total CPU=0.00 Elapsed=5.40 + X matrix: 95.577% of elements are nonzero + starting 8 OpenMP threads for REML setup + REML setup finished: matrix rows=240 cols=13; 109*1 cases; total CPU=0.00 Elapsed=5.41 + average case bandwidth = 16.58 ++ REML voxel loop: [8 threads]0123456789.0123456789.0123456789.012345 + ARMA voxel parameters estimated: total CPU=0.00 Elapsed=23.42 ++ Ljung-Box max lag parameter h = 31 (29 chi-squared DOF) ++ GLSQ loop:0123456789.0123456789.0123456789.0123456789.0123456789. + GLSQ regression done: total CPU=0.00 Elapsed=40.59 ++ creating FDR curves in dataset stats.sub-10871_REML+tlrc ++ Smallest FDR q [0 Full_Fstat] = 1.17999e-12 ++ Smallest FDR q [2 CONTROL#0_Tstat] = 0.000918181 ++ Smallest FDR q [4 TASK#0_Tstat] = 9.39416e-13 ++ Smallest FDR q [6 T-C#0_Tstat] = 3.26509e-07 ++ Smallest FDR q [8 meanTC#0_Tstat] = 4.92109e-11 + Added 5 FDR curves to dataset stats.sub-10871_REML+tlrc + unloading input dataset and REML matrices ++ 3dREMLfit is all done! total CPU=0.00 Elapsed=54.04 if ( 0 != 0 ) then 3dTcat -prefix all_runs.sub-10871 pb04.sub-10871.r01.scale+tlrc.HEAD ++ 3dTcat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ elapsed time = 10.4 s 3dTstat -mean -prefix rm.signal.all all_runs.sub-10871+tlrc[1dcat out.keep_trs_rall.txt] ++ 3dTstat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: KR Hammett & RW Cox 3dTstat -stdev -prefix rm.noise.all errts.sub-10871_REML+tlrc[1dcat out.keep_trs_rall.txt] ++ 3dTstat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: KR Hammett & RW Cox 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -expr a/b -prefix TSNR.sub-10871 ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands compute_ROI_stats.tcsh -out_dir tsnr_stats_regress -stats_file tsnr_stats_regress/stats_auto_brain.txt -dset_ROI mask_epi_anat.sub-10871+tlrc -dset_data TSNR.sub-10871+tlrc -rset_label brain -rval_list 1 ++ writing stats text to tsnr_stats_regress/stats_auto_brain.txt dset: brain (mask_epi_anat.sub-10871), Nroi: 1 ---------------------------------------------- ROI Nvox Nzer Dvox Tmin T25% Tmed T75% Tmax X Y Z ROI_name --- ---- ---- ---- ---- ---- ---- ---- ---- ----- ----- ----- -------- 1 63729 0 17.1 13 166 212 255 514 -7.5 31.5 28.5 NONE compute_ROI_stats.tcsh -out_dir tsnr_stats_regress -stats_file tsnr_stats_regress/stats_auto_MNI_2009c_asym.txt -dset_ROI ROI_import_MNI_2009c_asym_resam+tlrc -dset_data TSNR.sub-10871+tlrc -rset_label MNI_2009c_asym -rval_list ALL_LT ++ replacing ALL_LT with 12 entries from ROI_import_MNI_2009c_asym_resam+tlrc 10 11 12 13 14 20 21 22 23 24 30 31 ++ writing stats text to tsnr_stats_regress/stats_auto_MNI_2009c_asym.txt dset: MNI_2009c_asym (ROI_import_MNI_2009c_asym_resam), Nroi: 12 ---------------------------------------------------------------- ROI Nvox Nzer Dvox Tmin T25% Tmed T75% Tmax X Y Z ROI_name --- ---- ---- ---- ---- ---- ---- ---- ---- ----- ----- ----- -------- 10 252 0 1.7 8 136 187 233 403 4.5 91.5 1.5 SYAF-LH_VisCent_Striate_1 11 602 0 2.2 23 212 240 264 356 43.5 19.5 58.5 SYAF-LH_SomMotA_1 12 465 0 2.2 68 177 209 230 362 7.5 -13.5 37.5 SYAF-LH_SalVentAttnB_PFCmp_1 13 786 0 2.8 0 13 30 111 245 7.5 -16.5 -19.5 SYAF-LH_LimbicB_OFC_1 14 1142 18 2.4 1 7 14 37 241 22.5 7.5 -28.5 SYAF-LH_LimbicA_TempPole_1 20 499 0 2.0 9 144 180 213 400 -10.5 82.5 7.5 GHCP-R_Primary_Visual_Cortex 21 161 0 1.0 81 176 232 265 340 -13.5 31.5 82.5 GHCP-R_Primary_Sensory_Cortex 22 58 0 1.7 110 155 173 193 234 -4.5 -22.5 31.5 GHCP-R_Anterior_24_prime 23 194 0 2.0 1 12 22 31 126 -10.5 -25.5 -22.5 GHCP-R_Orbital_Frontal_Complex 24 384 0 2.2 0 11 25 76 189 -40.5 -19.5 -31.5 GHCP-R_Area_TG_dorsal 30 107 0 1.7 1 34 99 152 201 -25.5 1.5 -19.5 JULI-RH_Amygdala 31 20 0 1.0 26 88 113 126 146 -4.5 -10.5 -4.5 JULI-RH_Accumbens 3dTnorm -norm2 -prefix rm.errts.unit errts.sub-10871_REML+tlrc ++ 3dTnorm: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: RW Cox 3dmaskave -quiet -mask mask_epi_anat.sub-10871+tlrc rm.errts.unit+tlrc ++ 3dmaskave: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] +++ 63729 voxels survive the mask 3dTstat -sos -prefix - mean.errts.unit.1D' ++ 3dTstat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: KR Hammett & RW Cox echo -- GCOR = `cat out.gcor.1D` cat out.gcor.1D -- GCOR = 0.0551127 3dmaskave -quiet -mask mask_epi_anat.sub-10871+tlrc errts.sub-10871_REML+tlrc ++ 3dmaskave: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] +++ 63729 voxels survive the mask 3dTcorr1D -prefix corr_brain errts.sub-10871_REML+tlrc mean.errts.1D ++ 3dTcorr1D: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] + reading dataset file errts.sub-10871_REML+tlrc + reading 1D file mean.errts.1D + loading dataset ./errts.sub-10871_REML+tlrc.BRIK into memory ++ Start correlations: 311296 voxels X 1 time series(242); 1 threads ++ THD_Tcorr1D: 92719 voxels skipped because were constant in time ++ Wrote dataset: ./corr_brain+tlrc.BRIK 3dcalc -a all_runs.sub-10871+tlrc -b errts.sub-10871_REML+tlrc -expr a-b -prefix fitts.sub-10871_REML ++ 3dcalc: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: A cast of thousands 1dcat X.nocensor.xmat.1D[5] 1dcat X.nocensor.xmat.1D[6] 1d_tool.py -infile X.nocensor.xmat.1D -write_xstim X.stim.xmat.1D 3dTstat -sum -prefix sum_ideal.1D X.stim.xmat.1D ++ 3dTstat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: KR Hammett & RW Cox ++ Output dataset ./sum_ideal.1D touch blur_est.sub-10871.1D mkdir files_ACF touch blur.err_reml.1D foreach run ( 01 ) set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run $run` 1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 01 if ( 0..215,218..241 == ) continue 3dFWHMx -detrend -mask mask_epi_anat.sub-10871+tlrc -ACF files_ACF/out.3dFWHMx.ACF.err_reml.r01.1D errts.sub-10871_REML+tlrc[0..215,218..241] ++ 3dFWHMx: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: The Bob ++ Number of voxels in mask = 63729 ++ detrending start: 19 baseline funcs, 240 time points + detrending done (0.00 CPU s thus far) ++ start ACF calculations out to radius = 21.07 mm + ACF done (0.00 CPU s thus far) ++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.err_reml.r01.1D ++ 1dplot: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: RWC et al. + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.err_reml.r01.1D.png end set blurs = ( `3dTstat -mean -prefix - blur.err_reml.1D'{0..$(2)}'\'` ) 3dTstat -mean -prefix - blur.err_reml.1D{0..$(2)}' ++ 3dTstat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: KR Hammett & RW Cox echo average err_reml FWHM blurs: 0 0 0 0 average err_reml FWHM blurs: 0 0 0 0 echo 0 0 0 0 # err_reml FWHM blur estimates set blurs = ( `3dTstat -mean -prefix - blur.err_reml.1D'{1..$(2)}'\'` ) 3dTstat -mean -prefix - blur.err_reml.1D{1..$(2)}' ++ 3dTstat: AFNI version=AFNI_26.3.01 (Oct 8 2026) [64-bit] ++ Authored by: KR Hammett & RW Cox echo average err_reml ACF blurs: 0.647473 3.93749 12.0828 10.399 average err_reml ACF blurs: 0.647473 3.93749 12.0828 10.399 echo 0.647473 3.93749 12.0828 10.399 # err_reml ACF blur estimates gen_epi_review.py -script @epi_review.sub-10871 -dsets pb00.sub-10871.r01.tcat+orig.HEAD cat cat out.ap_uvars.txt afni_python_wrapper.py -eval data_file_to_json() gen_ss_review_scripts.py -exit0 -init_uvars_json out.ap_uvars.json -write_uvars_json out.ss_review_uvars.json ++ writing ss review basic: @ss_review_basic ++ writing ss review driver: @ss_review_driver ++ writing ss review drive commands: @ss_review_driver_commands rm -f rm.epi.1.r01+tlrc.BRIK.gz rm.epi.1.r01+tlrc.HEAD rm.epi.all1+orig.BRIK.gz rm.epi.all1+orig.HEAD rm.epi.min.r01+tlrc.BRIK.gz rm.epi.min.r01+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK.gz rm.epi.nomask.r01+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK.gz rm.epi.volreg.r01+orig.HEAD rm.errts.unit+tlrc.BRIK.gz rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK.gz rm.mask_r01+tlrc.HEAD rm.mean_r01+tlrc.BRIK.gz rm.mean_r01+tlrc.HEAD rm.noise.all+tlrc.BRIK.gz rm.noise.all+tlrc.HEAD rm.out.cen.r01.1D rm.resam.anat+tlrc.BRIK.gz rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK.gz rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK.gz rm.signal.all+tlrc.HEAD if ( -e @ss_review_basic ) then ./@ss_review_basic tee out.ss_review.sub-10871.txt subject ID : sub-10871 AFNI version : AFNI_26.3.01 AFNI package : linux_rocky_8 TR : 2.0 TRs removed (per run) : 0 multiband level : 1 slice timing pattern : alt+z2 num stim classes provided : 2 final anatomy dset : anat_final.sub-10871+tlrc.HEAD final stats dset : stats.sub-10871_REML+tlrc.HEAD orig voxel counts : 64 64 34 orig voxel resolution : 3.000000 3.000000 4.000000 orig volume center : -4.061523 -55.811874 -12.379280 final voxel resolution : 3.000000 3.000000 3.000000 motion limit : 0.3 num TRs above mot limit : 1 average motion (per TR) : 0.037265 average censored motion : 0.0357725 max motion displacement : 0.975222 max censored displacement : 0.975222 outlier limit : 0.05 average outlier frac (TR) : 0.000810496 num TRs above out limit : 1 flip guess : NO_FLIP num runs found : 1 num TRs per run : 242 num TRs per run (applied) : 240 num TRs per run (censored): 2 fraction censored per run : 0.00826446 TRs total (uncensored) : 242 TRs total : 240 degrees of freedom used : 13 degrees of freedom left : 227 final DF fraction : 0.938017 TRs censored : 2 censor fraction : 0.008264 num regs of interest : 2 num TRs per stim (orig) : 135 209 num TRs censored per stim : 0 2 fraction TRs censored : 0.000 0.010 ave mot per sresp (orig) : 0.032138 0.038306 ave mot per sresp (cens) : 0.032138 0.036593 TSNR average : 211.525 global correlation (GCOR) : 0.0551127 anat/EPI mask Dice coef : 0.909304 anat/templ mask Dice coef : 0.979462 maximum F-stat (masked) : 80.8373 blur estimates (ACF) : 0.647473 3.93749 12.0828 blur estimates (FWHM) : 0 0 0 apqc_make_tcsh.py -review_style pythonic -subj_dir . -uvar_json out.ss_review_uvars.json ++ Done making (executable) IC errts script: run_instacorr_errts.tcsh ++ Done making (executable) GV errts script: run_graphview_errts.tcsh ++ Done making (executable) IC pbrun script: run_instacorr_pbrun.tcsh ++ Done making (executable) GV pbrun script: run_graphview_pbrun.tcsh ++ APQC create: qc_00_vorig_EPI ++ APQC create: qc_01_vorig_EPI_variance ++ APQC create: qc_02_vorig_anat ++ APQC create: qc_03_vorig_olap ++ APQC create: qc_04_ve2a_epi2anat ++ APQC create: qc_05_va2t_anat2temp ++ APQC create: qc_06_va2t_mask2final ++ Found 5 stats items to use for vstat QC block ++ APQC create: qc_07_vstat_Full_Fstat ++ APQC create: qc_08_vstat_CONTROL_0_Coef ++ APQC create: qc_09_vstat_TASK_0_Coef ++ APQC create: qc_10_vstat_T-C_0_Coef ++ APQC create: qc_11_vstat_meanTC_0_Coef ++ APQC create: qc_12_mot_enormoutlr ++ APQC create: qc_13_mot_VR6 ++ APQC create: qc_14_mot_grayplot ++ APQC create: qc_15_regr_ideal ++ APQC create: qc_16_regr_stims ++ APQC create: qc_17_regr_df ++ APQC create: qc_18_regr_corr_errts ++ APQC create: qc_19_regr_tsnr_fin ++ APQC create: qc_20_regr_roi_tsnr_fin ++ APQC create: qc_21_radcor_rc_tcat run: r01/1 ++ APQC create: qc_22_radcor_rc_volreg run: r01/1 ++ APQC create: qc_23_warns_xmat ++ APQC create: qc_24_warns_cen_total ++ APQC create: qc_25_warns_cen_stim ++ APQC create: qc_26_warns_press ++ APQC create: qc_27_warns_sat_4095 ++ APQC create: qc_28_warns_flip ++ APQC create: qc_29_warns_vlines ++ APQC create: qc_30_qsumm_ssrev ++ APQC create: copy jsons to info dir ++ APQC create: copy ss_review_basic file ++ APQC create: display ss_review_basic info subject ID : sub-10871 AFNI version : AFNI_26.3.01 AFNI package : linux_rocky_8 TR : 2.0 TRs removed (per run) : 0 multiband level : 1 slice timing pattern : alt+z2 num stim classes provided : 2 final anatomy dset : anat_final.sub-10871+tlrc.HEAD final stats dset : stats.sub-10871_REML+tlrc.HEAD orig voxel counts : 64 64 34 orig voxel resolution : 3.000000 3.000000 4.000000 orig volume center : -4.061523 -55.811874 -12.379280 final voxel resolution : 3.000000 3.000000 3.000000 motion limit : 0.3 num TRs above mot limit : 1 average motion (per TR) : 0.037265 average censored motion : 0.0357725 max motion displacement : 0.975222 max censored displacement : 0.975222 outlier limit : 0.05 average outlier frac (TR) : 0.000810496 num TRs above out limit : 1 flip guess : NO_FLIP num runs found : 1 num TRs per run : 242 num TRs per run (applied) : 240 num TRs per run (censored): 2 fraction censored per run : 0.00826446 TRs total (uncensored) : 242 TRs total : 240 degrees of freedom used : 13 degrees of freedom left : 227 final DF fraction : 0.938017 TRs censored : 2 censor fraction : 0.008264 num regs of interest : 2 num TRs per stim (orig) : 135 209 num TRs censored per stim : 0 2 fraction TRs censored : 0.000 0.010 ave mot per sresp (orig) : 0.032138 0.038306 ave mot per sresp (cens) : 0.032138 0.036593 TSNR average : 211.525 global correlation (GCOR) : 0.0551127 anat/EPI mask Dice coef : 0.909304 anat/templ mask Dice coef : 0.979462 maximum F-stat (masked) : 80.8373 blur estimates (ACF) : 0.647473 3.93749 12.0828 blur estimates (FWHM) : 0 0 0 # ++++++++++++++ Check output of @ss_review_basic ++++++++++++++ # ------------------------------------------------------------------ ------------------------------------------------------------------ ++ Done setting up QC dir: QC_sub-10871 To create the APQC HTML, run either this (from any location): apqc_make_html.py -qc_dir /lscratch/32397853/sub-10871/sub-10871.results/QC_sub-10871 ... or this (from the afni_proc.py results directory): apqc_make_html.py -qc_dir QC_sub-10871 apqc_make_html.py -qc_dir QC_sub-10871 ++ Done! Wrote QC HTML. To view, run either this (without server): afni_open -b /lscratch/32397853/sub-10871/sub-10871.results/QC_sub-10871/index.html ... or this (with server): open_apqc.py -infiles /lscratch/32397853/sub-10871/sub-10871.results/QC_sub-10871/index.html echo \nconsider running: \n consider running: echo open_apqc.py -infiles sub-10871.results/QC_sub-10871/index.html open_apqc.py -infiles sub-10871.results/QC_sub-10871/index.html echo endif cd .. echo execution finished: `date` date execution finished: Fri Oct 9 17:35:54 EDT 2026