afni_ci_test_data/AFNI_data6/FT_analysis/results.clustsim.05/output.proc.FT

echo auto-generated by afni_proc.py, Tue Jan  9 09:34:33 2018
auto-generated by afni_proc.py, Tue Jan  9 09:34:33 2018
echo (version 6.02, December 12, 2017)
(version 6.02, December 12, 2017)
echo execution started: `date`
date
execution started: Tue Jan  9 09:34:33 EST 2018
afni -ver
Precompiled binary linux_fedora_25_64: Jan  8 2018 (Version AFNI_18.0.01)
afni_history -check_date 23 Sep 2016
-- is current: afni_history as new as: 23 Sep 2016
               most recent entry is:   06 Jan 2018
if ( 0 ) then
if ( 0 > 0 ) then
set subj = FT
endif
set output_dir = FT.results
if ( -d FT.results ) then
set runs = ( `count -digits 2 1 3` )
count -digits 2 1 3
mkdir FT.results
mkdir FT.results/stimuli
cp FT/AV1_vis.txt FT/AV2_aud.txt FT.results/stimuli
3dcopy FT/FT_anat+orig FT.results/FT_anat
++ 3dcopy: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
3dTcat -prefix FT.results/pb00.FT.r01.tcat FT/FT_epi_r1+orig[2..$]
++ 3dTcat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ elapsed time = 0.7 s
3dTcat -prefix FT.results/pb00.FT.r02.tcat FT/FT_epi_r2+orig[2..$]
++ 3dTcat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ elapsed time = 0.4 s
3dTcat -prefix FT.results/pb00.FT.r03.tcat FT/FT_epi_r3+orig[2..$]
++ 3dTcat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ elapsed time = 0.3 s
set tr_counts = ( 150 150 150 )
cd FT.results
touch out.pre_ss_warn.txt
foreach run ( 01 02 03 )
3dToutcount -automask -fraction -polort 3 -legendre pb00.FT.r01.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ 64203 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r01.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.FT.r02.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ 64323 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r02.1D{0} -expr step(a-0.4)
end
3dToutcount -automask -fraction -polort 3 -legendre pb00.FT.r03.tcat+orig
++ 3dToutcount: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ 64476 voxels passed mask/clip
if ( `1deval -a outcount.r$run.1D"{0}" -expr "step(a-0.4)"` ) then
1deval -a outcount.r03.1D{0} -expr step(a-0.4)
end
cat outcount.r01.1D outcount.r02.1D outcount.r03.1D
set minindex = `3dTstat -argmin -prefix - outcount_rall.1D\'`
3dTstat -argmin -prefix - outcount_rall.1D'
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
set ovals = ( `1d_tool.py -set_run_lengths $tr_counts                       
                          -index_to_run_tr $minindex` )
1d_tool.py -set_run_lengths 150 150 150 -index_to_run_tr 324
set minoutrun = 03
set minouttr = 24
echo min outlier: run 03, TR 24
tee out.min_outlier.txt
min outlier: run 03, TR 24
foreach run ( 01 02 03 )
3dTshift -tzero 0 -quintic -prefix pb01.FT.r01.tshift pb00.FT.r01.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
end
3dTshift -tzero 0 -quintic -prefix pb01.FT.r02.tshift pb00.FT.r02.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
end
3dTshift -tzero 0 -quintic -prefix pb01.FT.r03.tshift pb00.FT.r03.tcat+orig
++ 3dTshift: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
end
3dbucket -prefix vr_base_min_outlier pb01.FT.r03.tshift+orig[24]
++ 3dbucket: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
align_epi_anat.py -anat2epi -anat FT_anat+orig -save_skullstrip -suffix _al_junk -epi vr_base_min_outlier+orig -epi_base 0 -epi_strip 3dAutomask -volreg off -tshift off
#++ align_epi_anat version: 1.57
#++ turning off volume registration
#Script is running (command trimmed):
  3dAttribute DELTA ./vr_base_min_outlier+orig
#Script is running (command trimmed):
  3dAttribute DELTA ./vr_base_min_outlier+orig
#Script is running (command trimmed):
  3dAttribute DELTA ./FT_anat+orig
#++ Multi-cost is lpc
#++ Removing all the temporary files
#Script is running:
  \rm -f ./__tt_vr_base_min_outlier*
#Script is running:
  \rm -f ./__tt_FT_anat*
#Script is running (command trimmed):
  3dcopy ./FT_anat+orig ./__tt_FT_anat+orig
++ 3dcopy: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
#++ Removing skull from anat data
#Script is running (command trimmed):
  3dSkullStrip -orig_vol -input ./__tt_FT_anat+orig -prefix ./__tt_FT_anat_ns
#Script is running (command trimmed):
  3dinfo ./__tt_FT_anat_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /data/rickr/data/sample/AFNI_data6/FT_analysis/FT.results/__tt_FT_anat_ns+orig is not oblique
#Script is running (command trimmed):
  3dinfo ./vr_base_min_outlier+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /data/rickr/data/sample/AFNI_data6/FT_analysis/FT.results/vr_base_min_outlier+orig is not oblique
#++ using 0th sub-brick because only one found
#Script is running (command trimmed):
  3dbucket -prefix ./__tt_vr_base_min_outlier_ts ./vr_base_min_outlier+orig'[0]'
++ 3dbucket: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
#++ resampling epi to match anat data
#Script is running (command trimmed):
  3dresample -master ./__tt_FT_anat_ns+orig -prefix ./__tt_vr_base_min_outlier_ts_rs -inset ./__tt_vr_base_min_outlier_ts+orig'' -rmode Cu
#++ removing skull or area outside brain
#Script is running (command trimmed):
  3dAutomask -apply_prefix ./__tt_vr_base_min_outlier_ts_rs_ns ./__tt_vr_base_min_outlier_ts_rs+orig
++ 3dAutomask: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset ./__tt_vr_base_min_outlier_ts_rs+orig
++ Forming automask
 + Fixed clip level = 667.583984
 + Used gradual clip level = 556.494019 .. 744.586792
 + Number voxels above clip level = 1667294
 + Clustering voxels ...
 + Largest cluster has 1659813 voxels
 + Clustering voxels ...
 + Largest cluster has 1658234 voxels
 + Filled  1111 voxels in small holes; now have 1659345 voxels
 + Filled 20436 voxels in large holes; now have 1679781 voxels
 + Clustering voxels ...
 + Largest cluster has 1679774 voxels
 + Clustering non-brain voxels ...
 + Clustering voxels ...
 + Largest cluster has 9789026 voxels
 + Mask now has 1679774 voxels
++ 1679774 voxels in the mask [out of 11468800: 14.65%]
++ first  39 x-planes are zero [from A]
++ last   10 x-planes are zero [from P]
++ first  40 y-planes are zero [from S]
++ last  111 y-planes are zero [from I]
++ first  24 z-planes are zero [from L]
++ last   14 z-planes are zero [from R]
++ applying mask to original data
++ Writing masked data
++ Output dataset ./__tt_vr_base_min_outlier_ts_rs_ns+orig.BRIK
++ CPU time = 0.000000 sec
#++ Computing weight mask
#Script is running (command trimmed):
  3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_vr_base_min_outlier_ts_rs_ns+orig
#++ Applying threshold of 1674.000000 on /data/rickr/data/sample/AFNI_data6/FT_analysis/FT.results/__tt_vr_base_min_outlier_ts_rs_ns+orig
#Script is running (command trimmed):
  3dcalc -datum float -prefix ./__tt_vr_base_min_outlier_ts_rs_ns_wt -a ./__tt_vr_base_min_outlier_ts_rs_ns+orig -expr 'min(1,(a/1674.000000))'
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tt_vr_base_min_outlier_ts_rs_ns_wt+orig.BRIK
#++ Aligning anat data to epi data
#Script is running (command trimmed):
  3dAllineate -lpc -wtprefix ./__tt_FT_anat_ns_al_junk_wtal -weight ./__tt_vr_base_min_outlier_ts_rs_ns_wt+orig -source ./__tt_FT_anat_ns+orig -prefix ./FT_anat_al_junk -base ./__tt_vr_base_min_outlier_ts_rs_ns+orig -nocmass -1Dmatrix_save ./FT_anat_al_junk_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass 
++ 3dAllineate: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./__tt_FT_anat_ns+orig.HEAD
++ Base dataset:   ./__tt_vr_base_min_outlier_ts_rs_ns+orig.HEAD
++ Loading datasets
++ 2209675 voxels in -source_automask+4
++ Zero-pad: not needed
++ 1679771 voxels [14.6%] in weight mask
++ Output dataset ./__tt_FT_anat_ns_al_junk_wtal+orig.BRIK
++ Number of points for matching = 1679771
++ Local correlation: blok type = 'RHDD(6.54321)'
++ shift param auto-range: -55.9..55.9 -76.7..76.7 -76.7..76.7
 + Range param#4 [z-angle] = -6.000000 .. 6.000000
 + Range param#5 [x-angle] = -6.000000 .. 6.000000
 + Range param#6 [y-angle] = -6.000000 .. 6.000000
 + Range param#1 [x-shift] = -10.000000 .. 10.000000
 + Range param#2 [y-shift] = -10.000000 .. 10.000000
 + Range param#3 [z-shift] = -10.000000 .. 10.000000
 + 12 free parameters
++ Normalized convergence radius = 0.001000
++ OpenMP thread count = 7
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed =======
++ ========== sub-brick #0 ========== [total CPU to here=0.0 s]
++ *** Fine pass begins ***
 + * Enter alignment setup routine
 + - copying base image
 + - copying source image
 + - copying weight image
 + - using 1679771 points from base image [use_all=0]
 + * Exit alignment setup routine
 + 1601055 total points stored in 2639 'RHDD(6.54321)' bloks
 + - Initial  cost = -0.054441
 + - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
*******************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
 + - Finalish cost = -0.323382 ; 774 funcs
************
 + - Final    cost = -0.323504 ; 198 funcs
 + Final fine fit Parameters:
       x-shift= 2.4472   y-shift= 0.0825   z-shift= 4.9193
       z-angle=-0.1114   x-angle= 6.0000   y-angle=-0.0830
       x-scale= 1.0024   y-scale= 0.9728   z-scale= 0.9251
     y/x-shear= 0.0236 z/x-shear= 0.0066 z/y-shear= 0.0649
 + - Fine net CPU time = 0.0 s
++ Computing output image
++ image warp: parameters = 2.4472 0.0825 4.9193 -0.1114 6.0000 -0.0830 1.0024 0.9728 0.9251 0.0236 0.0066 0.0649
++ Output dataset ./FT_anat_al_junk+orig.BRIK
++ Wrote -1Dmatrix_save ./FT_anat_al_junk_mat.aff12.1D
++ 3dAllineate: total CPU time = 0.0 sec  Elapsed = 55.1
++ ###########################################################
++ #   Please check results visually for alignment quality   #
++ ###########################################################
++ #   '-autoweight' is recommended when using -lpc or -lpa  #
++ #   If your results are not good, please try again.       #
++ ###########################################################
#++ Creating final output: skullstripped anat data
copying from dataset /data/rickr/data/sample/AFNI_data6/FT_analysis/FT.results/__tt_FT_anat_ns+orig to /data/rickr/data/sample/AFNI_data6/FT_analysis/FT.results/FT_anat_ns+orig
#Script is running (command trimmed):
  3dcopy ./__tt_FT_anat_ns+orig FT_anat_ns
++ 3dcopy: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
#++ Creating final output: anat data aligned to epi
# copy is not necessary
#++ Saving history
#Script is running (command trimmed):
  3dNotes -h "align_epi_anat.py -anat2epi -anat FT_anat+orig -save_skullstrip \
 -suffix _al_junk -epi vr_base_min_outlier+orig -epi_base 0 -epi_strip \
 3dAutomask -volreg off -tshift off" \
 ./FT_anat_al_junk+orig

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

# Finished alignment successfully

@auto_tlrc -base TT_N27+tlrc -input FT_anat_ns+orig -no_ss
Center distance of 34.909285 mm
Padding ...
++ 3dZeropad: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ output dataset: ./__ats_tmp__ref_TT_N27_40pad+tlrc.BRIK
Resampling ...
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__resamp_step+orig.BRIK
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__resamp+tlrc.BRIK
Clipping -0.000100 2704.000100 ...
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__ats_tmp___rs_FT_anat_ns+tlrc.BRIK
++ 3drefit: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___rs_FT_anat_ns+tlrc.HEAD
 + changing dataset view code
 + Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD
 + changing dataset view code
 + Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD
 + changing dataset view code
 + Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
Registration (linear final interpolation) ...
++ 3dWarpDrive: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RW Cox
RMS[0] = 67.0839 47.1771   ITER = 12/137
67.0839

Warping has converged.

++ 3dcopy: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ 3dWarp: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RW Cox
Applying brain mask
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__reg_braintlrcstep+orig.BRIK
++ 3dWarp: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RW Cox
++ 3drename: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ THD_rename_dataset_files: rename __ats_tmp___pad40_FT_anat_ns+orig.HEAD -> __ats_tmp___pad40_FT_anat_ns.skl+orig.HEAD
++ THD_rename_dataset_files: rename __ats_tmp___pad40_FT_anat_ns+orig.BRIK -> __ats_tmp___pad40_FT_anat_ns.skl+orig.BRIK
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp___pad40_FT_anat_ns+orig.BRIK
Unpadding ...
++ 3dZeropad: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ output dataset: ./__ats_tmp___upad40_FT_anat_ns+orig.BRIK
++ 3drefit: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_FT_anat_ns+orig
*+ WARNING: Changing the space of an ORIG view dataset may cause confusion!
*+ WARNING:  NIFTI copies will be interpreted as TLRC view (not TLRC space).
*+ WARNING:  Consider changing the view of the dataset to TLRC view also
++ 3drefit processed 1 datasets
Changing view of transformed anatomy
++ 3drefit: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_FT_anat_ns+orig.HEAD
 + changing dataset view code
 + Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
Setting parent with 3drefit -wset FT_anat_ns+orig __ats_tmp___upad40_FT_anat_ns+tlrc
++ 3drefit: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_FT_anat_ns+tlrc
 + setting Warp parent
++ 3drefit processed 1 datasets
++ 3drename: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Warning: ignoring +tlrc on new_prefix.
++ THD_rename_dataset_files: rename __ats_tmp___upad40_FT_anat_ns+tlrc.HEAD -> FT_anat_ns+tlrc.HEAD
++ THD_rename_dataset_files: rename __ats_tmp___upad40_FT_anat_ns+tlrc.BRIK -> FT_anat_ns+tlrc.BRIK
Cleanup ...
cat_matvec FT_anat_ns+tlrc::WARP_DATA -I
if ( ! -f FT_anat_ns+tlrc.HEAD ) then
foreach run ( 01 02 03 )
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.FT.r01.tshift+orig
++ 3dvolreg: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RW Cox
++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK
++ Reading input dataset ./pb01.FT.r01.tshift+orig.BRIK
++ Edging: x=4 y=4 z=2
++ Creating mask for -maxdisp
 + Automask has 66765 voxels
 + 8106 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 150 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..
++ CPU time for realignment=0 s  [=0 s/sub-brick]
++ Min : roll=-0.127  pitch=-0.965  yaw=-0.104  dS=+0.014  dL=-0.051  dP=-0.439
++ Mean: roll=-0.071  pitch=+0.194  yaw=-0.043  dS=+0.214  dL=+0.022  dP=-0.319
++ Max : roll=+0.022  pitch=+0.396  yaw=+0.031  dS=+0.395  dL=+0.087  dP=-0.174
++ Max displacements (mm) for each sub-brick:
 0.83(0.00) 0.91(0.10) 0.91(0.03) 0.89(0.05) 0.87(0.06) 0.82(0.11) 0.79(0.04) 0.84(0.12) 0.83(0.03) 0.77(0.08) 0.80(0.08) 0.81(0.09) 0.77(0.05) 0.81(0.06) 0.76(0.09) 0.79(0.08) 0.83(0.07) 0.79(0.10) 0.76(0.07) 0.83(0.18) 0.79(0.06) 0.74(0.10) 0.77(0.04) 0.72(0.05) 0.74(0.03) 0.76(0.06) 0.76(0.06) 0.74(0.03) 0.78(0.09) 0.74(0.11) 0.71(0.06) 0.78(0.15) 0.74(0.09) 0.73(0.08) 0.75(0.08) 0.74(0.02) 0.68(0.08) 0.67(0.02) 0.67(0.05) 0.71(0.06) 0.70(0.07) 0.85(0.23) 1.94(2.62) 1.87(0.21) 0.84(2.59) 0.70(0.24) 0.74(0.07) 0.69(0.10) 0.68(0.03) 0.69(0.02) 0.63(0.13) 0.63(0.07) 0.62(0.06) 0.62(0.10) 0.57(0.08) 0.56(0.09) 0.57(0.07) 0.56(0.06) 0.68(0.24) 0.61(0.19) 0.56(0.08) 0.68(0.14) 0.66(0.12) 0.64(0.04) 0.63(0.05) 0.69(0.12) 0.59(0.24) 0.55(0.04) 0.62(0.11) 0.65(0.08) 0.62(0.08) 0.64(0.07) 0.71(0.10) 0.65(0.08) 0.80(0.17) 0.87(0.19) 0.80(0.21) 0.82(0.07) 0.73(0.18) 0.71(0.06) 0.73(0.05) 0.71(0.07) 0.73(0.07) 0.75(0.05) 0.75(0.02) 0.70(0.08) 0.69(0.03) 0.71(0.08) 0.69(0.10) 0.67(0.07) 0.70(0.14) 0.72(0.05) 0.71(0.11) 0.74(0.05) 0.75(0.06) 0.75(0.02) 0.72(0.04) 0.68(0.05) 0.69(0.06) 0.69(0.04) 0.69(0.02) 0.68(0.06) 0.70(0.07) 0.75(0.07) 0.72(0.06) 0.76(0.09) 0.70(0.14) 0.73(0.15) 0.71(0.05) 0.67(0.12) 0.68(0.05) 0.73(0.09) 0.76(0.10) 0.70(0.11) 0.72(0.10) 0.69(0.08) 0.68(0.06) 0.70(0.10) 0.67(0.11) 0.68(0.08) 0.72(0.14) 0.72(0.04) 0.70(0.03) 0.67(0.04) 0.70(0.08) 0.66(0.11) 0.64(0.05) 0.62(0.05) 0.62(0.01) 0.64(0.06) 0.64(0.03) 0.62(0.03) 0.62(0.04) 0.65(0.06) 0.61(0.06) 0.65(0.08) 0.68(0.05) 0.66(0.05) 0.69(0.07) 0.65(0.10) 0.61(0.07) 0.62(0.11) 0.59(0.06) 0.55(0.04) 0.60(0.10) 0.55(0.12) 0.58(0.04) 0.65(0.12) 0.68(0.04) 0.71(0.05)
++ Max displacement in automask = 1.94 (mm) at sub-brick 42
++ Max delta displ  in automask = 2.62 (mm) at sub-brick 42
++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK
3dcalc -overwrite -a pb01.FT.r01.tshift+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: input 'a' is not used in the expression
++ Output dataset ./rm.epi.all1+orig.BRIK
cat_matvec -ONELINE FT_anat_ns+tlrc::WARP_DATA -I FT_anat_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D
3dAllineate -base FT_anat_ns+tlrc -input pb01.FT.r01.tshift+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 2.5 -prefix rm.epi.nomask.r01
++ 3dAllineate: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./pb01.FT.r01.tshift+orig.HEAD
++ Base dataset:   ./FT_anat_ns+tlrc.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 2.5000 mm
++ OpenMP thread count = 7
++ ========== Applying transformation to 150 sub-bricks ==========
volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149
++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK
++ 3dAllineate: total CPU time = 0.0 sec  Elapsed = 10.7
++ ###########################################################
3dAllineate -base FT_anat_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 2.5 -final NN -quiet -prefix rm.epi.1.r01
++ 3dAllineate: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Output dataset ./rm.epi.1.r01+tlrc.BRIK
++ 3dAllineate: total CPU time = 0.0 sec  Elapsed = 9.5
3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.epi.min.r01+tlrc.BRIK
end
3dvolreg -verbose -zpad 1 -base vr_base_min_outlier+orig -1Dfile dfile.r02.1D -prefix rm.epi.volreg.r02 -cubic -1Dmatrix_save mat.r02.vr.aff12.1D pb01.FT.r02.tshift+orig
++ 3dvolreg: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RW Cox
++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK
++ Reading input dataset ./pb01.FT.r02.tshift+orig.BRIK
++ Edging: x=4 y=4 z=2
++ Creating mask for -maxdisp
 + Automask has 66969 voxels
 + 8176 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 150 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..
++ CPU time for realignment=0 s  [=0 s/sub-brick]
++ Min : roll=-0.108  pitch=-0.081  yaw=-0.013  dS=-0.159  dL=-0.062  dP=-0.165
++ Mean: roll=+0.016  pitch=+0.071  yaw=+0.026  dS=+0.139  dL=+0.018  dP=-0.041
++ Max : roll=+0.084  pitch=+0.266  yaw=+0.055  dS=+0.267  dL=+0.095  dP=+0.107
++ Max displacements (mm) for each sub-brick:
 0.66(0.00) 0.70(0.09) 0.67(0.07) 0.68(0.02) 0.64(0.06) 0.65(0.13) 0.62(0.08) 0.61(0.05) 0.58(0.07) 0.53(0.09) 0.53(0.06) 0.54(0.09) 0.54(0.07) 0.54(0.03) 0.48(0.08) 0.47(0.05) 0.44(0.07) 0.45(0.06) 0.47(0.10) 0.46(0.07) 0.48(0.09) 0.48(0.12) 0.39(0.10) 0.37(0.05) 0.39(0.03) 0.46(0.07) 0.43(0.09) 0.38(0.12) 0.38(0.05) 0.40(0.09) 0.43(0.04) 0.41(0.05) 0.35(0.07) 0.36(0.13) 0.32(0.08) 0.36(0.05) 0.35(0.02) 0.33(0.06) 0.35(0.11) 0.33(0.09) 0.38(0.07) 0.41(0.04) 0.35(0.12) 0.38(0.07) 0.34(0.05) 0.34(0.10) 0.40(0.09) 0.38(0.11) 0.36(0.06) 0.32(0.14) 0.33(0.05) 0.35(0.04) 0.35(0.05) 0.35(0.05) 0.38(0.09) 0.40(0.15) 0.38(0.09) 0.36(0.04) 0.34(0.04) 0.34(0.05) 0.34(0.04) 0.35(0.03) 0.35(0.05) 0.34(0.03) 0.35(0.09) 0.36(0.06) 0.36(0.03) 0.35(0.05) 0.31(0.06) 0.28(0.09) 0.28(0.04) 0.28(0.10) 0.26(0.07) 0.26(0.04) 0.31(0.15) 0.34(0.10) 0.31(0.09) 0.33(0.09) 0.29(0.12) 0.28(0.07) 0.35(0.09) 0.35(0.04) 0.32(0.10) 0.27(0.07) 0.28(0.03) 0.27(0.05) 0.29(0.08) 0.32(0.08) 0.29(0.05) 0.30(0.08) 0.27(0.09) 0.27(0.08) 0.26(0.06) 0.23(0.07) 0.30(0.17) 0.26(0.16) 0.23(0.07) 0.29(0.11) 0.24(0.11) 0.20(0.08) 0.28(0.11) 0.26(0.05) 0.27(0.12) 0.25(0.10) 0.29(0.08) 0.28(0.05) 0.33(0.09) 0.40(0.12) 0.37(0.06) 0.36(0.06) 0.33(0.06) 0.32(0.05) 0.31(0.06) 0.32(0.06) 0.29(0.10) 0.28(0.03) 0.57(0.56) 0.14(0.49) 0.15(0.20) 0.11(0.17) 0.08(0.05) 0.16(0.10) 0.17(0.11) 0.16(0.07) 0.19(0.07) 0.19(0.14) 0.18(0.03) 0.20(0.09) 0.21(0.07) 0.25(0.09) 0.28(0.14) 0.24(0.12) 0.27(0.07) 0.28(0.42) 0.20(0.17) 0.19(0.18) 0.15(0.11) 0.12(0.06) 0.16(0.10) 0.12(0.08) 0.14(0.04) 0.17(0.08) 0.19(0.03) 0.22(0.05) 0.19(0.04) 0.23(0.15) 0.20(0.14) 0.21(0.03) 0.22(0.13) 0.23(0.04)
++ Max displacement in automask = 0.70 (mm) at sub-brick 1
++ Max delta displ  in automask = 0.56 (mm) at sub-brick 116
++ Wrote dataset to disk in ./rm.epi.volreg.r02+orig.BRIK
3dcalc -overwrite -a pb01.FT.r02.tshift+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: input 'a' is not used in the expression
++ Output dataset ./rm.epi.all1+orig.BRIK
cat_matvec -ONELINE FT_anat_ns+tlrc::WARP_DATA -I FT_anat_al_junk_mat.aff12.1D -I mat.r02.vr.aff12.1D
3dAllineate -base FT_anat_ns+tlrc -input pb01.FT.r02.tshift+orig -1Dmatrix_apply mat.r02.warp.aff12.1D -mast_dxyz 2.5 -prefix rm.epi.nomask.r02
++ 3dAllineate: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./pb01.FT.r02.tshift+orig.HEAD
++ Base dataset:   ./FT_anat_ns+tlrc.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 2.5000 mm
++ OpenMP thread count = 7
++ ========== Applying transformation to 150 sub-bricks ==========
volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149
++ Output dataset ./rm.epi.nomask.r02+tlrc.BRIK
++ 3dAllineate: total CPU time = 0.0 sec  Elapsed = 10.9
++ ###########################################################
3dAllineate -base FT_anat_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r02.warp.aff12.1D -mast_dxyz 2.5 -final NN -quiet -prefix rm.epi.1.r02
++ 3dAllineate: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Output dataset ./rm.epi.1.r02+tlrc.BRIK
++ 3dAllineate: total CPU time = 0.0 sec  Elapsed = 9.7
3dTstat -min -prefix rm.epi.min.r02 rm.epi.1.r02+tlrc
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.epi.min.r02+tlrc.BRIK
end
3dvolreg -verbose -zpad 1 -base vr_base_min_outlier+orig -1Dfile dfile.r03.1D -prefix rm.epi.volreg.r03 -cubic -1Dmatrix_save mat.r03.vr.aff12.1D pb01.FT.r03.tshift+orig
++ 3dvolreg: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RW Cox
++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK
++ Reading input dataset ./pb01.FT.r03.tshift+orig.BRIK
++ Edging: x=4 y=4 z=2
++ Creating mask for -maxdisp
 + Automask has 66976 voxels
 + 8084 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 150 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..
++ CPU time for realignment=0 s  [=0 s/sub-brick]
++ Min : roll=-0.043  pitch=-0.023  yaw=-0.127  dS=-0.386  dL=-0.088  dP=-0.521
++ Mean: roll=+0.065  pitch=+0.150  yaw=-0.040  dS=-0.090  dL=-0.020  dP=-0.120
++ Max : roll=+0.156  pitch=+0.600  yaw=+0.013  dS=+0.083  dL=+0.031  dP=+0.105
++ Max displacements (mm) for each sub-brick:
 0.13(0.00) 0.29(0.21) 0.09(0.21) 0.14(0.05) 0.09(0.07) 0.09(0.06) 0.10(0.06) 0.08(0.05) 0.07(0.05) 0.08(0.03) 0.08(0.03) 0.10(0.06) 0.11(0.07) 0.16(0.15) 0.06(0.14) 0.10(0.07) 0.09(0.14) 0.07(0.09) 0.04(0.05) 0.08(0.06) 0.07(0.08) 0.06(0.12) 0.14(0.17) 0.04(0.11) 0.00(0.04) 0.07(0.07) 0.08(0.06) 0.09(0.07) 0.05(0.06) 0.03(0.03) 0.10(0.09) 0.07(0.07) 0.05(0.04) 0.06(0.05) 0.09(0.08) 0.10(0.06) 0.09(0.06) 0.13(0.07) 0.07(0.13) 0.08(0.05) 0.17(0.12) 0.15(0.05) 0.16(0.05) 0.17(0.15) 0.14(0.09) 0.15(0.09) 0.12(0.07) 0.08(0.06) 0.11(0.06) 0.14(0.07) 0.08(0.13) 0.28(0.30) 0.21(0.09) 0.15(0.23) 0.16(0.10) 0.14(0.09) 0.19(0.10) 0.16(0.16) 0.15(0.07) 0.25(0.15) 0.16(0.11) 0.17(0.10) 0.14(0.05) 0.14(0.05) 0.16(0.05) 0.14(0.05) 0.14(0.07) 0.14(0.02) 0.18(0.04) 0.16(0.11) 0.15(0.04) 0.14(0.05) 0.15(0.06) 0.17(0.13) 0.17(0.09) 0.15(0.04) 0.16(0.10) 0.14(0.03) 0.14(0.12) 0.14(0.05) 0.17(0.06) 0.14(0.04) 0.18(0.05) 0.19(0.06) 0.14(0.11) 0.14(0.05) 0.20(0.10) 0.16(0.05) 0.20(0.05) 0.38(0.21) 0.50(0.12) 0.48(0.11) 0.43(0.07) 0.49(0.14) 0.52(0.06) 0.47(0.09) 0.52(0.11) 0.64(0.14) 0.59(0.07) 0.60(0.09) 0.58(0.03) 0.62(0.05) 0.64(0.07) 0.63(0.05) 0.59(0.10) 0.58(0.04) 0.60(0.05) 0.61(0.07) 0.62(0.06) 0.66(0.07) 0.64(0.11) 0.62(0.09) 0.74(0.16) 0.72(0.10) 0.83(0.18) 0.81(0.12) 0.80(0.03) 0.72(0.30) 0.87(0.25) 1.00(0.30) 0.87(0.24) 0.90(0.04) 0.90(0.05) 0.95(0.09) 0.97(0.11) 1.06(0.13) 1.04(0.05) 1.06(0.06) 0.98(0.15) 1.03(0.09) 0.78(0.29) 0.90(0.14) 1.09(0.19) 0.99(0.21) 0.95(0.05) 1.07(0.18) 1.11(0.10) 1.06(0.09) 1.10(0.11) 1.14(0.07) 1.16(0.04) 1.21(0.10) 1.16(0.15) 1.23(0.10) 1.28(0.07) 1.28(0.09) 1.34(0.07) 1.42(0.21) 1.39(0.08) 1.37(0.10)
++ Max displacement in automask = 1.42 (mm) at sub-brick 147
++ Max delta displ  in automask = 0.30 (mm) at sub-brick 119
++ Wrote dataset to disk in ./rm.epi.volreg.r03+orig.BRIK
3dcalc -overwrite -a pb01.FT.r03.tshift+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: input 'a' is not used in the expression
++ Output dataset ./rm.epi.all1+orig.BRIK
cat_matvec -ONELINE FT_anat_ns+tlrc::WARP_DATA -I FT_anat_al_junk_mat.aff12.1D -I mat.r03.vr.aff12.1D
3dAllineate -base FT_anat_ns+tlrc -input pb01.FT.r03.tshift+orig -1Dmatrix_apply mat.r03.warp.aff12.1D -mast_dxyz 2.5 -prefix rm.epi.nomask.r03
++ 3dAllineate: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./pb01.FT.r03.tshift+orig.HEAD
++ Base dataset:   ./FT_anat_ns+tlrc.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 2.5000 mm
++ OpenMP thread count = 7
++ ========== Applying transformation to 150 sub-bricks ==========
volume 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149
++ Output dataset ./rm.epi.nomask.r03+tlrc.BRIK
++ 3dAllineate: total CPU time = 0.0 sec  Elapsed = 10.7
++ ###########################################################
3dAllineate -base FT_anat_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r03.warp.aff12.1D -mast_dxyz 2.5 -final NN -quiet -prefix rm.epi.1.r03
++ 3dAllineate: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Output dataset ./rm.epi.1.r03+tlrc.BRIK
++ 3dAllineate: total CPU time = 0.0 sec  Elapsed = 9.5
3dTstat -min -prefix rm.epi.min.r03 rm.epi.1.r03+tlrc
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.epi.min.r03+tlrc.BRIK
end
cat dfile.r01.1D dfile.r02.1D dfile.r03.1D
3dMean -datum short -prefix rm.epi.mean rm.epi.min.r01+tlrc.HEAD rm.epi.min.r02+tlrc.HEAD rm.epi.min.r03+tlrc.HEAD
++ 3dMean: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
3dcalc -a rm.epi.mean+tlrc -expr step(a-0.999) -prefix mask_epi_extents
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./mask_epi_extents+tlrc.BRIK
foreach run ( 01 02 03 )
3dcalc -a rm.epi.nomask.r01+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.FT.r01.volreg
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.FT.r01.volreg+tlrc.BRIK
end
3dcalc -a rm.epi.nomask.r02+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.FT.r02.volreg
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.FT.r02.volreg+tlrc.BRIK
end
3dcalc -a rm.epi.nomask.r03+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.FT.r03.volreg
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.FT.r03.volreg+tlrc.BRIK
end
cat_matvec -ONELINE FT_anat_ns+tlrc::WARP_DATA -I FT_anat_al_junk_mat.aff12.1D -I
3dAllineate -base FT_anat_ns+tlrc -input vr_base_min_outlier+orig -1Dmatrix_apply mat.basewarp.aff12.1D -mast_dxyz 2.5 -prefix final_epi_vr_base_min_outlier
++ 3dAllineate: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./vr_base_min_outlier+orig.HEAD
++ Base dataset:   ./FT_anat_ns+tlrc.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 2.5000 mm
++ OpenMP thread count = 7
++ ========== Applying transformation to 1 sub-bricks ==========
volume 0
++ Output dataset ./final_epi_vr_base_min_outlier+tlrc.BRIK
++ 3dAllineate: total CPU time = 0.0 sec  Elapsed = 0.1
++ ###########################################################
3dcopy FT_anat_ns+tlrc anat_final.FT
++ 3dcopy: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
3dAllineate -base final_epi_vr_base_min_outlier+tlrc -allcostX -input anat_final.FT+tlrc
tee out.allcostX.txt
++ 3dAllineate: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./anat_final.FT+tlrc.HEAD
++ Base dataset:   ./final_epi_vr_base_min_outlier+tlrc.HEAD
++ Loading datasets
++ 1364700 voxels in source_automask+0
++ Zero-pad: xbot=4 xtop=2
++ Computing -autobox
++ 262183 voxels [82.1%] in weight mask
++ Number of points for matching = 123226
++ Local correlation: blok type = 'RHDD(9.225)'
*+ WARNING: No output dataset will be calculated
++ OpenMP thread count = 7
volume 0
 + 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   = 0.248947
   sp   = 0.354302
   mi   = -0.524013
   crM  = 0.140429
   nmi  = 0.89318
   je   = 4.38153
   hel  = -0.10306
   crA  = 0.37474
   crU  = 0.375332
   lss  = 0.751053
   lpc  = 0.0782272
   lpa  = 0.921773
   lpc+ = 0.310739
   ncd  = 0.967007
++ 3dAllineate: total CPU time = 0.0 sec  Elapsed = 2.2
++ ###########################################################
3dAllineate -source FT_anat+orig -master anat_final.FT+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped
++ 3dAllineate: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: Zhark the Registrator
++ -1Dmatrix_apply: converting input 3x4 array to 1 row of 12 numbers
++ Source dataset: ./FT_anat+orig.HEAD
++ Base dataset:   (not given)
++ Loading datasets
++ OpenMP thread count = 7
++ ========== Applying transformation to 1 sub-bricks ==========
volume 0
++ wsinc5 interpolation setup:
 +   taper function  = Min sidelobe 3 term
 +   taper cut point = 0.000
 +   window radius   = 5 voxels
 +   window shape    = Cubical
 +   The above can be altered via the AFNI_WSINC5_* environment variables.
 +  (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.)
 +   wsinc5 CUBE(5) mask has 1000 points
++ Output dataset ./anat_w_skull_warped+tlrc.BRIK
++ 3dAllineate: total CPU time = 0.0 sec  Elapsed = 2.9
++ ###########################################################
foreach run ( 01 02 03 )
3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.FT.r01.blur pb02.FT.r01.volreg+tlrc
++ 3dmerge: AFNI version=AFNI_17.3.05 (Nov 28 2017) [64-bit]
++ default -1dindex = 0
++ default -1tindex = 1
Program 3dmerge 
3dmerge: edit and combine 3D datasets, by RW Cox
++ editing input dataset in memory (83.5 MB)
......................................................................................................................................................
-- Wrote edited dataset: ./pb03.FT.r01.blur+tlrc.BRIK
end
3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.FT.r02.blur pb02.FT.r02.volreg+tlrc
++ 3dmerge: AFNI version=AFNI_17.3.05 (Nov 28 2017) [64-bit]
++ default -1dindex = 0
++ default -1tindex = 1
Program 3dmerge 
3dmerge: edit and combine 3D datasets, by RW Cox
++ editing input dataset in memory (83.5 MB)
......................................................................................................................................................
-- Wrote edited dataset: ./pb03.FT.r02.blur+tlrc.BRIK
end
3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.FT.r03.blur pb02.FT.r03.volreg+tlrc
++ 3dmerge: AFNI version=AFNI_17.3.05 (Nov 28 2017) [64-bit]
++ default -1dindex = 0
++ default -1tindex = 1
Program 3dmerge 
3dmerge: edit and combine 3D datasets, by RW Cox
++ editing input dataset in memory (83.5 MB)
......................................................................................................................................................
-- Wrote edited dataset: ./pb03.FT.r03.blur+tlrc.BRIK
end
foreach run ( 01 02 03 )
3dAutomask -dilate 1 -prefix rm.mask_r01 pb03.FT.r01.blur+tlrc
++ 3dAutomask: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset pb03.FT.r01.blur+tlrc
++ Forming automask
 + Fixed clip level = 664.820679
 + Used gradual clip level = 534.349304 .. 733.529419
 + Number voxels above clip level = 70158
 + Clustering voxels ...
 + Largest cluster has 69993 voxels
 + Clustering voxels ...
 + Largest cluster has 69957 voxels
 + Filled    54 voxels in small holes; now have 70011 voxels
 + Clustering voxels ...
 + Largest cluster has 70011 voxels
 + Clustering non-brain voxels ...
 + Clustering voxels ...
 + Largest cluster has 221829 voxels
 + Mask now has 70011 voxels
++ Dilating automask
 + Clustering voxels ...
 + Largest cluster has 212725 voxels
++ 79115 voxels in the mask [out of 291840: 27.11%]
++ first   4 x-planes are zero [from R]
++ last    5 x-planes are zero [from L]
++ first   5 y-planes are zero [from A]
++ last    4 y-planes are zero [from P]
++ first  16 z-planes are zero [from I]
++ last    6 z-planes are zero [from S]
++ Output dataset ./rm.mask_r01+tlrc.BRIK
++ CPU time = 0.000000 sec
end
3dAutomask -dilate 1 -prefix rm.mask_r02 pb03.FT.r02.blur+tlrc
++ 3dAutomask: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset pb03.FT.r02.blur+tlrc
++ Forming automask
 + Fixed clip level = 662.259827
 + Used gradual clip level = 539.891174 .. 730.324829
 + Number voxels above clip level = 70277
 + Clustering voxels ...
 + Largest cluster has 70132 voxels
 + Clustering voxels ...
 + Largest cluster has 70106 voxels
 + Filled    50 voxels in small holes; now have 70156 voxels
 + Clustering voxels ...
 + Largest cluster has 70156 voxels
 + Clustering non-brain voxels ...
 + Clustering voxels ...
 + Largest cluster has 221684 voxels
 + Mask now has 70156 voxels
++ Dilating automask
 + Clustering voxels ...
 + Largest cluster has 212558 voxels
++ 79282 voxels in the mask [out of 291840: 27.17%]
++ first   4 x-planes are zero [from R]
++ last    5 x-planes are zero [from L]
++ first   5 y-planes are zero [from A]
++ last    4 y-planes are zero [from P]
++ first  16 z-planes are zero [from I]
++ last    6 z-planes are zero [from S]
++ Output dataset ./rm.mask_r02+tlrc.BRIK
++ CPU time = 0.000000 sec
end
3dAutomask -dilate 1 -prefix rm.mask_r03 pb03.FT.r03.blur+tlrc
++ 3dAutomask: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset pb03.FT.r03.blur+tlrc
++ Forming automask
 + Fixed clip level = 663.061523
 + Used gradual clip level = 547.176270 .. 729.621277
 + Number voxels above clip level = 70351
 + Clustering voxels ...
 + Largest cluster has 70219 voxels
 + Clustering voxels ...
 + Largest cluster has 70193 voxels
 + Filled    57 voxels in small holes; now have 70250 voxels
 + Clustering voxels ...
 + Largest cluster has 70250 voxels
 + Clustering non-brain voxels ...
 + Clustering voxels ...
 + Largest cluster has 221590 voxels
 + Mask now has 70250 voxels
++ Dilating automask
 + Clustering voxels ...
 + Largest cluster has 212500 voxels
++ 79340 voxels in the mask [out of 291840: 27.19%]
++ first   4 x-planes are zero [from R]
++ last    5 x-planes are zero [from L]
++ first   5 y-planes are zero [from A]
++ last    4 y-planes are zero [from P]
++ first  16 z-planes are zero [from I]
++ last    6 z-planes are zero [from S]
++ Output dataset ./rm.mask_r03+tlrc.BRIK
++ CPU time = 0.000000 sec
end
3dmask_tool -inputs rm.mask_r01+tlrc.HEAD rm.mask_r02+tlrc.HEAD rm.mask_r03+tlrc.HEAD -union -prefix full_mask.FT
++ processing 3 input datasets...
++ padding all datasets by 0 (for dilations)
++ frac 0 over 3 volumes gives min count 0
++ voxel limits: 0 clipped, 79514 survived, 212326 were zero
++ writing result full_mask.FT...
++ Output dataset ./full_mask.FT+tlrc.BRIK
3dresample -master full_mask.FT+tlrc -input FT_anat_ns+tlrc -prefix rm.resam.anat
3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.FT
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 5 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 92162 survived, 199678 were zero
++ filled 0 holes (0 voxels)
++ writing result mask_anat.FT...
++ Output dataset ./mask_anat.FT+tlrc.BRIK
3dABoverlap -no_automask full_mask.FT+tlrc mask_anat.FT+tlrc
tee out.mask_ae_overlap.txt
++ 3dOverlap: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
#A=./full_mask.FT+tlrc.BRIK  B=./mask_anat.FT+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)
79514        92162        99644        72032        7482         20130         9.4097     21.8420     0.9467     0.9037     1.5722
3ddot -dodice full_mask.FT+tlrc mask_anat.FT+tlrc
tee out.mask_ae_dice.txt
0.839162	
3dresample -master full_mask.FT+tlrc -prefix ./rm.resam.group -input /home/rickr/abin/TT_N27+tlrc
3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 5 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 95647 survived, 196193 were zero
++ filled 0 holes (0 voxels)
++ writing result mask_group...
++ Output dataset ./mask_group+tlrc.BRIK
foreach run ( 01 02 03 )
3dTstat -prefix rm.mean_r01 pb03.FT.r01.blur+tlrc
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.mean_r01+tlrc.BRIK
3dcalc -a pb03.FT.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.FT.r01.scale
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb04.FT.r01.scale+tlrc.BRIK
end
3dTstat -prefix rm.mean_r02 pb03.FT.r02.blur+tlrc
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.mean_r02+tlrc.BRIK
3dcalc -a pb03.FT.r02.blur+tlrc -b rm.mean_r02+tlrc -c mask_epi_extents+tlrc -expr c * min(200, a/b*100)*step(a)*step(b) -prefix pb04.FT.r02.scale
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb04.FT.r02.scale+tlrc.BRIK
end
3dTstat -prefix rm.mean_r03 pb03.FT.r03.blur+tlrc
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.mean_r03+tlrc.BRIK
3dcalc -a pb03.FT.r03.blur+tlrc -b rm.mean_r03+tlrc -c mask_epi_extents+tlrc -expr c * min(200, a/b*100)*step(a)*step(b) -prefix pb04.FT.r03.scale
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb04.FT.r03.scale+tlrc.BRIK
end
1d_tool.py -infile dfile_rall.1D -set_nruns 3 -demean -write motion_demean.1D
1d_tool.py -infile dfile_rall.1D -set_nruns 3 -derivative -demean -write motion_deriv.1D
1d_tool.py -infile dfile_rall.1D -set_nruns 3 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_FT
total number of censored TRs (simple form) = 6
set ktrs = `1d_tool.py -infile motion_${subj}_censor.1D                  
                       -show_trs_uncensored encoded`
1d_tool.py -infile motion_FT_censor.1D -show_trs_uncensored encoded
3dDeconvolve -input pb04.FT.r01.scale+tlrc.HEAD pb04.FT.r02.scale+tlrc.HEAD pb04.FT.r03.scale+tlrc.HEAD -censor motion_FT_censor.1D -polort 3 -num_stimts 8 -stim_times 1 stimuli/AV1_vis.txt BLOCK(20,1) -stim_label 1 vis -stim_times 2 stimuli/AV2_aud.txt BLOCK(20,1) -stim_label 2 aud -stim_file 3 motion_demean.1D[0] -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D[1] -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D[2] -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D[3] -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D[4] -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D[5] -stim_base 8 -stim_label 8 dP -jobs 2 -gltsym SYM: vis -aud -glt_label 1 V-A -gltsym SYM: 0.5*vis +0.5*aud -glt_label 2 mean.VA -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -errts errts.FT -bucket stats.FT
++ 3dDeconvolve: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: B. Douglas Ward, et al.
++ current memory malloc-ated = 485,662 bytes (about 486 thousand [kilo])
++ loading dataset pb04.FT.r01.scale+tlrc.HEAD pb04.FT.r02.scale+tlrc.HEAD pb04.FT.r03.scale+tlrc.HEAD
++ current memory malloc-ated = 263,370,853 bytes (about 263 million [mega])
++ Auto-catenated input datasets treated as multiple imaging runs
++ Auto-catenated datasets start at:  0 150 300
++ STAT automask has 161983 voxels (out of 291840 = 55.5%)
++ Skipping check for initial transients
++ Input polort=3; Longest run=300.0 s; Recommended minimum polort=3 ++ 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 1 using LOCAL times
++ ** GUESSED ** -stim_times 2 using LOCAL times
------------------------------------------------------------
GLT matrix from 'SYM: vis -aud':
   0   0   0   0   0   0   0   0   0   0   0   0   1  -1   0   0   0   0   0   0 
 
------------------------------------------------------------
GLT matrix from 'SYM: 0.5*vis +0.5*aud':
          0          0          0          0          0          0          0          0          0          0          0          0        0.5        0.5          0          0          0          0          0          0 
 
++ Number of time points: 450 (before censor) ; 444 (after)
 + Number of parameters:  20 [18 baseline ; 2 signal]
++ total shared memory needed = 540,487,680 bytes (about 540 million [mega])
++ current memory malloc-ated = 263,682,665 bytes (about 264 million [mega])
++ mmap() memory allocated: 540,487,680 bytes (about 540 million [mega])
++ Memory required for output bricks = 540,487,680 bytes (about 540 million [mega])
++ 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.FT.r01.scale+tlrc.HEAD pb04.FT.r02.scale+tlrc.HEAD pb04.FT.r03.scale+tlrc.HEAD" \
 -fout -tout -Rbuck stats.FT_REML -Rvar stats.FT_REMLvar \
 -Rerrts errts.FT_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] (444x20):  3.70922  ++ VERY GOOD ++
++ ----- Signal-only matrix condition [X] (444x2):  1.00007  ++ VERY GOOD ++
++ ----- Baseline-only matrix condition [X] (444x18):  3.67957  ++ VERY GOOD ++
++ ----- stim_base-only matrix condition [X] (444x6):  2.3891  ++ VERY GOOD ++
++ ----- polort-only matrix condition [X] (444x12):  1.03493  ++ VERY GOOD ++
++ +++++ Matrix inverse average error = 1.37734e-15  ++ VERY GOOD ++
++ Matrix setup time = 1.79 s
++ Voxels in dataset: 291840
++ Voxels per job:    145920
++ Job #1: processing voxels 145920 to 291839; elapsed time=4.742
++ Job #0: processing voxels 0 to 145919; elapsed time=4.752
++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789.
++ Job #0 waiting for children to finish; elapsed time=31.337
++ Job #1 finished; elapsed time=31.557
++ Job #0 now finishing up; elapsed time=31.576
++ Smallest FDR q [0 Full_Fstat] = 1.26814e-14
++ Smallest FDR q [2 vis#0_Tstat] = 1.81285e-14
++ Smallest FDR q [3 vis_Fstat] = 1.81292e-14
++ Smallest FDR q [5 aud#0_Tstat] = 2.13952e-14
++ Smallest FDR q [6 aud_Fstat] = 2.13948e-14
++ Smallest FDR q [8 V-A_GLT#0_Tstat] = 1.98312e-13
++ Smallest FDR q [9 V-A_GLT_Fstat] = 1.98331e-13
++ Smallest FDR q [11 mean.VA_GLT#0_Tstat] = 1.75581e-14
++ Smallest FDR q [12 mean.VA_GLT_Fstat] = 1.75594e-14
++ Wrote bucket dataset into ./stats.FT+tlrc.BRIK
 + created 9 FDR curves in bucket header
++ Wrote 3D+time dataset into ./errts.FT+tlrc.BRIK
++ Program finished; elapsed time=48.238
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:      -0.612       0.000  (12 vs. 13)  vis#0  vs.  aud#0

3dTcat -prefix all_runs.FT pb04.FT.r01.scale+tlrc.HEAD pb04.FT.r02.scale+tlrc.HEAD pb04.FT.r03.scale+tlrc.HEAD
++ 3dTcat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ elapsed time = 0.7 s
3dTstat -mean -prefix rm.signal.all all_runs.FT+tlrc[0..40,45..264,267..449]
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.signal.all+tlrc.BRIK
3dTstat -stdev -prefix rm.noise.all errts.FT+tlrc[0..40,45..264,267..449]
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.noise.all+tlrc.BRIK
3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.FT+tlrc -expr c*a/b -prefix TSNR.FT
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./TSNR.FT+tlrc.BRIK
3dTnorm -norm2 -prefix rm.errts.unit errts.FT+tlrc
++ 3dTnorm: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RW Cox
++ Output dataset ./rm.errts.unit+tlrc.BRIK
3dmaskave -quiet -mask full_mask.FT+tlrc rm.errts.unit+tlrc
++ 3dmaskave: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
+++ 79514 voxels survive the mask
3dTstat -sos -prefix - gmean.errts.unit.1D'
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
echo -- GCOR = `cat out.gcor.1D`
cat out.gcor.1D
-- GCOR =  0.0573639
3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr a*b -prefix rm.DP
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./rm.DP+tlrc.BRIK
3dTstat -sum -prefix corr_brain rm.DP+tlrc
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./corr_brain+tlrc.BRIK
3dcalc -a all_runs.FT+tlrc -b errts.FT+tlrc -expr a-b -prefix fitts.FT
++ 3dcalc: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./fitts.FT+tlrc.BRIK
1dcat X.nocensor.xmat.1D[12]
1dcat X.nocensor.xmat.1D[13]
set reg_cols = `1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest`
1d_tool.py -infile X.nocensor.xmat.1D -show_indices_interest
3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D[12,13]
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
++ Output dataset ./sum_ideal.1D
1dcat X.nocensor.xmat.1D[12,13]
touch blur_est.FT.1D
mkdir files_ACF
touch blur.epits.1D
foreach run ( 01 02 03 )
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..40,45..149 ==  ) continue
3dFWHMx -detrend -mask full_mask.FT+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r01.1D all_runs.FT+tlrc[0..40,45..149]
++ 3dFWHMx: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: The Bob
++ Number of voxels in mask = 79514
*+ WARNING: removed 1255 voxels from mask because they are constant in time
++ detrending start: 11 baseline funcs, 146 time points
 + detrending done (0.00 CPU s thus far)
++ start ACF calculations out to radius = 17.57 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.epits.r01.1D
++ 1dplot: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RWC et al.
 + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.epits.r01.1D.png
end
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 02
if ( 150..264,267..299 ==  ) continue
3dFWHMx -detrend -mask full_mask.FT+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r02.1D all_runs.FT+tlrc[150..264,267..299]
++ 3dFWHMx: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: The Bob
++ Number of voxels in mask = 79514
*+ WARNING: removed 1255 voxels from mask because they are constant in time
++ detrending start: 11 baseline funcs, 148 time points
 + detrending done (0.00 CPU s thus far)
++ start ACF calculations out to radius = 17.82 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.epits.r02.1D
++ 1dplot: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RWC et al.
 + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.epits.r02.1D.png
end
set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded 
                          -show_trs_run $run`
1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 03
if ( 300..449 ==  ) continue
3dFWHMx -detrend -mask full_mask.FT+tlrc -ACF files_ACF/out.3dFWHMx.ACF.epits.r03.1D all_runs.FT+tlrc[300..449]
++ 3dFWHMx: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: The Bob
++ Number of voxels in mask = 79514
*+ WARNING: removed 1255 voxels from mask because they are constant in time
++ detrending start: 13 baseline funcs, 150 time points
 + detrending done (0.00 CPU s thus far)
++ start ACF calculations out to radius = 17.62 mm
 + ACF done (0.00 CPU s thus far)
++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.epits.r03.1D
++ 1dplot: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RWC et al.
 + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.epits.r03.1D.png
end
set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{0..$(2)}'\'` )
3dTstat -mean -prefix - blur.epits.1D{0..$(2)}'
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
echo average epits FWHM blurs: 0 0 0 0
average epits FWHM blurs: 0 0 0 0
echo 0 0 0 0   # epits FWHM blur estimates
set blurs = ( `3dTstat -mean -prefix - blur.epits.1D'{1..$(2)}'\'` )
3dTstat -mean -prefix - blur.epits.1D{1..$(2)}'
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
echo average epits ACF blurs: 0.627097 3.16447 12.0673 8.76114
average epits ACF blurs: 0.627097 3.16447 12.0673 8.76114
echo 0.627097 3.16447 12.0673 8.76114   # epits ACF blur estimates
touch blur.errts.1D
foreach run ( 01 02 03 )
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..40,45..149 ==  ) continue
3dFWHMx -detrend -mask full_mask.FT+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r01.1D errts.FT+tlrc[0..40,45..149]
++ 3dFWHMx: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: The Bob
++ Number of voxels in mask = 79514
*+ WARNING: removed 1255 voxels from mask because they are constant in time
++ detrending start: 11 baseline funcs, 146 time points
 + detrending done (0.00 CPU s thus far)
++ start ACF calculations out to radius = 17.16 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.errts.r01.1D
++ 1dplot: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RWC et al.
 + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.errts.r01.1D.png
end
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 02
if ( 150..264,267..299 ==  ) continue
3dFWHMx -detrend -mask full_mask.FT+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r02.1D errts.FT+tlrc[150..264,267..299]
++ 3dFWHMx: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: The Bob
++ Number of voxels in mask = 79514
*+ WARNING: removed 1255 voxels from mask because they are constant in time
++ detrending start: 11 baseline funcs, 148 time points
 + detrending done (0.00 CPU s thus far)
++ start ACF calculations out to radius = 17.43 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.errts.r02.1D
++ 1dplot: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RWC et al.
 + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.errts.r02.1D.png
end
set trs = `1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded 
                          -show_trs_run $run`
1d_tool.py -infile X.xmat.1D -show_trs_uncensored encoded -show_trs_run 03
if ( 300..449 ==  ) continue
3dFWHMx -detrend -mask full_mask.FT+tlrc -ACF files_ACF/out.3dFWHMx.ACF.errts.r03.1D errts.FT+tlrc[300..449]
++ 3dFWHMx: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: The Bob
++ Number of voxels in mask = 79514
*+ WARNING: removed 1255 voxels from mask because they are constant in time
++ detrending start: 13 baseline funcs, 150 time points
 + detrending done (0.00 CPU s thus far)
++ start ACF calculations out to radius = 17.23 mm
 + ACF done (0.00 CPU s thus far)
++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to files_ACF/out.3dFWHMx.ACF.errts.r03.1D
++ 1dplot: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RWC et al.
 + and 1dplot-ed to file files_ACF/out.3dFWHMx.ACF.errts.r03.1D.png
end
set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{0..$(2)}'\'` )
3dTstat -mean -prefix - blur.errts.1D{0..$(2)}'
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
echo average errts FWHM blurs: 0 0 0 0
average errts FWHM blurs: 0 0 0 0
echo 0 0 0 0   # errts FWHM blur estimates
set blurs = ( `3dTstat -mean -prefix - blur.errts.1D'{1..$(2)}'\'` )
3dTstat -mean -prefix - blur.errts.1D{1..$(2)}'
++ 3dTstat: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
echo average errts ACF blurs: 0.657691 3.19123 10.3821 8.47382
average errts ACF blurs: 0.657691 3.19123 10.3821 8.47382
echo 0.657691 3.19123 10.3821 8.47382   # errts ACF blur estimates
mkdir files_ClustSim
set params = ( `grep ACF blur_est.$subj.1D | tail -n 1` )
tail -n 1
grep ACF blur_est.FT.1D
3dClustSim -both -mask full_mask.FT+tlrc -acf 0.657691 3.19123 10.3821 -cmd 3dClustSim.ACF.cmd -prefix files_ClustSim/ClustSim.ACF
++ 3dClustSim: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RW Cox and BD Ward
++ 79514 voxels in mask (27.25% of total)
++ Kernel function radius = 29.48 mm
++ ACF(0.66,3.19,10.38) => FWHM=8.47 => 64x76x60 pads to 96x120x96
 + Kernel image dimensions 47 x 59 x 47
++ Startup clock time = 0.2 s
++ Using 7 OpenMP threads
Simulating:0123456789.0123456789.0123456789.0123456789.0123456789.!
++ Clock time now = 539.5 s
++ Command fragment to put cluster results into a dataset header;
 + (also echoed to file 3dClustSim.ACF.cmd for your scripting pleasure)
 + Append the name of the datasets to be patched to this command:
 3drefit -atrstring AFNI_CLUSTSIM_NN1_1sided file:files_ClustSim/ClustSim.ACF.NN1_1sided.niml -atrstring AFNI_CLUSTSIM_MASK file:files_ClustSim/ClustSim.ACF.mask -atrstring AFNI_CLUSTSIM_NN2_1sided file:files_ClustSim/ClustSim.ACF.NN2_1sided.niml -atrstring AFNI_CLUSTSIM_NN3_1sided file:files_ClustSim/ClustSim.ACF.NN3_1sided.niml -atrstring AFNI_CLUSTSIM_NN1_2sided file:files_ClustSim/ClustSim.ACF.NN1_2sided.niml -atrstring AFNI_CLUSTSIM_NN2_2sided file:files_ClustSim/ClustSim.ACF.NN2_2sided.niml -atrstring AFNI_CLUSTSIM_NN3_2sided file:files_ClustSim/ClustSim.ACF.NN3_2sided.niml -atrstring AFNI_CLUSTSIM_NN1_bisided file:files_ClustSim/ClustSim.ACF.NN1_bisided.niml -atrstring AFNI_CLUSTSIM_NN2_bisided file:files_ClustSim/ClustSim.ACF.NN2_bisided.niml -atrstring AFNI_CLUSTSIM_NN3_bisided file:files_ClustSim/ClustSim.ACF.NN3_bisided.niml 
set cmd = ( `cat 3dClustSim.ACF.cmd` )
cat 3dClustSim.ACF.cmd
3drefit -atrstring AFNI_CLUSTSIM_NN1_1sided file:files_ClustSim/ClustSim.ACF.NN1_1sided.niml -atrstring AFNI_CLUSTSIM_MASK file:files_ClustSim/ClustSim.ACF.mask -atrstring AFNI_CLUSTSIM_NN2_1sided file:files_ClustSim/ClustSim.ACF.NN2_1sided.niml -atrstring AFNI_CLUSTSIM_NN3_1sided file:files_ClustSim/ClustSim.ACF.NN3_1sided.niml -atrstring AFNI_CLUSTSIM_NN1_2sided file:files_ClustSim/ClustSim.ACF.NN1_2sided.niml -atrstring AFNI_CLUSTSIM_NN2_2sided file:files_ClustSim/ClustSim.ACF.NN2_2sided.niml -atrstring AFNI_CLUSTSIM_NN3_2sided file:files_ClustSim/ClustSim.ACF.NN3_2sided.niml -atrstring AFNI_CLUSTSIM_NN1_bisided file:files_ClustSim/ClustSim.ACF.NN1_bisided.niml -atrstring AFNI_CLUSTSIM_NN2_bisided file:files_ClustSim/ClustSim.ACF.NN2_bisided.niml -atrstring AFNI_CLUSTSIM_NN3_bisided file:files_ClustSim/ClustSim.ACF.NN3_bisided.niml stats.FT+tlrc
++ 3drefit: AFNI version=AFNI_18.0.01 (Jan  8 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset stats.FT+tlrc
 + atrcopy
++ applying attributes
++ 3drefit processed 1 datasets
gen_epi_review.py -script @epi_review.FT -dsets pb00.FT.r01.tcat+orig.HEAD pb00.FT.r02.tcat+orig.HEAD pb00.FT.r03.tcat+orig.HEAD
gen_ss_review_scripts.py -mot_limit 0.3 -exit0
++ 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.DP+tlrc.BRIK rm.DP+tlrc.HEAD rm.epi.1.r01+tlrc.BRIK rm.epi.1.r01+tlrc.HEAD rm.epi.1.r02+tlrc.BRIK rm.epi.1.r02+tlrc.HEAD rm.epi.1.r03+tlrc.BRIK rm.epi.1.r03+tlrc.HEAD rm.epi.all1+orig.BRIK rm.epi.all1+orig.HEAD rm.epi.mean+tlrc.BRIK rm.epi.mean+tlrc.HEAD rm.epi.min.r01+tlrc.BRIK rm.epi.min.r01+tlrc.HEAD rm.epi.min.r02+tlrc.BRIK rm.epi.min.r02+tlrc.HEAD rm.epi.min.r03+tlrc.BRIK rm.epi.min.r03+tlrc.HEAD rm.epi.nomask.r01+tlrc.BRIK rm.epi.nomask.r01+tlrc.HEAD rm.epi.nomask.r02+tlrc.BRIK rm.epi.nomask.r02+tlrc.HEAD rm.epi.nomask.r03+tlrc.BRIK rm.epi.nomask.r03+tlrc.HEAD rm.epi.volreg.r01+orig.BRIK rm.epi.volreg.r01+orig.HEAD rm.epi.volreg.r02+orig.BRIK rm.epi.volreg.r02+orig.HEAD rm.epi.volreg.r03+orig.BRIK rm.epi.volreg.r03+orig.HEAD rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK rm.mask_r01+tlrc.HEAD rm.mask_r02+tlrc.BRIK rm.mask_r02+tlrc.HEAD rm.mask_r03+tlrc.BRIK rm.mask_r03+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.mean_r02+tlrc.BRIK rm.mean_r02+tlrc.HEAD rm.mean_r03+tlrc.BRIK rm.mean_r03+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.resam.anat+tlrc.BRIK rm.resam.anat+tlrc.HEAD rm.resam.group+tlrc.BRIK rm.resam.group+tlrc.HEAD rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD
if ( -e @ss_review_basic ) ./@ss_review_basic
tee out.ss_review.FT.txt
./@ss_review_basic

subject ID                : FT
TRs removed (per run)     : 2
num stim classes provided : 2
final anatomy dset        : anat_final.FT+tlrc.HEAD
final stats dset          : stats.FT+tlrc.HEAD
final voxel resolution    : 2.500000	2.500000	2.500000

motion limit              : 0.3
num TRs above mot limit   : 3
average motion (per TR)   : 0.075313
average censored motion   : 0.0689467
max motion displacement   : 1.65986
max censored displacement : 1.0295
outlier limit             : 0.1
average outlier frac (TR) : 0.00276734
num TRs above out limit   : 1

num runs found            : 3
num TRs per run           : 150 150 150
num TRs per run (applied) : 146 148 150
num TRs per run (censored): 4 2 0
fraction censored per run : 0.0266667 0.0133333 0
TRs total (uncensored)    : 450
TRs total                 : 444
degrees of freedom used   : 20
degrees of freedom left   : 424

TRs censored              : 6
censor fraction           : 0.013333
num regs of interest      : 2
num TRs per stim (orig)   : 240 239
num TRs censored per stim : 6 0
fraction TRs censored     : 0.025 0.000
ave mot per sresp (orig)  : 0.078156 0.071051
ave mot per sresp (cens)  : 0.066231 0.071051

TSNR average              : 202.793
global correlation (GCOR) : 0.0573639
anat/EPI mask Dice coef   : 0.839162
maximum F-stat (masked)   : 904.824
blur estimates (ACF)      : 0.657691 3.19123 10.3821
blur estimates (FWHM)     : 0 0 0


cd ..
echo execution finished: `date`
date
execution finished: Tue Jan  9 09:53:14 EST 2018