++ have nslices : 34
++ copying pb00.sub-024.r01.tcat+orig.HEAD[0..$] to ts.0.orig.r01.nii.gz
++ 3dTcat: AFNI version=AFNI_24.1.22 (Jun 21 2024) [64-bit]
++ elapsed time = 6.2 s
++ creating automask from first dset
++ 3dAutomask: AFNI version=AFNI_24.1.22 (Jun 21 2024) [64-bit]
++ Authored by: Emperor Zhark
[7m*+ WARNING:[0m   If you are performing spatial transformations on an oblique dset,
  such as /lscratch/30511576/sub-024/sub-024.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/30511576/sub-024/sub-024.results/vlines.pb00.tcat/ts.0.orig.r01.nii.gz is 35.151749 degrees from plumb.
++ Loading dataset ts.0.orig.r01.nii.gz
++ Forming automask
 + Fixed clip level = 310.765869
 + Used gradual clip level = 243.884857 .. 357.807892
 + Number voxels above clip level = 36714
 + Clustering voxels ...
 + Largest cluster has 35316 voxels
 + Clustering voxels ...
 + Largest cluster has 34762 voxels
 + Filled   498 voxels in small holes; now have 35260 voxels
 + Clustering voxels ...
 + Largest cluster has 35260 voxels
 + Clustering non-brain voxels ...
 + Clustering voxels ...
 + Largest cluster has 103976 voxels
 + Mask now has 35288 voxels
++ 35288 voxels in the mask [out of 139264: 25.34%]
++ first  12 x-planes are zero [from R]
++ last   10 x-planes are zero [from L]
++ first   2 y-planes are zero [from P]
++ last    4 y-planes are zero [from A]
++ first   0 z-planes are zero [from I]
++ last    2 z-planes are zero [from S]
++ Output dataset ./mask.nii.gz
++ CPU time = 0.000000 sec

-- will apply mask mask.nii.gz
++ eroding mask.nii.gz by 2 voxels
++ no -frac option: defaulting to -union
++ processing 1 input dataset(s), NN=2...
++ padding all datasets by 0 (for dilations)
[7m*+ WARNING:[0m   If you are performing spatial transformations on an oblique dset,
  such as /lscratch/30511576/sub-024/sub-024.results/vlines.pb00.tcat/tmp.mask.nii.gz,
  or viewing/combining it with volumes of differing obliquity,
  you should consider running: 
     3dWarp -deoblique 
  on this and  other oblique datasets in the same session.
 See 3dWarp -help for details.
++ Oblique dataset:/lscratch/30511576/sub-024/sub-024.results/vlines.pb00.tcat/tmp.mask.nii.gz is 35.151749 degrees from plumb.
++ have 1 volumes of input to combine
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 20355 survived, 118909 were zero
++ writing result mask.nii.gz...
++ Output dataset ./mask.nii.gz

++ requiring 5 voxels in mask columns
++ 3dLocalstat: AFNI version=AFNI_24.1.22 (Jun 21 2024) [64-bit]
++ Authored by: Emperor Zhark
[7m*+ WARNING:[0m   If you are performing spatial transformations on an oblique dset,
  such as /lscratch/30511576/sub-024/sub-024.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/30511576/sub-024/sub-024.results/vlines.pb00.tcat/mask.nii.gz is 35.151749 degrees from plumb.
++ Number of voxels in mask = 20355
++ Oblique dataset:/lscratch/30511576/sub-024/sub-024.results/vlines.pb00.tcat/mask.nii.gz is 35.151749 degrees from plumb.
++ Neighborhood comprises 69 voxels
++ Start sub-brick [0]
++ Output dataset ./tmp.mask.col.count.nii.gz
++ 3dcalc: AFNI version=AFNI_24.1.22 (Jun 21 2024) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./mask.nii.gz

-- detrend -polort 4, new eset = ts.1.det.r01.nii.gz
++ 3dTproject: AFNI version=AFNI_24.1.22 (Jun 21 2024) [64-bit]
++ Authored by: Cox the Algebraic (Linear)
[7m*+ WARNING:[0m   If you are performing spatial transformations on an oblique dset,
  such as /lscratch/30511576/sub-024/sub-024.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/30511576/sub-024/sub-024.results/vlines.pb00.tcat/ts.0.orig.r01.nii.gz is 35.151749 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
[7m*+ WARNING:[0m 3dTproject input data :: 2176 vectors are constant

++ 3dTstat: AFNI version=AFNI_24.1.22 (Jun 21 2024) [64-bit]
++ Authored by: KR Hammett & RW Cox
[7m*+ WARNING:[0m   If you are performing spatial transformations on an oblique dset,
  such as /lscratch/30511576/sub-024/sub-024.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/30511576/sub-024/sub-024.results/vlines.pb00.tcat/ts.1.det.r01.nii.gz is 35.151749 degrees from plumb.
++ Output dataset ./tmp.stdev.nii.gz
++ 3dcalc: AFNI version=AFNI_24.1.22 (Jun 21 2024) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./var.0.orig.r01.nii.gz
[7m*+ WARNING:[0m   If you are performing spatial transformations on an oblique dset,
  such as /lscratch/30511576/sub-024/sub-024.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/30511576/sub-024/sub-024.results/vlines.pb00.tcat/mask.nii.gz is 35.151749 degrees from plumb.
++ Oblique dataset:/lscratch/30511576/sub-024/sub-024.results/vlines.pb00.tcat/var.0.orig.r01.nii.gz is 35.151749 degrees from plumb.
++ 3dcalc: AFNI version=AFNI_24.1.22 (Jun 21 2024) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./var.1.scale.r01.nii.gz
++ 3dLocalstat: AFNI version=AFNI_24.1.22 (Jun 21 2024) [64-bit]
++ Authored by: Emperor Zhark
[7m*+ WARNING:[0m   If you are performing spatial transformations on an oblique dset,
  such as /lscratch/30511576/sub-024/sub-024.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/30511576/sub-024/sub-024.results/vlines.pb00.tcat/mask.nii.gz is 35.151749 degrees from plumb.
++ Number of voxels in mask = 20061
++ Oblique dataset:/lscratch/30511576/sub-024/sub-024.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 35.151749 degrees from plumb.
++ Neighborhood comprises 69 voxels
++ Start sub-brick [0]
++ Output dataset ./proj.r01.nii.gz
++ Neighborhood definition (NN=3) accepted
[7m*+ WARNING:[0m   If you are performing spatial transformations on an oblique dset,
  such as /lscratch/30511576/sub-024/sub-024.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/30511576/sub-024/sub-024.results/vlines.pb00.tcat/proj.r01.nii.gz is 35.151749 degrees from plumb.
++ User input stat threshold: -1
++ User input stat threshold: 0.95
++ Data volume:      [0] 'MEAN'
++ Threshold volume: [0] 'MEAN'
++ How many sides to this stat? 0
++ Looks like clustering is *not* being performed on a stat value; won't worry about sidedness, then.
++ Opt code: 2sided,-1,0.95,NN3
[7m*+ WARNING:[0m No mask being used? That *could* be OK, but thought I'd let you know...
++ Threshold volume [0] does *not* appear to be a stat!
++ Sorting clusters by size.
#
#  Cluster report 
#[ Dataset prefix      = proj.r01.nii.gz ]
#[ Threshold vol       = [0] 'MEAN' ]
#[ Supplement dat vol  = [0] 'MEAN' ]
#[ Option summary      = 2sided,-1,0.95,NN3 ]
#[ Threshold value(s)  = left-tail thr=-1.000000;  right-tail thr=0.950000 ]
#[ Aux. stat. info.    = not a stat! ]
#[ Nvoxel threshold    = 0;  Volume threshold = 0.000 ]
#[ Single voxel volume = 36.000 (microliters) ]
#[ Neighbor type, NN   = 3 ]
#[ 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
#------  -----  -----  -----  -----  -----  -----  -----  -----  -----  -------  -------  -------  -----  -----  -----
      5    7.9  -135.4  -70.3    7.9    7.9  -135.4  -135.4  -78.3  -62.3   0.9702  5.3e-05   0.9702    7.9  -135.4  -78.3 
   7.90 -135.40  -52.34

-- evaluating intersection...
++ 3dMean: AFNI version=AFNI_24.1.22 (Jun 21 2024) [64-bit]
++ WARNING: Have only 1 dset.
[7m*+ WARNING:[0m   If you are performing spatial transformations on an oblique dset,
  such as /lscratch/30511576/sub-024/sub-024.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/30511576/sub-024/sub-024.results/vlines.pb00.tcat/proj.r01.nii.gz is 35.151749 degrees from plumb.
++ Neighborhood definition (NN=3) accepted
[7m*+ WARNING:[0m   If you are performing spatial transformations on an oblique dset,
  such as /lscratch/30511576/sub-024/sub-024.results/vlines.pb00.tcat/proj.min.nii.gz,
  or viewing/combining it with volumes of differing obliquity,
  you should consider running: 
     3dWarp -deoblique 
  on this and  other oblique datasets in the same session.
 See 3dWarp -help for details.
++ Oblique dataset:/lscratch/30511576/sub-024/sub-024.results/vlines.pb00.tcat/proj.min.nii.gz is 35.151749 degrees from plumb.
++ User input stat threshold: -1
++ User input stat threshold: 0.95
++ Data volume:      [0] 'MEAN'
++ Threshold volume: [0] 'MEAN'
++ How many sides to this stat? 0
++ Looks like clustering is *not* being performed on a stat value; won't worry about sidedness, then.
++ Opt code: 2sided,-1,0.95,NN3
[7m*+ WARNING:[0m No mask being used? That *could* be OK, but thought I'd let you know...
++ Threshold volume [0] does *not* appear to be a stat!
++ Sorting clusters by size.
#
#  Cluster report 
#[ Dataset prefix      = proj.min.nii.gz ]
#[ Threshold vol       = [0] 'MEAN' ]
#[ Supplement dat vol  = [0] 'MEAN' ]
#[ Option summary      = 2sided,-1,0.95,NN3 ]
#[ Threshold value(s)  = left-tail thr=-1.000000;  right-tail thr=0.950000 ]
#[ Aux. stat. info.    = not a stat! ]
#[ Nvoxel threshold    = 0;  Volume threshold = 0.000 ]
#[ Single voxel volume = 36.000 (microliters) ]
#[ Neighbor type, NN   = 3 ]
#[ 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
#------  -----  -----  -----  -----  -----  -----  -----  -----  -----  -------  -------  -------  -----  -----  -----
      5    7.9  -135.4  -70.3    7.9    7.9  -135.4  -135.4  -78.3  -62.3   0.9702  5.3e-05   0.9702    7.9  -135.4  -78.3 
   7.90 -135.40  -52.34
++ Check about making images
++ 3dcalc: AFNI version=AFNI_24.1.22 (Jun 21 2024) [64-bit]
++ Authored by: A cast of thousands
[7m*+ WARNING:[0m input 'a' is not used in the expression
++ Symbol k using predefined value
++ Symbol x using predefined value
++ Symbol y using predefined value
++ Output dataset ./__tmp_dash_line.nii.gz
++ olay_alpha has known value: Yes
++ My command:
   @chauffeur_afni -ulay var.1.scale.r01.nii.gz -olay __tmp_dash_line.nii.gz -pbar_posonly -cbar Reds_and_Blues_Inv -func_range 1 -set_subbricks 0 0 0 -thr_olay 0.5 -olay_alpha Yes -olay_boxed Yes -set_dicom_xyz 7.90 -135.40 -52.34 -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_24.1.22
++ chauffeur ver  : 6.7

------------------ 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_3KdrtdZetqE
++ 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/30511576/sub-024/sub-024.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/30511576/sub-024/sub-024.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 35.151749 degrees from plumb.
*+ WARNING:   If you are performing spatial transformations on an oblique dset,
  such as /lscratch/30511576/sub-024/sub-024.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/30511576/sub-024/sub-024.results/vlines.pb00.tcat/var.1.scale.r01.nii.gz is 35.151749 degrees from plumb.
++ Ulay to be visualized within user range:
  [0%, 98%] -> [0.000000, 1.000000]
++ 3dcalc: AFNI version=AFNI_24.1.22 (Jun 21 2024) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_3KdrtdZetqE/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_24.1.22 (Jun 21 2024) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_3KdrtdZetqE/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 7.90 -135.40 -52.34

------------------- end of optionizing -------------------

 -- trying to start Xvfb :387 
[1] 3276011
+/lscratch/30511576/sub-024/sub-024.results/vlines.pb00.tcat/__tmp_chauf_3KdrtdZetqE++ Writing one 256x180 image to filter '/usr/bin/pnmtopng -compression 9 > ./img_r01_01.sag.png'

AFNI QUITTs!

+++ Command Echo:
   afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY  tmp_olay.nii -com SEE_OVERLAY     + -com OPEN_WINDOW sagittalimage opacity=9 mont=1x1:64:0: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 7.90 -135.40 -52.34 -com SAVE_PNG sagittalimage ./img_r01_01.sag blowup=4 -com QUITT ./__tmp_chauf_3KdrtdZetqE 


+* Removing temporary image directory './__tmp_chauf_3KdrtdZetqE'.

[1]    Done                          Xvfb :387 -screen 0 1024x768x24

++ DONE (good exit)
   see: ./img_r01_01*

+++ Have 1 images. Will wrap to fill 7x1 matrix
+++ Transforming all input to rgb for a good reason 
+++ Writing image to QC_var_lines.jpg
+++ Arranging 1 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: 1
   found questionable intersected regions  : 1

=============== bad_coords.inter.txt ===============
   7.90 -135.40  -52.34

=============== bad_coords.r01.txt ===============
   7.90 -135.40  -52.34

