afni.nimh.nih.gov

Here's the full listing for the command run:
********* Starting @SSwarper for TDT_101 Visit1 ************
******************************************
Running .cshrc
++ Starting: @SSwarper v2.2
++ Default OMP_NUM_THREADS is 12

++ Based on input, the output directory will be:
.

++ SSW Step 1
++ 3dUnifize: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as TDT_101_anat.nii,
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:TDT_101_anat.nii is 15.967682 degrees from plumb.
+ Pre-processing: ADV................UW[s75897]Gm
++ Output dataset ./anatU.TDT_101.nii
++ ===== CPU time = 472.6 sec Elapsed = 60.8
++ 3danisosmooth: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: Daniel Glen
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./anatU.TDT_101.nii,
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:./anatU.TDT_101.nii is 15.967682 degrees from plumb.
++ total voxels 10485760, voxels completely inside mask 4319205, voxels on edge of mask 426212
++ loading original data
++ iteration 0
++ computing structure tensor
++ applying structure tensor
++ --- Output dataset ./anatUA.TDT_101.nii
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./anatUA.TDT_101.nii,
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:./anatUA.TDT_101.nii is 15.967682 degrees from plumb.
++ 3dcalc: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././anatUAC.TDT_101.nii
++ SSW Step 2
++ Notice SUMA_BrainWrap_ParseInput (SUMA_3dSkullStrip.c:1244 @10:49:42):
Setting fill_hole to 10
++ Notice 3dSkullStrip (SUMA_3dSkullStrip.c:1600 @10:49:42):
Loading dset, performing Spatial Normalization
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./anatUAC.TDT_101.nii,
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:./anatUAC.TDT_101.nii is 15.967682 degrees from plumb.
3dSkullStrip:
Original resolution 1.000000, 1.000000, 1.000000
SpatNorm resolution 1.000000, 1.000000, 1.000000
++mri_brainormalize: normalizing
++mri_brainormalize: top clip above slice 232
++mri_brainormalize: bot clip below slice 62
++mri_brainormalize: Rescaling.
++mri_brainormalize: Eroding, clustering ...
+ Eroded 759207 voxels
+ Restored 680470 eroded voxels
+ Clustering voxels ...
+ Largest cluster has 2706318 voxels
+ Clustering voxels ...
+ Largest cluster has 3472051 voxels
++mri_brainormalize: Clipping extreme values.
+ scaling by fac=0.0690683
3dSkullStrip: -spatnorm: Expecting 6195700 voxels in in_vol dset (167 212 175)
3dSkullStrip: Edge threshold set to 79.376221. (minimum acceptable was 23.673152)
(92.000000 percentile =79.376221, 99.999001 percentile = 236.731522)
3dSkullStrip: Prepping volume...
SUMA_LoadPrepInVol: Volume 2723458.000000, radius 86.631828
3dSkullStrip: Beginning brain extraction...
3dSkullStrip: Have surface, OK for 1st entry.
3dSkullStrip: Stretching to avoid ventricles.
SO->Center is [0.400050 21.408291 -7.290159]
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: pastarea = 75542.833038
SUMA_StretchToFitLeCerveau:
Stage1: MaxExp = 0.678188, darea = 0.000000, going for more...
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 4529 troubled nodes, going for more...
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.563701 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.168016 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.080900 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.054269 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.038488 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.030568 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: -0.000751 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Stage converged. Moving to new Stage or Type.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
Stage 3, type 2: 1.000000 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
3dSkullStrip: Checking for self intersection...
3dSkullStrip: No intersections found.
3dSkullStrip: Final smoothing of 72
3dSkullStrip: Touchup correction, pass 1 ...
3dSkullStrip: The beauty treatment smoothing.
3dSkullStrip: Locating voxels inside surface ...
3dSkullStrip: Setting output to orig_vol (iset = 0x7f98d2814a00) (osnd = 0x7f98d3816200)...
3dSkullStrip: Coercing...
3dSkullStrip: Writing masked volume ...
3dSkullStrip: Applying a bit of erosion and dilatation
++ SSW Step 3
++ OpenMP thread count = 12

+++ Command Echo:
3dQwarp -lite -base /Users/knutsonk/abin/MNI152_2009_template_SSW.nii.gz[1] -lpa -warpscale 1 -source ./anatUAC.TDT_101.nii -weight /Users/knutsonk/abin/MNI152_2009_template_SSW.nii.gz[2] -allineate -noneg -maxlev 5 -iwarp -awarp -wtgaus 4.5 -inedge -workhard:3:5 -nopenalty -prefix ./junk.SSwarper.iC0C39AtVM7_TAL5.nii

++ 3dQwarp: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./anatUAC.TDT_101.nii,
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:./anatUAC.TDT_101.nii is 15.967682 degrees from plumb.
++ ###############################################################
+ Starting 3dAllineate (affine register) command:

3dAllineate -base /Users/knutsonk/abin/MNI152_2009_template_SSW.nii.gz[1] -source ./anatUAC.TDT_101.nii -prefix ./junk.SSwarper.iC0C39AtVM7_TAL5_Allin.nii -1Dmatrix_save ./junk.SSwarper.iC0C39AtVM7_TAL5_Allin -cmass -final wsinc5 -float -master BASE -twobest 7 -weight /Users/knutsonk/abin/MNI152_2009_template_SSW.nii.gz[2] -zclip -cost lpa+ZZ -fineblur 4.44
+ ###############################################################
++ 3dAllineate: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./anatUAC.TDT_101.nii,
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:./anatUAC.TDT_101.nii is 15.967682 degrees from plumb.
++ lpa+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration]
*+ WARNING: '-source_automask' is strongly recommended when using -lpc or -lpa
++ Source dataset: ./anatUAC.TDT_101.nii
++ Base dataset: /Users/knutsonk/abin/MNI152_2009_template_SSW.nii.gz
++ Loading datasets into memory
++ NOTE: base and source coordinate systems have different handedness
+ Orientations: base=Right handed (LPI); source=Left handed (ASR)
+ - It is nothing to worry about: 3dAllineate aligns based on coordinates.
+ - But it is always important to check the alignment visually to be sure.
++ Local correlation: blok type = 'RHDD(6.54321)'
++ lpa+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration]
++ OpenMP thread count = 12
++ ======= Allineation of 1 sub-bricks using Local Pearson Abs + Others =======
++ *** Coarse pass begins ***
++ *** Fine pass begins ***
+ Final fine fit Parameters:
x-shift= 14.4633 y-shift= 5.6927 z-shift= 33.9463 ... enorm= 37.3356 mm
z-angle= -0.6470 x-angle= 13.8857 y-angle= 0.8761 ... total= 13.9233 deg
x-scale= 0.9593 y-scale= 0.9533 z-scale= 0.8578 ... vol3D= 0.7844 = base bigger than source
y/x-shear= -0.0210 z/x-shear= -0.0192 z/y-shear= -0.0135
++ Output dataset ./junk.SSwarper.iC0C39AtVM7_TAL5_Allin.nii
++ Wrote -1Dmatrix_save ./junk.SSwarper.iC0C39AtVM7_TAL5_Allin.aff12.1D
++ 3dAllineate: total CPU time = 2541.4 sec Elapsed = 949.8
++ ###########################################################
++ # Please check results visually for alignment quality #
++ ###########################################################
++ # '-autoweight' is recommended when using -lpc or -lpa #
++ # If your results are not good, please try again. #
++ ###########################################################

++ 3dQwarp: replacing source dataset with 3dAllineate result ./junk.SSwarper.iC0C39AtVM7_TAL5_Allin.nii
# mat44 3dAllineate matrix:
0.959131 -0.007311 -0.014240 14.463300
-0.009673 0.925549 0.229081 5.692670
-0.007767 -0.218347 0.829814 33.946301
++ Dataset zero-pad: xbot=15 xtop=14 ybot=13 ytop=22 zbot=15 ztop=9 voxels
++ +++++++++++ Begin warp optimization: base=/Users/knutsonk/abin/MNI152_2009_template_SSW.nii.gz source=./junk.SSwarper.iC0C39AtVM7_TAL5_Allin.nii
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21..200 26..238 21..195 [clock= 16m 24s 743ms]
lev=0 0..221 0..263 0..216: [first cost=-2.04045] .... done [cost:-2.04045==>-2.76744]
lev=1 patch=167x197x163 [clock= 19m 5s 544ms]........ done [cost:-2.76744==>-6.54723 ; 8 patches optimized, 0 skipped]
lev=2 patch=125x149x123 [clock= 19m 36s 384ms]......................... done [cost:-6.54723==>-5.72616 ; 25 patches optimized, 2 skipped]
lev=3 patch=93x111x91 [clock= 20m 42s 69ms].................:[cost=-5.45052]:............. done [cost:-5.72616==>-5.70162 ; 84 patches optimized, 44 skipped]
lev=4 patch=71x83x69 [clock= 22m 31s 120ms]...........:[cost=-5.11998]:................ done [cost:-5.70162==>-5.16012 ; 164 patches optimized, 86 skipped]
lev=5 patch=53x63x51 [clock= 24m 23s 570ms].................:[cost=-5.42544]:................. done [cost:-5.16012==>-5.93053 ; 405 patches optimized, 281 skipped]
++ ====== total number of parameters 'optimized' = 8379
+ initial unpenalized cost = -2.04045
+ final unpenalized cost = -5.93053
+ final penalized cost = -5.93053
++ Output dataset ./junk.SSwarper.iC0C39AtVM7_TAL5_AWARP.nii
++ Output dataset ./junk.SSwarper.iC0C39AtVM7_TAL5.nii
++ Output dataset ./junk.SSwarper.iC0C39AtVM7_TAL5_WARP.nii
++ Inverting warp ********.............:...
++ Output dataset ./junk.SSwarper.iC0C39AtVM7_TAL5_WARPINV.nii
++ ===== CPU time = 3635.1 sec clock time = 27m 6s 864ms
++ SSW Step 4
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 2 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 2117569 survived, 6412452 were zero
++ writing result junk.SSwarper.iC0C39AtVM7_MASK.nii...
++ Output dataset ./junk.SSwarper.iC0C39AtVM7_MASK.nii
++ 3dcalc: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././junk.SSwarper.iC0C39AtVM7_TAL5mm.nii
++ SSW Step 5

+++ Command Echo:
3dNwarpApply -nwarp ./junk.SSwarper.iC0C39AtVM7_TAL5_WARPINV.nii -master ./anatS.TDT_101.nii -source ./junk.SSwarper.iC0C39AtVM7_TAL5mm.nii -prefix ./junk.SSwarper.iC0C39AtVM7_TAL5ww.nii

++ 3dNwarpApply: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is './anatS.TDT_101.nii'
** AFNI converts NIFTI_datatype=2 (UINT8) in file ./junk.SSwarper.iC0C39AtVM7_TAL5mm.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ opened source dataset './junk.SSwarper.iC0C39AtVM7_TAL5mm.nii'
++ Processing -nwarp
++ Warping:.Z
++ Output dataset ./junk.SSwarper.iC0C39AtVM7_TAL5ww.nii
++ total CPU time = 94.5 sec Elapsed = 12.3

+++ Command Echo:
3dmask_tool -input /Users/knutsonk/abin/MNI152_2009_template_SSW.nii.gz[3] -dilate_input 3 -prefix ./junk.SSwarper.iC0C39AtVM7_MASK.nii

++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 3 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 2237335 survived, 6292686 were zero
++ writing result junk.SSwarper.iC0C39AtVM7_MASK.nii...
++ Output dataset ./junk.SSwarper.iC0C39AtVM7_MASK.nii
++ 3dNwarpApply: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is './anatS.TDT_101.nii'
++ opened source dataset './junk.SSwarper.iC0C39AtVM7_MASK.nii'
++ Processing -nwarp
++ Warping:.Z
++ Output dataset ./junk.SSwarper.iC0C39AtVM7_MASKO.nii
++ total CPU time = 80.0 sec Elapsed = 10.8
++ 3dcalc: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././anatSS.TDT_101.nii
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 0 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 1581696 survived, 8904064 were zero
++ writing result junk.SSwarper.iC0C39AtVM7_de3.nii...
++ Output dataset ./junk.SSwarper.iC0C39AtVM7_de3.nii
++ 3dcalc: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././anatSSc.TDT_101.nii
++ 3dAutomask: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset ./anatSSc.TDT_101.nii
++ Forming automask
+ Fixed clip level = 449.564484
+ Used gradual clip level = 418.801331 .. 464.351929
+ Number voxels above clip level = 1413798
+ Clustering voxels ...
+ Largest cluster has 1413207 voxels
+ Clustering voxels ...
+ Largest cluster has 1404582 voxels
+ Filled 22512 voxels in small holes; now have 1427094 voxels
+ Filled 86072 voxels in large holes; now have 1513166 voxels
+ Clustering voxels ...
+ Largest cluster has 1513165 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 8972595 voxels
+ Mask now has 1513165 voxels
++ 1513165 voxels in the mask [out of 10485760: 14.43%]
++ first 47 x-planes are zero [from A]
++ last 37 x-planes are zero [from P]
++ first 37 y-planes are zero [from S]
++ last 80 y-planes are zero [from I]
++ first 11 z-planes are zero [from R]
++ last 12 z-planes are zero [from L]
++ applying mask to original data
++ Writing masked data
++ Output dataset ./anatSSd.TDT_101.nii
++ CPU time = 2.030000 sec
++ SSW Step 6
++ SSW Step 6 ... piece 0
++ 3dAllineate: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: Zhark the Registrator
** AFNI converts NIFTI_datatype=2 (UINT8) in file ./junk.SSwarper.iC0C39AtVM7_TAL5mm.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ lpa+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration]
++ Source dataset: ./anatSS.TDT_101.nii
++ Base dataset: (not given)
++ Loading datasets into memory
++ Local correlation: blok type = 'RHDD(6.54321)'
++ lpa+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration]
+ -cmass x y z shifts = 0.000 0.000 0.000
+ shift search range is +/- = 51.039 81.855 81.855
++ OpenMP thread count = 12
++ ========== Applying transformation to 1 sub-bricks ==========
++ wsinc5 interpolation setup:
+ taper function = Min sidelobe 3 term
+ taper cut point = 0.000
+ window radius = 5 voxels
+ window shape = Cubical
+ The above can be altered via the AFNI_WSINC5_* environment variables.
+ (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.)
+ wsinc5 CUBE(5) mask has 1000 points
++ Output dataset ./junk.SSwarper.iC0C39AtVM7_AffSS.nii
++ 3dAllineate: total CPU time = 25.4 sec Elapsed = 3.9
++ ###########################################################
++ SSW Step 6 ... piece 1
++ OpenMP thread count = 12

+++ Command Echo:
3dQwarp -lite -base /Users/knutsonk/abin/MNI152_2009_template_SSW.nii.gz[0] -source ./junk.SSwarper.iC0C39AtVM7_AffSS.nii -iniwarp ./junk.SSwarper.iC0C39AtVM7_TAL5_AWARP.nii -warpscale 1 -lpa -inilev 1 -maxlev 5 -wtgaus 4.5 -inedge -pblur -workhard:5:5 -nodset -prefix ./junk.SSwarper.iC0C39AtVM7_QQ5.nii

++ 3dQwarp: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=15 xtop=14 ybot=13 ytop=22 zbot=15 ztop=9 voxels
++ Weightizing the base image: FWHM = 4.5 (vox)
++ +++++++++++ Begin warp optimization: base=/Users/knutsonk/abin/MNI152_2009_template_SSW.nii.gz source=./junk.SSwarper.iC0C39AtVM7_AffSS.nii
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34..188 33..223 16..179 [clock= 20s 373ms]
lev=1 patch=145x177x149 [clock= 21s 706ms][first cost=-18.25406] ... done [cost:-18.25406==>-17.59986 ; 3 patches optimized, 5 skipped]
lev=2 patch=109x133x113 [clock= 30s 822ms][first cost=-15.91180] ................. done [cost:-17.59986==>-16.18772 ; 17 patches optimized, 10 skipped]
lev=3 patch=81x99x85 [clock= 55s 650ms][first cost=-11.96368] ......... done [cost:-16.18772==>-13.40290 ; 34 patches optimized, 30 skipped]
lev=4 patch=61x75x63 [clock= 1m 35s 833ms][first cost=-9.00451] ........... done [cost:-13.40290==>-10.70988 ; 78 patches optimized, 47 skipped]
lev=5 patch=45x57x47 [clock= 2m 25s 936ms][first cost=-8.18368] ............:[cost=-9.68777]:........... done [cost:-10.70988==>-10.14562 ; 386 patches optimized, 300 skipped]
++ ====== total number of parameters 'optimized' = 6216
+ initial unpenalized cost = -18.2541
+ final unpenalized cost = -11.4522
+ final penalized cost = -10.1456
++ Output dataset ./junk.SSwarper.iC0C39AtVM7_QQ5_WARP.nii
++ ===== CPU time = 1754.6 sec clock time = 4m 43s 973ms
++ SSW Step 6 ... piece 2
++ OpenMP thread count = 12

+++ Command Echo:
3dQwarp -lite -base /Users/knutsonk/abin/MNI152_2009_template_SSW.nii.gz[0] -source ./junk.SSwarper.iC0C39AtVM7_AffSS.nii -iniwarp ./junk.SSwarper.iC0C39AtVM7_QQ5_WARP.nii -warpscale 1 -pcl -inilev 6 -maxlev 7 -workhard:6:7 -wtgaus 4.5 -inedge -pblur -nodset -prefix ./junk.SSwarper.iC0C39AtVM7_QQ7.nii

++ 3dQwarp: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=15 xtop=14 ybot=13 ytop=22 zbot=15 ztop=9 voxels
++ Weightizing the base image: FWHM = 4.5 (vox)
++ +++++++++++ Begin warp optimization: base=/Users/knutsonk/abin/MNI152_2009_template_SSW.nii.gz source=./junk.SSwarper.iC0C39AtVM7_AffSS.nii

Fatal Signal 11 (SIGSEGV) received
IW3D_setup_for_improvement
IW3D_warpomatic
IW3D_warp_s2bim
3dQwarp
Bottom of Debug Stack
** AFNI version = AFNI_20.1.06 Compile date = May 4 2020
** [[Precompiled binary macos_10.12_local: May 4 2020]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /Users/knutsonk/.afni.crashlog
++ SSW Step 6 ... piece 3a
++ OpenMP thread count = 12

+++ Command Echo:
3dQwarp -lite -base /Users/knutsonk/abin/MNI152_2009_template_SSW.nii.gz[0] -source ./junk.SSwarper.iC0C39AtVM7_AffSS.nii -iniwarp ./junk.SSwarper.iC0C39AtVM7_QQ7_WARP.nii -warpscale 1 -pcl -inilev 8 -minpatch 17 -wtgaus 4.5 -inedge -pblur -nodset -prefix ./junk.SSwarper.iC0C39AtVM7_QQ9.nii

++ 3dQwarp: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
** ERROR: Can't open warp dataset './junk.SSwarper.iC0C39AtVM7_QQ7_WARP.nii'
** FATAL ERROR: Cannot open -iniwarp ./junk.SSwarper.iC0C39AtVM7_QQ7_WARP.nii
** Program compile date = May 4 2020
++ SSW Step 6 ... piece 3b
++ OpenMP thread count = 12

+++ Command Echo:
3dQwarp -lite -base /Users/knutsonk/abin/MNI152_2009_template_SSW.nii.gz[0] -source ./junk.SSwarper.iC0C39AtVM7_AffSS.nii -iniwarp ./junk.SSwarper.iC0C39AtVM7_QQ9_WARP.nii -warpscale 1 -pcl -inilev 10 -wtgaus 4.5 -inedge -pblur -minpatch 11 -prefix ./anatQQ.TDT_101.nii

++ 3dQwarp: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
** ERROR: Can't open warp dataset './junk.SSwarper.iC0C39AtVM7_QQ9_WARP.nii'
** FATAL ERROR: Cannot open -iniwarp ./junk.SSwarper.iC0C39AtVM7_QQ9_WARP.nii
** Program compile date = May 4 2020
++ SSW: done warping. Finalize.
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 0 (for dilations)
** FATAL ERROR: failed to open mask dataset './anatQQ.TDT_101.nii'
** Program compile date = May 4 2020
++ 3dcalc: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset ./anatQQ.TDT_101.nii
** Program compile date = May 4 2020
mv: rename ./anatQQc.TDT_101.nii to ./anatQQ.TDT_101.nii: No such file or directory
++ SSW Step 7
Running .cshrc
** ERROR: @snapshot_volreg can't find ./anatQQ.TDT_101.nii
Running .cshrc
** ERROR: @snapshot_volreg can't find ./anatQQ.TDT_101.nii
++ 3dcalc: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././junk.SSwarper.iC0C39AtVM7_mask.nii
Running .cshrc
++ My command:
@chauffeur_afni -ulay ./anatU.TDT_101.nii -ulay_range 2% 98% -olay ./junk.SSwarper.iC0C39AtVM7_mask.nii -func_range_perc_nz 1 -set_subbricks 0 0 0 -box_focus_slices ./junk.SSwarper.iC0C39AtVM7_mask.nii -cbar Reds_and_Blues_Inv -opacity 4 -prefix ./junk.SSwarper.iC0C39AtVM7_MONT1 -save_ftype JPEG -montx 9 -monty 1 -montgap 3 -set_xhairs OFF -label_mode 1 -label_size 3
\n------------------ start of optionizing ------------------\n
++ Found input file: ./anatU.TDT_101.nii
++ Found input file: ./junk.SSwarper.iC0C39AtVM7_mask.nii
++ Found focus refbox file: ./junk.SSwarper.iC0C39AtVM7_mask.nii
++ Using blowup factor: 2
++ Using opacity: 4
++ Making temporary work directory to copy vis files: ./__tmp_chauf_sWZwlkoY07f
++ 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 ./anatU.TDT_101.nii,
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:./anatU.TDT_101.nii is 15.967682 degrees from plumb.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./anatU.TDT_101.nii,
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:./anatU.TDT_101.nii is 15.967682 degrees from plumb.
++ Ulay to be visualized within user range:
[2%, 98%] -> [0.000000, 1136.991943]
++ 3dcalc: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_sWZwlkoY07f/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_sWZwlkoY07f/tmp_olay.nii
++ For olay, the 1%ile value leads to
--> upper range value: 1.000000
++ Dimensions (xyzt): 256 256 160 1
++ (initial) Slice spacing ordered (x,y,z) is: Running .cshrc 17 28 28
++ Resample refbox to match ulay
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./anatU.TDT_101.nii,
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:./anatU.TDT_101.nii is 15.967682 degrees from plumb.
++ 3dAutobox: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Auto bbox: x=47..218 y=37..175 z=11..147
++ 3dAutobox: output dataset = ./__tmp_chauf_sWZwlkoY07f/ulay_box_0.nii
(standard_in) 1: illegal character: R
(standard_in) 1: parse error
(standard_in) 1: illegal character: R
(standard_in) 1: parse error
(standard_in) 1: parse error
(standard_in) 1: parse error
++ 3dmaskdump: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=./__tmp_chauf_sWZwlkoY07f/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/8s/xk5nvfx539132klws39brmnh00znzr/T/ argv[8]=-prefix argv[9]=3dcalc_XYZ_9J9ykiIUdO5wmnpOAYEH4w argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0: no scale factor
++ Computing output statistics
++ Output dataset /var/folders/8s/xk5nvfx539132klws39brmnh00znzr/T/3dcalc_XYZ_9J9ykiIUdO5wmnpOAYEH4w+orig.BRIK
++ 3275396 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ How many coors? 5
++ Will have the ref box central coors : SET_DICOM_XYZ Running .cshrc 15.46435 -63.0221 -38.06531
++ Will have the ref box central gapord: Running .cshrc 15 19 15
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :330
[1] 36050
Precompiled binary macos_10.12_local: May 4 2020 (Version AFNI_20.1.06 'Otho')

+++ Command Echo:
afni -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=4 mont=9x1:Running:3:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=9x1:.cshrc:3:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=9x1:15:3: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 1136.991943 -com SET_FUNC_RANGE 1.000000 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_DICOM_XYZ Running .cshrc 15.46435 -63.0221 -38.06531 -com SAVE_JPEG sagittalimage ./junk.SSwarper.iC0C39AtVM7_MONT1.sag blowup=2 -com SAVE_JPEG coronalimage ./junk.SSwarper.iC0C39AtVM7_MONT1.cor blowup=2 -com SAVE_JPEG axialimage ./junk.SSwarper.iC0C39AtVM7_MONT1.axi blowup=2 -com QUITT ./__tmp_chauf_sWZwlkoY07f


Thanks go to M Furey for useful feedback

Initializing: X11[The X.Org Foundation v 11804000].. Widgets...... Input files:+/Volumes/shares/BNU/cnsraid/kknutson_fMRI/***/TDT_101/Visit1/MPRAGE/__tmp_chauf_sWZwlkoY07f
session # 1 = __tmp_chauf_sWZwlkoY07f/ ==> 4 datasets
Catenated 2 sessions = All_Datasets has 5 datasets
dataset count = 4
Time series = 0 files read
Plugins = 0 libraries read
*+ WARNING: Bad drive AFNI result from 'SET_DICOM_XYZ Running .cshrc 15.46435 -63.0221 -38.06531'
++ Writing one 4608x512 image to filter '/usr/local/bin/cjpeg -quality 95 > ./junk.SSwarper.iC0C39AtVM7_MONT1.sag.jpg'
++ Writing one 2880x512 image to filter '/usr/local/bin/cjpeg -quality 95 > ./junk.SSwarper.iC0C39AtVM7_MONT1.cor.jpg'
++ Writing one 2928x512 image to filter '/usr/local/bin/cjpeg -quality 95 > ./junk.SSwarper.iC0C39AtVM7_MONT1.axi.jpg'

AFNI QUITTs!
\n+* Removing temporary image directory './__tmp_chauf_sWZwlkoY07f'.\n
[1] + Done Xvfb :330 -screen 0 1024x768x24

++ DONE (good exit)
see: ./junk.SSwarper.iC0C39AtVM7_MONT1*

+++ Arranging 3 images (each 2928x512) into a 1x3 matrix.
+++ Transforming all input to rgb for a good reason
+++ Writing image to ./QC_anatSS.TDT_101.jpg
You can view image ./QC_anatSS.TDT_101.jpg with:
aiv ./QC_anatSS.TDT_101.jpg
Running .cshrc
++ 3dcalc: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset ./anatQQ.TDT_101.nii
** Program compile date = May 4 2020
** FATAL ERROR: Can't open dataset '__eac_tmp_flOARWyk4W9_0_cp.nii'
** Program compile date = May 4 2020
++ 3dAllineate: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: Zhark the Registrator
** FATAL ERROR: can't open -master dataset './anatQQ.TDT_101.nii'
** Program compile date = May 4 2020
++ 3dAutomask: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: Emperor Zhark
** FATAL ERROR: Can't open dataset '__eac_tmp_flOARWyk4W9_2_res.nii'
** Program compile date = May 4 2020
++ 3dMedianFilter: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
** FATAL ERROR: Can't open dataset '__eac_tmp_flOARWyk4W9_2_res.nii'
** Program compile date = May 4 2020
++ 3dedge3: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
** ERROR: can't open dataset (null)
++ 3dcalc: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset __eac_tmp_flOARWyk4W9_3_mask.nii
** Program compile date = May 4 2020
** FATAL ERROR: Can't open dataset '__eac_tmp_flOARWyk4W9_6_edge_mskd.nii'
** Program compile date = May 4 2020
vvv: Subscript out of range.
2dcat: No match.
++ SSW cleanup
--------------------------------------------------------
++ DONE with SSW. Check QC images:
./AMTDT_101.jpg ./MATDT_101.jpg ./QC_anatSS.TDT_101.jpg ./QC_anatQQ.TDT_101.jpg

In ref/base space (check warping):
ulay=anat, olay=base edges : ./AMTDT_101.jpg
ulay=base edges, olay=anat : ./MATDT_101.jpg
ulay=anat, olay=base edges : ./QC_anatQQ.TDT_101.jpg

In native space (check skullstripping):
ulay=anat, olay=SS mask : ./QC_anatSS.TDT_101.jpg

--------------------------------------------------------
******************************************
********* Finished @SSwarper for TDT_101 Visit1 ************
******************************************