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AFNI Message Board
Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| May 16, 2020 05:28AM | |
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 ************
******************************************
********* 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 ************
******************************************
| Subject | Author | Posted |
|---|---|---|
|
krisknut | May 15, 2020 05:09PM |
|
krisknut | May 16, 2020 05:28AM |
|
krisknut | May 22, 2020 09:03AM |
|
kxd344 | June 29, 2020 01:01PM |
|
krisknut | June 29, 2020 03:12PM |
|
kxd344 | June 29, 2020 10:13PM |
