bic@bic-iMac:~/Desktop/1.7.6_output/PythonScripts$ python3 /home/bic/Desktop/1.7.6_output/PythonScripts/tissue_seg.py
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/BRAINSFit --fixedVolume /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd --movingVolume /home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/template.mha --outputTransform /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/output_affine_transform.txt --useRigid --initializeTransformMode useCenterOfHeadAlign
Original Fixed image origin[-130.97, 107.242, 133.116, 0]
TranformTypes: Rigid(1 of 1).

Initializing transform with useCenterOfHeadAlign
ListSample TotalFrequency is  9000000
984 ValidHistogramsEntries,  9000000 TotalFrequency
0.001 ---> 0
0.999 ---> 899
LowHigh Thresholds: [349,2147483647]
maxSIDirection = 199
Computing Sampled Distance Computations
ListSample TotalFrequency is  16777216
138 ValidHistogramsEntries,  16777216 TotalFrequency
0.001 ---> 0
0.999 ---> 113
LowHigh Thresholds: [43,2147483647]
maxSIDirection = 133.116
Computing Sampled Distance Computations
Initializing transform with useCenterOfHeadAlign to 
VersorRigid3DTransform (0x375ddb0)
  RTTI typeinfo:   itk::VersorRigid3DTransform<double>
  Reference Count: 2
  Modified Time: 2756
  Debug: Off
  Object Name: 
  Observers: 
    none
  Matrix: 
    0.994522 0.103242 -0.0163519 
    -0.104528 0.982278 -0.155578 
    0 0.156434 0.987688 
  Offset: [101.151, 124.18, 101.041]
  Center: [-0.116031, -7.8283, -1.62563]
  Translation: [100.37, 124.584, 99.8368]
  Inverse: 
    0.994522 -0.104528 0 
    0.103242 0.982278 0.156434 
    -0.0163519 -0.155578 0.987688 
  Singular: 0
  Versor: [ 0.0783516, -0.00410623, -0.0521746, 0.995551 ]

===============================================



=============================== ITKv4 Registration: Starting Transform Estimations for Rigid(1 of 1).===============================

   0    -0.375917   [ 0.0789469 -0.0054252 -0.0524534 100.337 124.617 99.8199 ]
   1    -0.376465   [ 0.0790152 -0.00696646 -0.052157 100.323 124.663 99.8335 ]
   2    -0.377234   [ 0.079468 -0.00655364 -0.0510691 100.314 124.71 99.8451 ]
   3    -0.377226   [ 0.0780548 -0.00693262 -0.0522384 100.292 124.755 99.851 ]
   4    -0.377268   [ 0.0799382 -0.00566769 -0.0501678 100.323 124.789 99.8323 ]
   5    -0.376832   [ 0.0772336 -0.00748714 -0.051298 100.316 124.829 99.8036 ]
   6    -0.377151   [ 0.0780968 -0.0083109 -0.0515373 100.327 124.854 99.7619 ]
   7    -0.377669   [ 0.0787395 -0.00925679 -0.0515525 100.343 124.87 99.7171 ]
   8    -0.378079   [ 0.0790323 -0.0106142 -0.0511166 100.368 124.881 99.6753 ]
   9    -0.378688   [ 0.0801995 -0.0118571 -0.0500232 100.397 124.907 99.6446 ]
  10    -0.379376   [ 0.0804546 -0.0131172 -0.0500426 100.406 124.914 99.5961 ]
  11    -0.379597   [ 0.0790227 -0.0137197 -0.0489755 100.398 124.928 99.5488 ]
  12    -0.379875   [ 0.0796688 -0.0140649 -0.0473436 100.39 124.963 99.5149 ]
  13    -0.380446   [ 0.079173 -0.0142846 -0.0458485 100.419 124.962 99.4741 ]
  14    -0.380903   [ 0.0782166 -0.0146134 -0.0450656 100.393 124.962 99.4314 ]
  15    -0.381553   [ 0.0776715 -0.0152149 -0.0442782 100.386 124.967 99.3823 ]
  16    -0.381773   [ 0.0783477 -0.0156746 -0.043372 100.355 124.982 99.3454 ]
  17    -0.382342   [ 0.0788358 -0.0164075 -0.042106 100.354 125.005 99.3011 ]
  18    -0.383089   [ 0.0780385 -0.0172559 -0.0406163 100.391 125.015 99.2696 ]
  19    -0.383635   [ 0.077875 -0.0181502 -0.0404839 100.433 125.02 99.2425 ]
  20    -0.384121   [ 0.0778085 -0.0188372 -0.0401945 100.473 125.017 99.2124 ]
  21    -0.384615   [ 0.077905 -0.0197367 -0.0393449 100.515 125.014 99.1856 ]
  22    -0.385115   [ 0.0782 -0.0207206 -0.0382376 100.539 125.029 99.1448 ]
  23    -0.385367   [ 0.0771914 -0.022206 -0.0387508 100.574 125.032 99.109 ]
  24    -0.385377   [ 0.0786118 -0.0224276 -0.0388138 100.611 125.05 99.0806 ]
  25    -0.385732   [ 0.0799478 -0.0225186 -0.039108 100.634 125.078 99.0464 ]
  26    -0.386066   [ 0.0794602 -0.0231959 -0.0382697 100.639 125.113 99.0115 ]
  27    -0.386063   [ 0.0804262 -0.0221626 -0.0375335 100.653 125.138 98.9707 ]
  28    -0.386594   [ 0.0802624 -0.0228932 -0.0371032 100.669 125.15 98.986 ]
  29    -0.386555   [ 0.0802256 -0.0223639 -0.0374483 100.686 125.156 98.9692 ]
  30    -0.386673   [ 0.0801587 -0.0227013 -0.0373553 100.68 125.167 98.9685 ]
  31    -0.386662   [ 0.0801595 -0.0227747 -0.0373983 100.683 125.177 98.9616 ]
  32    -0.386699   [ 0.0801233 -0.0228166 -0.0374676 100.688 125.187 98.9553 ]
  33     -0.38669   [ 0.0800375 -0.0228887 -0.0375263 100.693 125.196 98.9484 ]
  34    -0.386712   [ 0.0799481 -0.0229371 -0.0376283 100.699 125.204 98.9413 ]
  35     -0.38676   [ 0.0799071 -0.023098 -0.0377282 100.705 125.213 98.934 ]
  36    -0.386771   [ 0.0800274 -0.0231094 -0.0378951 100.71 125.22 98.9252 ]
  37    -0.386762   [ 0.0795881 -0.0238091 -0.0377588 100.716 125.23 98.922 ]
  38    -0.386694   [ 0.0798901 -0.0233415 -0.0378614 100.713 125.229 98.9168 ]
  39    -0.386802   [ 0.0800783 -0.0231389 -0.0379361 100.716 125.227 98.9168 ]
  40    -0.386765   [ 0.0799241 -0.0233217 -0.0378957 100.715 125.227 98.9181 ]
Stop condition from optimizer.RegularStepGradientDescentOptimizerv4: Step too small after 41 iterations. Current step (0.00078125) is less than minimum step (0.001).

exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/WarpImageMultiTransform 3 /home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/template.mha /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_affine.nrrd /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/output_affine_transform.txt -R /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
AFFINE: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/output_affine_transform.txt
moving_image_filename: /home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/template.mha components 1
output_image_filename: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_affine.nrrd
reference_image_filename: /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
[0/1]: AFFINE: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/output_affine_transform.txt
User Linear interpolation 
 You are doing something more complex -- we wont check syntax in this case 
output origin: [-130.97, 107.242, 133.116]
output size: [256, 256, 256]
output spacing: [1, 1, 1]
output direction: 1 0 0
0 -0 -1
0 -1 -0


exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ANTS 3 -m CC[/home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd,/home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/template.mha,1,4] -i 100x50x25 -o /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_ -t SyN[0.25] -r Gauss[3,0]
 Run Reg 
 values 1
  Fixed image file: /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
  Moving image file: /home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/template.mha
Metric 0:  Not a Point-set
  Fixed image file: /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
  Moving image file: /home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/template.mha
  similarity metric weight: 1
  Radius: [4, 4, 4]
  radius: [4, 4, 4]
Use identity affine transform as initial affine para.
aff_init.IsNull()==1
Use identity affine transform as initial fixed affine para.
fixed_aff_init.IsNull()==1
Continue affine registration from the input
affine_opt.use_rotation_header = 0
affine_opt.ignore_void_orgin = 0
transform_initial: IsNotNull():0
OptAffine: metric_type=AffineWithMutualInformation
MI_bins=32 MI_samples=32000
number_of_seeds=0 time_seed=1592927414
number_of_levels=3
number_of_iteration_list=[10000,10000,10000]
graident_scales=[1,1,1,1,1,1,1,1,1,1,0.0001,0.0001,0.0001]
is_rigid = 0
mask null: 1
maximum_step_length=0.1
relaxation_factor=0.5
minimum_step_length=0.0001
translation_scales=0.0001
opt.transform_initial.IsNull(): 1
 opt.use_rotation_header: 0
 opt.ignore_void_orgin: 0
input affine center: [-0.10471, -7.96155, -1.57875]
input affine para: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 100.32017777781192, 118.45319333526895, 91.05563400865785]
level 0, iter 554, size: fix[64, 64, 64]-mov[50, 56, 50], affine para: [0.07649805709893333, -0.02512937528227103, -0.028070890792130463, 0.9963576601041151, 0.9982180417936809, 1.0496797309467178, 1.0106262822343979, 0.013279082160718032, 0.0026967139128111317, -0.05683166290409736, 100.19261074560502, 125.45739899056436, 98.56000274289889]
    reach oscillation, current step: 9.76563e-05<0.0001
level 1, iter 118, size: fix[128, 128, 128]-mov[100, 113, 100], affine para: [0.07047947842296362, -0.03369276721510702, -0.037603661483926146, 0.9962346135331867, 0.9977312381007678, 1.0476965596341474, 1.0207792046149848, 0.0064870768777572025, 0.006104425458149719, -0.06849176794818775, 100.3378331368746, 125.83753190115652, 99.26952789743012]
    reach oscillation, current step: 9.76563e-05<0.0001
level 2, iter 492, size: fix[256, 256, 256]-mov[200, 225, 200], affine para: [0.07169662508525074, -0.02899677869856428, -0.03118986763769434, 0.9965169205453736, 1.0056786740235424, 1.0559270104168421, 1.024150303947286, 0.009949409485277593, 0.010218658836296905, -0.06903026665070551, 100.38131582043684, 125.67375838955999, 98.4521068938571]
    reach oscillation, current step: 9.76563e-05<0.0001
A=1 0 0 
0 1 0 
0 0 1 

rotation R1 0 0 
0 1 0 
0 0 1 

upper R1 0 0 
0 1 0 
0 0 1 

s=0.25 u=0 v=0 w0 r=1
m_Rotation from vnl0 0 0 1
level 0, iter 4581, size: fix[50, 56, 50]-mov[64, 64, 64], affine para: [-0.07332717594981428, 0.029189017361097063, 0.02795568285046167, 0.9964886383341672, 0.9674227449727383, 0.9028968840517516, 0.9434925659134376, -0.016391373848967068, -0.0110010439595381, 0.01774088633035939, -91.84454842833027, -132.2269111641177, -69.63705103892485]
    reach oscillation, current step: 9.76563e-05<0.0001
level 1, iter 10000, size: fix[100, 113, 100]-mov[128, 128, 128], affine para: [-0.07537609410104931, 0.034269173823340736, 0.023403473547999307, 0.9962912955503644, 0.983746964212401, 0.9270280799394882, 0.9722107418433117, -0.020572240993879002, -0.013858589334017478, 0.03531534186497361, -94.41497131473868, -136.7592629027898, -70.10704543005677]
    does not reach oscillation, current step: 0.000195313>0.0001
level 2, iter 397, size: fix[200, 225, 200]-mov[256, 256, 256], affine para: [-0.07719642569077431, 0.03272616727314386, 0.023782304377449482, 0.9961948162054837, 0.9844792608327425, 0.9239525698716323, 0.9747464463825137, -0.02183332551039977, -0.008885164018746082, 0.03978566853947077, -94.41525145544678, -136.67838828965878, -69.92875851958946]
    reach oscillation, current step: 9.76563e-05<0.0001
 v1 -0.400478 v2 -0.407301
 last params [0.07169662508525074, -0.02899677869856428, -0.03118986763769434, 0.9965169205453736, 1.0056786740235424, 1.0559270104168421, 1.024150303947286, 0.009949409485277593, 0.010218658836296905, -0.06903026665070551, 100.38131582043684, 125.67375838955999, 98.4521068938571]
 my params [-0.07719642569077431, 0.03272616727314386, 0.023782304377449482, 0.9961948162054837, 0.9844792608327425, 0.9239525698716323, 0.9747464463825137, -0.02183332551039977, -0.008885164018746082, 0.03978566853947077, -94.41525145544678, -136.67838828965878, -69.92875851958946]
A=1.01171 0.067598 -0.0654501 
-0.0592637 1.06184 -0.205022 
0.0631256 0.159387 1.01148 

rotation R0.996358 0.0486793 -0.0700113 
-0.0583645 0.987896 -0.143717 
0.0621678 0.14728 0.987139 

upper R1.01541 0.0152867 0.00963606 
0 1.07575 -0.056756 
0 0 1.03252 

s=0.250899 u=0.0730107 v=-0.0331636 w-0.0268572 r=0.996418
m_Rotation from vnl0.0730107 -0.0331636 -0.0268572 0.996418
 new params [0.0730106864738273, -0.033163584836780224, -0.026857159376196718, 0.9964177383465409, 1.0154059588154105, 1.0757543085232415, 1.032521938691277, 0.015054775953600753, 0.009489864033915416, -0.05275929190135414, 100.182970651136, 125.19842796482753, 98.47653319283827]
outputput affine center: [-0.10471, -7.96155, -1.57875]
output affine para: [0.0730106864738273, -0.033163584836780224, -0.026857159376196718, 0.9964177383465409, 1.0154059588154105, 1.0757543085232415, 1.032521938691277, 0.015054775953600753, 0.009489864033915416, -0.05275929190135414, 100.182970651136, 125.19842796482753, 98.47653319283827]
initial measure value (MMI): rval = -0.301015
final measure value (MMI): rval = -0.433212
finish affine registeration...
 Requested Transformation Model:  SyN : Using 
SyN diffeomorphic model for transformation. 
  Grad Step 0.25 total-smoothing 0 gradient-smoothing 3
 setting N-TimeSteps = 1 trunc 256
 ScaleFactor 4 nlev 3 curl 0
 allocated def field 1 0 0
0 -0 -1
0 -1 -0

 Its at this level 100
 Allocating 
 Allocating Done 
 iteration 1 energy 0 : -22532.5
 iteration 2 energy 0 : -24353.8
 iteration 3 energy 0 : -25766.4
 iteration 4 energy 0 : -26797
 iteration 5 energy 0 : -27723.9
 iteration 6 energy 0 : -28545
 iteration 7 energy 0 : -29072.4
 iteration 8 energy 0 : -29248.4
 iteration 9 energy 0 : -29415.6
 iteration 10 energy 0 : -29684.3
 iteration 11 energy 0 : -29747.7
 iteration 12 energy 0 : -30123.3
 E-Slope 0.00951333 iteration 13 energy 0 : -30161.8
 E-Slope 0.00716597 iteration 14 energy 0 : -30285.3
 E-Slope 0.00541632 iteration 15 energy 0 : -30331.3
 E-Slope 0.00413337 iteration 16 energy 0 : -30475.9
 E-Slope 0.00322886 iteration 17 energy 0 : -30510.8
 E-Slope 0.00274175 iteration 18 energy 0 : -30634.8
 E-Slope 0.00243675 iteration 19 energy 0 : -30655.3
 E-Slope 0.0021564 iteration 20 energy 0 : -30763.9
 E-Slope 0.0018431 iteration 21 energy 0 : -30770.5
 E-Slope 0.00164877 iteration 22 energy 0 : -30870.6
 E-Slope 0.0013703 iteration 23 energy 0 : -30860.5
 E-Slope 0.00128075 iteration 24 energy 0 : -30913.1
 E-Slope 0.00112232 iteration 25 energy 0 : -30904.6
 E-Slope 0.00100709 iteration 26 energy 0 : -30963.9
 E-Slope 0.000842422 iteration 27 energy 0 : -30951.3
 E-Slope 0.000739865 iteration 28 energy 0 : -30990
 E-Slope 0.000601254 iteration 29 energy 0 : -30979.9
 E-Slope 0.000530608 iteration 30 energy 0 : -31023.1
 E-Slope 0.000428192 iteration 31 energy 0 : -31012.4
 E-Slope 0.000390112 iteration 32 energy 0 : -31048.1
 E-Slope 0.000321425 iteration 33 energy 0 : -31038.5
 E-Slope 0.00032156 iteration 34 energy 0 : -31077.9
 E-Slope 0.000285454 iteration 35 energy 0 : -31067.6
 E-Slope 0.000288159 iteration 36 energy 0 : -31104.6
 E-Slope 0.000257604 iteration 37 energy 0 : -31094.2
 E-Slope 0.000273056 iteration 38 energy 0 : -31132.6
 E-Slope 0.000253215 iteration 39 energy 0 : -31120.7
 E-Slope 0.000264183 iteration 40 energy 0 : -31155.9
 E-Slope 0.000241205 iteration 41 energy 0 : -31142.9
 E-Slope 0.000249498 iteration 42 energy 0 : -31172.9
 E-Slope 0.000224188 iteration 43 energy 0 : -31159
 E-Slope 0.000224553 iteration 44 energy 0 : -31186.2
 E-Slope 0.00019259 iteration 45 energy 0 : -31170.6
 E-Slope 0.000188589 iteration 46 energy 0 : -31194.3
 E-Slope 0.000153586 iteration 47 energy 0 : -31177.4
 E-Slope 0.000147618 iteration 48 energy 0 : -31200.9
 E-Slope 0.000112705 iteration 49 energy 0 : -31183.2
 E-Slope 0.00011082 iteration 50 energy 0 : -31207.3
 E-Slope 8.10698e-05 iteration 51 energy 0 : -31188.7
 Converged due to oscillation in optimization  metric 0 bad 15  
 ScaleFactor 2 nlev 3 curl 1
 Its at this level 50
 iteration 1 energy 0 : -152904
 iteration 2 energy 0 : -156966
 iteration 3 energy 0 : -163093
 iteration 4 energy 0 : -167378
 iteration 5 energy 0 : -170641
 iteration 6 energy 0 : -173331
 iteration 7 energy 0 : -175866
 iteration 8 energy 0 : -177782
 iteration 9 energy 0 : -179290
 iteration 10 energy 0 : -180538
 iteration 11 energy 0 : -181550
 iteration 12 energy 0 : -182410
 E-Slope 0.00722322 iteration 13 energy 0 : -183282
 E-Slope 0.0058063 iteration 14 energy 0 : -184166
 E-Slope 0.00481579 iteration 15 energy 0 : -185056
 E-Slope 0.00406373 iteration 16 energy 0 : -185703
 E-Slope 0.00337669 iteration 17 energy 0 : -185430
 E-Slope 0.00285768 iteration 18 energy 0 : -186297
 E-Slope 0.00239155 iteration 19 energy 0 : -186007
 E-Slope 0.00206459 iteration 20 energy 0 : -186854
 E-Slope 0.00171811 iteration 21 energy 0 : -186478
 E-Slope 0.00149009 iteration 22 energy 0 : -187396
 E-Slope 0.00121744 iteration 23 energy 0 : -186919
 E-Slope 0.00105616 iteration 24 energy 0 : -187854
 E-Slope 0.000850797 iteration 25 energy 0 : -187273
 E-Slope 0.00078629 iteration 26 energy 0 : -188252
 E-Slope 0.000704966 iteration 27 energy 0 : -187738
 E-Slope 0.000741579 iteration 28 energy 0 : -188621
 E-Slope 0.000620864 iteration 29 energy 0 : -187931
 E-Slope 0.000657827 iteration 30 energy 0 : -188909
 E-Slope 0.000568837 iteration 31 energy 0 : -188480
 E-Slope 0.000586279 iteration 32 energy 0 : -188975
 E-Slope 0.00045193 iteration 33 energy 0 : -188328
 E-Slope 0.000489347 iteration 34 energy 0 : -189283
 E-Slope 0.000384592 iteration 35 energy 0 : -188781
 E-Slope 0.000401713 iteration 36 energy 0 : -189215
 E-Slope 0.000273131 iteration 37 energy 0 : -188710
 E-Slope 0.000292584 iteration 38 energy 0 : -189271
 E-Slope 0.000183806 iteration 39 energy 0 : -188794
 E-Slope 0.000210181 iteration 40 energy 0 : -189279
 E-Slope 0.000101678 iteration 41 energy 0 : -188870
 E-Slope 0.000175305 iteration 42 energy 0 : -189657
 E-Slope 0.0001342 iteration 43 energy 0 : -189140
 E-Slope 0.000179358 iteration 44 energy 0 : -189515
 E-Slope 9.84147e-05 iteration 45 energy 0 : -189115
 Converged due to oscillation in optimization  metric 0 bad 15  
 ScaleFactor 1 nlev 3 curl 2
 Its at this level 25
 iteration 1 energy 0 : -1.16725e+06
 iteration 2 energy 0 : -1.18745e+06
 iteration 3 energy 0 : -1.21275e+06
 iteration 4 energy 0 : -1.23308e+06
 iteration 5 energy 0 : -1.24992e+06
 iteration 6 energy 0 : -1.26462e+06
 iteration 7 energy 0 : -1.27691e+06
 iteration 8 energy 0 : -1.28756e+06
 iteration 9 energy 0 : -1.29706e+06
 iteration 10 energy 0 : -1.30551e+06
 iteration 11 energy 0 : -1.31316e+06
 iteration 12 energy 0 : -1.31996e+06
 E-Slope 0.00539611 iteration 13 energy 0 : -1.32615e+06
 E-Slope 0.00463068 iteration 14 energy 0 : -1.33172e+06
 E-Slope 0.00402832 iteration 15 energy 0 : -1.33662e+06
 E-Slope 0.00353698 iteration 16 energy 0 : -1.34097e+06
 E-Slope 0.00312459 iteration 17 energy 0 : -1.34486e+06
 E-Slope 0.00277831 iteration 18 energy 0 : -1.34842e+06
 E-Slope 0.00247891 iteration 19 energy 0 : -1.35171e+06
 E-Slope 0.00221749 iteration 20 energy 0 : -1.35481e+06
 E-Slope 0.00199115 iteration 21 energy 0 : -1.35777e+06
 E-Slope 0.00179613 iteration 22 energy 0 : -1.36056e+06
 E-Slope 0.00163049 iteration 23 energy 0 : -1.36318e+06
 E-Slope 0.00149035 iteration 24 energy 0 : -1.36566e+06
 E-Slope 0.00137422 iteration 25 energy 0 : -1.36804e+06
 tired convergence: reached max iterations 
 Registration Done 
 begin writing /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_
 WARNING! we are guessing you want .nii.gz for your image output instead of: .6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_
 writing /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_ affine 
 writing /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_ def 
filename /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz

exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/WarpImageMultiTransform 3 /home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/template.mha /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template.mha /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Affine.txt -R /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
FIELD: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz
AFFINE: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Affine.txt
moving_image_filename: /home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/template.mha components 1
output_image_filename: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template.mha
reference_image_filename: /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
[0/2]: FIELD: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz
[1/2]: AFFINE: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Affine.txt
User Linear interpolation 
  We check the syntax of your call .... 
 syntax probably ok. 
output origin: [-130.97, 107.242, 133.116]
output size: [256, 256, 256]
output spacing: [1, 1, 1]
output direction: 1 0 0
0 -0 -1
0 -1 -0


exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/WarpImageMultiTransform 3 /home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/4.mha /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/4.mha /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Affine.txt -R /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
FIELD: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz
AFFINE: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Affine.txt
moving_image_filename: /home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/4.mha components 1
output_image_filename: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/4.mha
reference_image_filename: /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
[0/2]: FIELD: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz
[1/2]: AFFINE: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Affine.txt
User Linear interpolation 
  We check the syntax of your call .... 
 syntax probably ok. 
output origin: [-130.97, 107.242, 133.116]
output size: [256, 256, 256]
output spacing: [1, 1, 1]
output direction: 1 0 0
0 -0 -1
0 -1 -0


exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/WarpImageMultiTransform 3 /home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/2.mha /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/2.mha /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Affine.txt -R /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
FIELD: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz
AFFINE: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Affine.txt
moving_image_filename: /home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/2.mha components 1
output_image_filename: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/2.mha
reference_image_filename: /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
[0/2]: FIELD: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz
[1/2]: AFFINE: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Affine.txt
User Linear interpolation 
  We check the syntax of your call .... 
 syntax probably ok. 
output origin: [-130.97, 107.242, 133.116]
output size: [256, 256, 256]
output spacing: [1, 1, 1]
output direction: 1 0 0
0 -0 -1
0 -1 -0


exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/WarpImageMultiTransform 3 /home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/3.mha /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/3.mha /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Affine.txt -R /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
FIELD: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz
AFFINE: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Affine.txt
moving_image_filename: /home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/3.mha components 1
output_image_filename: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/3.mha
reference_image_filename: /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
[0/2]: FIELD: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz
[1/2]: AFFINE: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Affine.txt
User Linear interpolation 
  We check the syntax of your call .... 
 syntax probably ok. 
output origin: [-130.97, 107.242, 133.116]
output size: [256, 256, 256]
output spacing: [1, 1, 1]
output direction: 1 0 0
0 -0 -1
0 -1 -0


exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/WarpImageMultiTransform 3 /home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/1.mha /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/1.mha /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Affine.txt -R /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
FIELD: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz
AFFINE: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Affine.txt
moving_image_filename: /home/bic/Desktop/Adult_Atlas_rev1/Adult_Atlas/BrainsegAtlas/adult-atlas-asym-T1-RAI/1.mha components 1
output_image_filename: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/1.mha
reference_image_filename: /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
[0/2]: FIELD: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Warp.nii.gz
[1/2]: AFFINE: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas/template_to_T1_Affine.txt
User Linear interpolation 
  We check the syntax of your call .... 
 syntax probably ok. 
output origin: [-130.97, 107.242, 133.116]
output size: [256, 256, 256]
output spacing: [1, 1, 1]
output direction: 1 0 0
0 -0 -1
0 -1 -0


exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ABC_CLI /home/bic/Desktop/1.7.6_output/ABC_Segmentation/ABCparam.xml
Reading /home/bic/Desktop/1.7.6_output/ABC_Segmentation/ABCparam.xml...
ABC: Atlas Based Classification
========================================
Version 1.5.1
Program compiled on: May 29 2020

Marcel Prastawa - prastawa@sci.utah.edu
This software is provided for research purposes only

Using ITK version 4.8.2

=== Parameters ===
Suffix: EMS
Atlas Directory: /home/bic/Desktop/1.7.6_output/ABC_Segmentation/TissueSegmentationAtlas
Atlas Orientation: file
Atlas Format: mha
Output Directory: /home/bic/Desktop/1.7.6_output/ABC_Segmentation
Output Format: Nrrd
Input images: 
  [file] /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
  [file] 
Non-linear filtering, method: Curvature flow, 10 iterations, dt = 0.01
Prior weight scales: 1.3 1 0.7 0.8 
Max bias polynomial degree: 4
Initial Distribution Estimator: robust
Atlas warping: 0
Atlas warp fluid iterations: 50
Atlas warp fluid max step: 0.1
Atlas warp kernel width: 10

=== Start ===
Registering images using affine transform...
Attempting to read previous registration results...
Reading /home/bic/Desktop/1.7.6_output/ABC_Segmentation/T1_stripped_to_template_EMS.affine...
mu::Exception, in /work/jprieto/source/auto_EACSF-build/ABC/Engine/register/PairRegistrationMethod.txx line 1073Reading /home/bic/Desktop/1.7.6_output/ABC_Segmentation/T1_stripped_to__EMS.affine...
mu::Exception, in /work/jprieto/source/auto_EACSF-build/ABC/Engine/register/PairRegistrationMethod.txx line 1073Registering and resampling images...
Reading image 1: /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd...
Reading image 2: ...

Run without any arguments to see command line options

Failed opening /home/bic/Desktop/1.7.6_output/ABC_Segmentation/T1_stripped_to_template_EMS.affine

Failed opening /home/bic/Desktop/1.7.6_output/ABC_Segmentation/T1_stripped_to__EMS.affine

itk::ImageFileReaderException (0x2181560)
Location: "void itk::ImageFileReader<TOutputImage, ConvertPixelTraits>::GenerateOutputInformation() [with TOutputImage = itk::Image<float, 3u>; ConvertPixelTraits = itk::DefaultConvertPixelTraits<float>]" 
File: /work/jprieto/source/auto_EACSF-build/ABC-build/ITK-install/include/ITK-4.8/itkImageFileReader.hxx
Line: 87
Description: FileName must be specified