main_script.py

Running /home/bic/Desktop/1.7.6_output/PythonScripts/skull_strip.py
/usr/bin/python3 /home/bic/Desktop/1.7.6_output/PythonScripts/skull_strip.py
Skull stripping ...
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/T1.nii -mask /home/bic/Desktop/brainmask.nii -outfile /home/bic/Desktop/1.7.6_output/SkullStripping/T1_stripped.nrrd
exit with success

exit with success
Running /home/bic/Desktop/1.7.6_output/PythonScripts/tissue_seg.py
/usr/bin/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 (0x2f63db0)
  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    -0.379401   [ 0.0782102 -0.00486804 -0.0513532 100.39 124.58 99.7913 ]
   1    -0.380317   [ 0.0779289 -0.00618992 -0.0507215 100.421 124.567 99.754 ]
   2    -0.381767   [ 0.0773748 -0.00808544 -0.0499623 100.459 124.561 99.7225 ]
   3    -0.383148   [ 0.0775722 -0.00968123 -0.0486547 100.466 124.572 99.6745 ]
   4       -0.384   [ 0.0782482 -0.0112955 -0.0481701 100.45 124.574 99.6275 ]
   5    -0.384555   [ 0.0783468 -0.0119238 -0.0484261 100.437 124.569 99.5794 ]
   6     -0.38507   [ 0.0784405 -0.0126888 -0.0484647 100.426 124.567 99.5307 ]
   7    -0.385417   [ 0.0787765 -0.0133164 -0.0480163 100.422 124.573 99.4811 ]
   8    -0.385855   [ 0.0791627 -0.0136613 -0.0471433 100.429 124.581 99.4323 ]
   9     -0.38642   [ 0.0793054 -0.0141654 -0.045954 100.446 124.587 99.3857 ]
  10    -0.387036   [ 0.0804021 -0.014958 -0.0452107 100.451 124.581 99.3364 ]
  11     -0.38761   [ 0.0816654 -0.0161804 -0.0442085 100.41 124.589 99.3097 ]
  12    -0.388378   [ 0.0820812 -0.0172416 -0.0442851 100.41 124.62 99.2702 ]
  13    -0.388713   [ 0.0832216 -0.0179101 -0.0425911 100.414 124.662 99.2445 ]
  14    -0.389118   [ 0.0840076 -0.0182647 -0.0425338 100.403 124.687 99.2028 ]
  15    -0.389367   [ 0.0839128 -0.0178845 -0.0414298 100.397 124.705 99.1565 ]
  16    -0.389436   [ 0.0827056 -0.0185609 -0.0437374 100.361 124.737 99.1446 ]
  17    -0.389125   [ 0.0860972 -0.0192593 -0.0427824 100.379 124.768 99.111 ]
  18    -0.389312   [ 0.0848355 -0.0192481 -0.0424114 100.353 124.768 99.0684 ]
  19    -0.389778   [ 0.0844094 -0.0189193 -0.0430897 100.336 124.815 99.0622 ]
  20    -0.389909   [ 0.0847175 -0.0197715 -0.0406942 100.366 124.844 99.0352 ]
  21    -0.389481   [ 0.085852 -0.0189359 -0.0441791 100.362 124.857 98.988 ]
  22     -0.38959   [ 0.086388 -0.0195058 -0.0402794 100.373 124.874 98.9428 ]
  23    -0.390242   [ 0.0870694 -0.020538 -0.0419133 100.367 124.894 98.8976 ]
  24    -0.390469   [ 0.085483 -0.0203785 -0.0411161 100.341 124.923 98.8659 ]
  25    -0.390798   [ 0.086061 -0.0209548 -0.0422249 100.332 124.945 98.8226 ]
  26    -0.390831   [ 0.0860211 -0.0198838 -0.040088 100.336 124.943 98.7731 ]
  27    -0.390733   [ 0.0855549 -0.0219324 -0.0443575 100.302 124.954 98.7405 ]
  28    -0.390348   [ 0.0865845 -0.0240874 -0.0409938 100.309 124.975 98.6967 ]
  29    -0.390863   [ 0.0868454 -0.0210059 -0.0388463 100.306 124.992 98.7133 ]
  30    -0.390538   [ 0.0883586 -0.0218243 -0.0394593 100.291 125.012 98.7137 ]
  31    -0.390981   [ 0.0870713 -0.0227777 -0.0389427 100.274 125.03 98.714 ]
  32    -0.390899   [ 0.0879616 -0.0226858 -0.039612 100.252 125.041 98.7123 ]
  33    -0.391123   [ 0.0880322 -0.0231109 -0.0386275 100.247 125.065 98.717 ]
  34    -0.391221   [ 0.0884288 -0.0228639 -0.038979 100.235 125.087 98.713 ]
  35    -0.391257   [ 0.0888828 -0.023063 -0.0386233 100.225 125.109 98.7175 ]
  36    -0.391345   [ 0.0894491 -0.0228241 -0.0386899 100.219 125.133 98.7235 ]
  37    -0.391528   [ 0.0894872 -0.0231205 -0.0389122 100.21 125.153 98.735 ]
  38    -0.391574   [ 0.0898713 -0.0226773 -0.0385862 100.216 125.177 98.7306 ]
  39    -0.391508   [ 0.0893763 -0.023115 -0.038996 100.207 125.179 98.7385 ]
  40    -0.391556   [ 0.0895192 -0.0229784 -0.0388689 100.211 125.181 98.7338 ]
  41    -0.391595   [ 0.0896084 -0.0229461 -0.0387292 100.214 125.184 98.7295 ]
  42    -0.391582   [ 0.0895264 -0.0230008 -0.0388363 100.212 125.185 98.7322 ]
  43    -0.391584   [ 0.089549 -0.0229835 -0.0388115 100.214 125.186 98.7314 ]
  44    -0.391562   [ 0.0895252 -0.023016 -0.0388324 100.214 125.187 98.732 ]
  45    -0.391584   [ 0.0895534 -0.0229961 -0.0388068 100.215 125.187 98.7312 ]
Stop condition from optimizer.RegularStepGradientDescentOptimizerv4: Step too small after 46 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=1592857697
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 196, size: fix[64, 64, 64]-mov[50, 56, 50], affine para: [0.07748029554407235, -0.02535762326058937, -0.037762695317994595, 0.9959557086473763, 0.9980736766671306, 1.0465334942253266, 1.012661978883193, 0.0009688583581911313, 0.00174976818174943, -0.04659640043355795, 100.37910607675563, 125.76688859569184, 98.6955326326732]
    reach oscillation, current step: 9.76563e-05<0.0001
level 1, iter 129, size: fix[128, 128, 128]-mov[100, 113, 100], affine para: [0.07517981677151697, -0.026673437806614478, -0.03385074240399082, 0.9962382496694636, 0.9927290795538325, 1.0413890897361382, 1.0157092538933237, 0.006217945345835279, 0.0033108331918905664, -0.058667748067016245, 100.28699073174683, 125.47118421072578, 98.36813889495386]
    reach oscillation, current step: 9.76563e-05<0.0001
level 2, iter 114, size: fix[256, 256, 256]-mov[200, 225, 200], affine para: [0.07020061152459067, -0.028369547745645554, -0.028155749424065426, 0.9967318077981911, 1.000480166657857, 1.0500103948807586, 1.0246065583720494, 0.003427308306861096, -0.0003759013334379519, -0.062075444343628834, 100.40287900978984, 125.48730283387273, 98.3643279776724]
    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 7098, size: fix[50, 56, 50]-mov[64, 64, 64], affine para: [-0.07558081235921062, 0.027069906555317352, 0.034134486592954656, 0.9961875314353437, 0.9650611927577911, 0.9045356575594791, 0.9410993528982938, -0.010043710075995893, 0.0017414455144425273, 0.050349409764042855, -91.43144861160663, -136.32162475037347, -68.65628918524187]
    reach oscillation, current step: 9.76563e-05<0.0001
level 1, iter 4035, size: fix[100, 113, 100]-mov[128, 128, 128], affine para: [-0.07672935743668197, 0.025520616740547206, 0.032983111326903736, 0.996179410646362, 0.9817552450836634, 0.9285308547255601, 0.9681032210887911, -0.015668115212698574, -0.005981929473554177, 0.04952333396650343, -91.79411635236337, -139.88455019930663, -70.51042159674309]
    reach oscillation, current step: 9.76563e-05<0.0001
level 2, iter 5976, size: fix[200, 225, 200]-mov[256, 256, 256], affine para: [-0.08077679610918713, 0.024299367777886993, 0.026567642546568057, 0.9960817287278427, 0.985646918734971, 0.9246810572938107, 0.9781740795276577, -0.017938142921816533, -0.005334435636344415, 0.04406418672893532, -93.35341260283795, -138.91025674722144, -70.68508207993335]
    reach oscillation, current step: 9.76563e-05<0.0001
 v1 -0.400431 v2 -0.403808
 last params [0.07020061152459067, -0.028369547745645554, -0.028155749424065426, 0.9967318077981911, 1.000480166657857, 1.0500103948807586, 1.0246065583720494, 0.003427308306861096, -0.0003759013334379519, -0.062075444343628834, 100.40287900978984, 125.48730283387273, 98.3643279776724]
 my params [-0.08077679610918713, 0.024299367777886993, 0.026567642546568057, 0.9960817287278427, 0.985646918734971, 0.9246810572938107, 0.9781740795276577, -0.017938142921816533, -0.005334435636344415, 0.04406418672893532, -93.35341260283795, -138.91025674722144, -70.68508207993335]
A=1.01103 0.0695873 -0.0519852 
-0.0634709 1.05851 -0.217038 
0.0451006 0.165831 1.00776 

rotation R0.997048 0.055062 -0.0535185 
-0.0625929 0.986532 -0.15112 
0.0444767 0.154024 0.987066 

upper R1.01403 0.0105024 0.00657531 
0 1.07362 -0.0617575 
0 0 1.03031 

s=0.250922 u=0.0765676 v=-0.0245892 w-0.0295222 r=0.996324
m_Rotation from vnl0.0765676 -0.0245892 -0.0295222 0.996324
 new params [0.07656758322364719, -0.02458917894318307, -0.029522249942868103, 0.99632385007913, 1.0140275727382058, 1.0736246413446882, 1.0303108784297996, 0.01035710010150285, 0.006484352521145518, -0.05752239146598248, 100.37525768714833, 125.77093548415242, 98.47987065866266]
outputput affine center: [-0.10471, -7.96155, -1.57875]
output affine para: [0.07656758322364719, -0.02458917894318307, -0.029522249942868103, 0.99632385007913, 1.0140275727382058, 1.0736246413446882, 1.0303108784297996, 0.01035710010150285, 0.006484352521145518, -0.05752239146598248, 100.37525768714833, 125.77093548415242, 98.47987065866266]
initial measure value (MMI): rval = -0.293334
final measure value (MMI): rval = -0.414306
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 : -22688.9
 iteration 2 energy 0 : -24644.7
 iteration 3 energy 0 : -25972.1
 iteration 4 energy 0 : -26961.2
 iteration 5 energy 0 : -27811.5
 iteration 6 energy 0 : -28610.8
 iteration 7 energy 0 : -29282.2
 iteration 8 energy 0 : -29449.5
 iteration 9 energy 0 : -29584.9
 iteration 10 energy 0 : -29863.6
 iteration 11 energy 0 : -29888.3
 iteration 12 energy 0 : -30293.8
 E-Slope 0.00936659 iteration 13 energy 0 : -30277.3
 E-Slope 0.00717697 iteration 14 energy 0 : -30516.1
 E-Slope 0.00545644 iteration 15 energy 0 : -30476.2
 E-Slope 0.00430815 iteration 16 energy 0 : -30829.3
 E-Slope 0.00340798 iteration 17 energy 0 : -30774.4
 E-Slope 0.00284623 iteration 18 energy 0 : -30824.8
 E-Slope 0.00251907 iteration 19 energy 0 : -30787.2
 E-Slope 0.0022551 iteration 20 energy 0 : -30971.9
 E-Slope 0.0018948 iteration 21 energy 0 : -30929.9
 E-Slope 0.0016715 iteration 22 energy 0 : -31055
 E-Slope 0.00131302 iteration 23 energy 0 : -31007.2
 E-Slope 0.00121204 iteration 24 energy 0 : -31126.7
 E-Slope 0.000978962 iteration 25 energy 0 : -31071.6
 E-Slope 0.000895135 iteration 26 energy 0 : -31163.4
 E-Slope 0.000680961 iteration 27 energy 0 : -31108.6
 E-Slope 0.000722922 iteration 28 energy 0 : -31220.1
 E-Slope 0.000642031 iteration 29 energy 0 : -31163.1
 E-Slope 0.000607952 iteration 30 energy 0 : -31250.3
 E-Slope 0.000467703 iteration 31 energy 0 : -31193.3
 E-Slope 0.000476286 iteration 32 energy 0 : -31286.5
 E-Slope 0.000385292 iteration 33 energy 0 : -31228.8
 E-Slope 0.00039988 iteration 34 energy 0 : -31306.5
 E-Slope 0.000317208 iteration 35 energy 0 : -31249.6
 E-Slope 0.000328451 iteration 36 energy 0 : -31307
 E-Slope 0.000244565 iteration 37 energy 0 : -31251.4
 E-Slope 0.000206016 iteration 38 energy 0 : -31253.3
 E-Slope 8.89674e-05 iteration 39 energy 0 : -31209.6
 Converged due to oscillation in optimization  metric 0 bad 14  
 ScaleFactor 2 nlev 3 curl 1
 Its at this level 50
 iteration 1 energy 0 : -153592
 iteration 2 energy 0 : -157891
 iteration 3 energy 0 : -163908
 iteration 4 energy 0 : -168192
 iteration 5 energy 0 : -171524
 iteration 6 energy 0 : -174551
 iteration 7 energy 0 : -177025
 iteration 8 energy 0 : -178892
 iteration 9 energy 0 : -180356
 iteration 10 energy 0 : -181430
 iteration 11 energy 0 : -182268
 iteration 12 energy 0 : -182977
 E-Slope 0.00708281 iteration 13 energy 0 : -183649
 E-Slope 0.00558867 iteration 14 energy 0 : -184340
 E-Slope 0.00450806 iteration 15 energy 0 : -185113
 E-Slope 0.003704 iteration 16 energy 0 : -185940
 E-Slope 0.00311209 iteration 17 energy 0 : -186764
 E-Slope 0.00270535 iteration 18 energy 0 : -187342
 E-Slope 0.00233143 iteration 19 energy 0 : -186840
 E-Slope 0.00210426 iteration 20 energy 0 : -187763
 E-Slope 0.00188445 iteration 21 energy 0 : -187714
 E-Slope 0.00168892 iteration 22 energy 0 : -188067
 E-Slope 0.00142145 iteration 23 energy 0 : -187634
 E-Slope 0.00124072 iteration 24 energy 0 : -188618
 E-Slope 0.000999115 iteration 25 energy 0 : -188183
 E-Slope 0.0008526 iteration 26 energy 0 : -189018
 E-Slope 0.000652365 iteration 27 energy 0 : -188319
 E-Slope 0.0005982 iteration 28 energy 0 : -189282
 E-Slope 0.000560246 iteration 29 energy 0 : -189021
 E-Slope 0.000577569 iteration 30 energy 0 : -189305
 E-Slope 0.000438467 iteration 31 energy 0 : -188733
 E-Slope 0.000463746 iteration 32 energy 0 : -189620
 E-Slope 0.000398263 iteration 33 energy 0 : -189136
 E-Slope 0.000419877 iteration 34 energy 0 : -189844
 E-Slope 0.000291742 iteration 35 energy 0 : -189172
 E-Slope 0.00034596 iteration 36 energy 0 : -190065
 E-Slope 0.000277348 iteration 37 energy 0 : -189596
 E-Slope 0.00032004 iteration 38 energy 0 : -189965
 E-Slope 0.000213705 iteration 39 energy 0 : -189495
 E-Slope 0.000288039 iteration 40 energy 0 : -190363
 E-Slope 0.000258967 iteration 41 energy 0 : -189854
 E-Slope 0.000281587 iteration 42 energy 0 : -190201
 E-Slope 0.000173785 iteration 43 energy 0 : -189743
 E-Slope 0.000237711 iteration 44 energy 0 : -190571
 E-Slope 0.000172533 iteration 45 energy 0 : -190020
 E-Slope 0.000212632 iteration 46 energy 0 : -190396
 E-Slope 0.000118017 iteration 47 energy 0 : -189955
 E-Slope 0.000189848 iteration 48 energy 0 : -190692
 E-Slope 0.000135064 iteration 49 energy 0 : -190104
 E-Slope 0.000155337 iteration 50 energy 0 : -190513
 tired convergence: reached max iterations 
 ScaleFactor 1 nlev 3 curl 2
 Its at this level 25
 iteration 1 energy 0 : -1.17353e+06
 iteration 2 energy 0 : -1.18912e+06
 iteration 3 energy 0 : -1.21536e+06
 iteration 4 energy 0 : -1.2386e+06
 iteration 5 energy 0 : -1.25807e+06
 iteration 6 energy 0 : -1.27414e+06
 iteration 7 energy 0 : -1.28798e+06
 iteration 8 energy 0 : -1.29999e+06
 iteration 9 energy 0 : -1.30999e+06
 iteration 10 energy 0 : -1.31858e+06
 iteration 11 energy 0 : -1.3262e+06
 iteration 12 energy 0 : -1.33316e+06
 E-Slope 0.00584477 iteration 13 energy 0 : -1.33952e+06
 E-Slope 0.00497407 iteration 14 energy 0 : -1.34522e+06
 E-Slope 0.00426056 iteration 15 energy 0 : -1.35041e+06
 E-Slope 0.00369313 iteration 16 energy 0 : -1.35526e+06
 E-Slope 0.0032426 iteration 17 energy 0 : -1.35985e+06
 E-Slope 0.00288066 iteration 18 energy 0 : -1.36424e+06
 E-Slope 0.00259395 iteration 19 energy 0 : -1.36852e+06
 E-Slope 0.00236766 iteration 20 energy 0 : -1.37248e+06
 E-Slope 0.00218193 iteration 21 energy 0 : -1.37616e+06
 E-Slope 0.0020246 iteration 22 energy 0 : -1.37963e+06
 E-Slope 0.00188316 iteration 23 energy 0 : -1.38256e+06
 E-Slope 0.00172528 iteration 24 energy 0 : -1.38329e+06
 E-Slope 0.00152995 iteration 25 energy 0 : -1.38237e+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: ...



/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath  -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/T1_MID00.nrrd -mask /home/bic/Desktop/brainmask.nii
Cutting below AC-PC line
Creating coronal mask
Coronal mask created
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/T1_MID00.nrrd -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/_MID01.nrrd -mask /home/bic/Desktop/1.7.6_output/FinalMasking/coronal_mask_70.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/_MID01.nrrd -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/_MID02.nrrd -extractLabel 3
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/_MID02.nrrd -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/_MID03.nrrd -conComp 1
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/brainmask.nii -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion00.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion00.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -threshold 0,0 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01_inv.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/_MID03.nrrd -mask /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01_inv.nrrd -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/_Partial_CSF.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/_Partial_CSF.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_Ero.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion01.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion.nrrd -erode 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion.nrrd
exit with success
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_Ero.nrrd -mask /home/bic/Desktop/1.7.6_output/FinalMasking/brainmask_Erosion.nrrd -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_Masking.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_Masking.nrrd -conComp 1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp.nrrd -dilate 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd

/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd -dilate 1,1 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd -threshold 0,0 -outfile /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageMath /home/bic/Desktop/1.7.6_output/FinalMasking/_Partial_CSF.nrrd -mask /home/bic/Desktop/1.7.6_output/FinalMasking/Partial_conComp_dil.nrrd -outfile /home/bic/Desktop/1.7.6_output/_FINAL_QCistern.nrrd
/home/bic/Desktop/Auto_EACSF-1.7.6-Linux/bin/ImageStat /home/bic/Desktop/1.7.6_output/_FINAL_QCistern.nrrd -label /home/bic/Desktop/1.7.6_output/_FINAL_QCistern.nrrd -volumeSummary
Auto_EACSF finished

Auto_EACSF pipeline exited with code 0