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Copy pathforloop_nifty_deeds_output.txt
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forloop_nifty_deeds_output.txt
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[reg_aladin]
[reg_aladin] Command line:
[reg_aladin] reg_aladin -ref bucket/RESECT/RESECT/NIFTI/Case1/output/deeds/Case1-US.nii.gz -flo bucket/RESECT/RESECT/NIFTI/Case1/output/deeds/Case1-MRI_in_US.nii.gz -res bucket/RESECT/RESECT/NIFTI/Case1/output/deeds/Case1-MRI_to_US_result_affine.nii.gz -rmask bucket/RESECT/RESECT/NIFTI/Case1/output/deeds/mask_US.nii.gz -fmask bucket/RESECT/RESECT/NIFTI/Case1/output/deeds/mask_US.nii.gz -aff bucket/RESECT/RESECT/NIFTI/Case1/output/deeds/affine_matrix.txt -rigOnly
[reg_aladin]
[reg_aladin] OpenMP is used with 8 thread(s)
[reg_aladin_sym] Parameters
[reg_aladin_sym] Platform: cpu_platform
[reg_aladin_sym] Reference image name: bucket/RESECT/RESECT/NIFTI/Case1/output/deeds/Case1-US.nii.gz
[reg_aladin_sym] 151x136x119 voxels
[reg_aladin_sym] 0.498613x0.497928x0.499973 mm
[reg_aladin_sym] Floating image name: bucket/RESECT/RESECT/NIFTI/Case1/output/deeds/Case1-MRI_in_US.nii.gz
[reg_aladin_sym] 151x136x119 voxels
[reg_aladin_sym] 0.498613x0.497928x0.499973 mm
[reg_aladin_sym] Maximum iteration number: 5
[reg_aladin_sym] (10 during the first level)
[reg_aladin_sym] Percentage of blocks: 50 %
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Current level 1 / 3
[reg_aladin_sym] reference image size: 38x34x60 voxels 1.99445x1.99171x0.999946 mm
[reg_aladin_sym] floating image size: 38x34x60 voxels 1.99445x1.99171x0.999946 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [10 9 15]
[reg_aladin_sym] Backward Block number = [10 9 15]
[reg_aladin_sym] Initial forward transformation matrix::
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9972102 0.06352999 -0.03918939 5.37393
-0.06530061 0.9968191 -0.04568912 4.979452
0.03616211 0.04812074 0.9981867 1.187068
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9972102 -0.06530061 0.0361621 -5.076704
0.06352999 0.9968191 0.04812075 -5.36214
-0.03918939 -0.04568911 0.9981867 -0.7468074
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin_sym] Current level 2 / 3
[reg_aladin_sym] reference image size: 76x68x60 voxels 0.997225x0.995856x0.999946 mm
[reg_aladin_sym] floating image size: 76x68x60 voxels 0.997225x0.995856x0.999946 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [19 17 15]
[reg_aladin_sym] Backward Block number = [19 17 15]
[reg_aladin_sym] Initial forward transformation matrix::
0.9972102 0.06352999 -0.03918939 5.37393
-0.06530061 0.9968191 -0.04568912 4.979452
0.03616211 0.04812074 0.9981867 1.187068
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
0.9972102 -0.06530061 0.0361621 -5.076704
0.06352999 0.9968191 0.04812075 -5.36214
-0.03918939 -0.04568911 0.9981867 -0.7468074
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9994356 0.03160486 0.01138528 2.22697
-0.0313495 0.9992675 -0.02194989 2.924339
-0.01207065 0.02158055 0.9996943 2.426681
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9994356 -0.03134949 -0.01207066 -2.104745
0.03160486 0.9992674 0.02158058 -3.044949
0.01138527 -0.02194986 0.9996942 -2.387105
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin_sym] Current level 3 / 3
[reg_aladin_sym] reference image size: 151x136x119 voxels 0.498613x0.497928x0.499973 mm
[reg_aladin_sym] floating image size: 151x136x119 voxels 0.498613x0.497928x0.499973 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [38 34 30]
[reg_aladin_sym] Backward Block number = [38 34 30]
[reg_aladin_sym] Initial forward transformation matrix::
0.9994356 0.03160486 0.01138528 2.22697
-0.0313495 0.9992675 -0.02194989 2.924339
-0.01207065 0.02158055 0.9996943 2.426681
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
0.9994356 -0.03134949 -0.01207066 -2.104745
0.03160486 0.9992674 0.02158058 -3.044949
0.01138527 -0.02194986 0.9996942 -2.387105
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9986953 0.04508761 0.02397758 1.019273
-0.04408501 0.9981937 -0.0408167 3.8545
-0.0257746 0.03970638 0.9988788 3.140961
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9986952 -0.044085 -0.02577459 -0.7670602
0.04508761 0.9981936 0.03970639 -4.018209
0.02397758 -0.04081668 0.998879 -3.004551
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin] Registration performed in 0 min 12 sec
[reg_aladin] Have a good day !
Transforming Case1-MRI-landmarks.nii.gz into Case1-MRI-landmarks_linear.nii.gz
Reading affine matrix file: affine_matrix.txt
+0.999 | +0.045 | +0.024 | +1.019
-0.044 | +0.998 | -0.041 | +3.855
-0.026 | +0.040 | +0.999 | +3.141
+0.000 | +0.000 | +0.000 | +1.000
Reading displacements from:
/vol/bitbucket/mt3215/RESECT/RESECT/NIFTI/Case1/output/deeds/zero_displacements.dat
=============================================================
grid step 4
Transforming Case1-MRI_in_US.nii.gz into Case1-MRI_in_US_linear.nii.gz
Reading affine matrix file: affine_matrix.txt
+0.999 | +0.045 | +0.024 | +1.019
-0.044 | +0.998 | -0.041 | +3.855
-0.026 | +0.040 | +0.999 | +3.141
+0.000 | +0.000 | +0.000 | +1.000
Reading displacements from:
/vol/bitbucket/mt3215/RESECT/RESECT/NIFTI/Case1/output/deeds/zero_displacements.dat
=============================================================
grid step 4
Starting registration of Case1-US.nii.gz and Case1-MRI_in_US.nii.gz
=============================================================
Reading affine matrix file: affine_matrix.txt
+0.999 | +0.045 | +0.024 | +1.019
-0.044 | +0.998 | -0.041 | +3.855
-0.026 | +0.040 | +0.999 | +3.141
+0.000 | +0.000 | +0.000 | +1.000
MIND STEPS, 3, 3, 2, 2, 1
==========================================================
Level 0 grid=8 with sizes: 18x17x14 hw=8 quant=5
==========================================================
TMdDSTMdDS
Time: MIND=0.440594, data=1.35462, MST-reg=0.440455, transf.=0.304654
speed=2.34501e+07 dof/s
std(J)=0.85 (J<0)=0e-7 SSD before registration: 8379.6 and after 8379.6
==========================================================
Level 1 grid=7 with sizes: 21x19x17 hw=7 quant=4
==========================================================
TMdDSTMdDS
Time: MIND=0.22036, data=0.99375, MST-reg=0.491672, transf.=0.305545
speed=3.08231e+07 dof/s
std(J)=1.06 (J<0)=0e-7 SSD before registration: 8379.6 and after 6879.98
==========================================================
Level 2 grid=6 with sizes: 25x22x19 hw=6 quant=3
==========================================================
TMdDSTMdDS
Time: MIND=0.434597, data=0.607518, MST-reg=0.44265, transf.=0.307434
speed=4.37238e+07 dof/s
std(J)=1.23 (J<0)=0e-7 SSD before registration: 8379.6 and after 6069.32
==========================================================
Level 3 grid=5 with sizes: 30x27x23 hw=5 quant=2
==========================================================
TMdDSTMdDS
Time: MIND=0.215955, data=0.459035, MST-reg=0.419989, transf.=0.306862
speed=5.64183e+07 dof/s
std(J)=1.28 (J<0)=0e-7 SSD before registration: 8379.6 and after 5781.31
==========================================================
Level 4 grid=4 with sizes: 37x34x29 hw=4 quant=1
==========================================================
TMdDSTMdDS
Time: MIND=0.393274, data=0.65511, MST-reg=0.415046, transf.=0.300296
speed=4.97037e+07 dof/s
std(J)=1.19 (J<0)=0e-7 SSD before registration: 8379.6 and after 5814.47
SSD before registration: 8391.34 and after 6756.7
outputseg /vol/bitbucket/mt3215/RESECT/RESECT/NIFTI/Case1/output/deeds/Case1-deeds_deformed_seg.nii.gz
Finished. Total time: 9.59673 sec. (0 sec. for MIND+data+reg+trans)
('landmark error (vox)', 5.148045112842608)
[reg_aladin]
[reg_aladin] Command line:
[reg_aladin] reg_aladin -ref bucket/RESECT/RESECT/NIFTI/Case2/output/deeds/Case2-US.nii.gz -flo bucket/RESECT/RESECT/NIFTI/Case2/output/deeds/Case2-MRI_in_US.nii.gz -res bucket/RESECT/RESECT/NIFTI/Case2/output/deeds/Case2-MRI_to_US_result_affine.nii.gz -rmask bucket/RESECT/RESECT/NIFTI/Case2/output/deeds/mask_US.nii.gz -fmask bucket/RESECT/RESECT/NIFTI/Case2/output/deeds/mask_US.nii.gz -aff bucket/RESECT/RESECT/NIFTI/Case2/output/deeds/affine_matrix.txt -rigOnly
[reg_aladin]
[reg_aladin] OpenMP is used with 8 thread(s)
[reg_aladin_sym] Parameters
[reg_aladin_sym] Platform: cpu_platform
[reg_aladin_sym] Reference image name: bucket/RESECT/RESECT/NIFTI/Case2/output/deeds/Case2-US.nii.gz
[reg_aladin_sym] 128x161x106 voxels
[reg_aladin_sym] 0.497621x0.497762x0.498787 mm
[reg_aladin_sym] Floating image name: bucket/RESECT/RESECT/NIFTI/Case2/output/deeds/Case2-MRI_in_US.nii.gz
[reg_aladin_sym] 128x161x106 voxels
[reg_aladin_sym] 0.497621x0.497762x0.498787 mm
[reg_aladin_sym] Maximum iteration number: 5
[reg_aladin_sym] (10 during the first level)
[reg_aladin_sym] Percentage of blocks: 50 %
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Current level 1 / 3
[reg_aladin_sym] reference image size: 32x41x53 voxels 1.99048x1.99105x0.997573 mm
[reg_aladin_sym] floating image size: 32x41x53 voxels 1.99048x1.99105x0.997573 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [8 11 14]
[reg_aladin_sym] Backward Block number = [8 11 14]
[reg_aladin_sym] Initial forward transformation matrix::
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9665042 -0.1899414 -0.1726038 25.50125
0.2022796 0.9776798 0.05679024 -9.465215
0.1579645 -0.08980222 0.9833528 6.867827
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9665041 0.2022796 0.1579645 -23.81732
-0.1899413 0.9776798 -0.08980223 14.71444
-0.1726038 0.05679022 0.9833528 -1.814352
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin_sym] Current level 2 / 3
[reg_aladin_sym] reference image size: 64x81x53 voxels 0.995241x0.995524x0.997573 mm
[reg_aladin_sym] floating image size: 64x81x53 voxels 0.995241x0.995524x0.997573 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [16 21 14]
[reg_aladin_sym] Backward Block number = [16 21 14]
[reg_aladin_sym] Initial forward transformation matrix::
0.9665042 -0.1899414 -0.1726038 25.50125
0.2022796 0.9776798 0.05679024 -9.465215
0.1579645 -0.08980222 0.9833528 6.867827
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
0.9665041 0.2022796 0.1579645 -23.81732
-0.1899413 0.9776798 -0.08980223 14.71444
-0.1726038 0.05679022 0.9833528 -1.814352
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9871931 -0.1332686 -0.08768847 15.93332
0.1315825 0.9909959 -0.02476168 -3.324872
0.09019885 0.01290627 0.9958402 0.8702193
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9871931 0.1315825 0.09019886 -15.37026
-0.1332686 0.9909959 0.01290629 5.407114
-0.08768845 -0.02476165 0.9958401 0.4482392
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin_sym] Current level 3 / 3
[reg_aladin_sym] reference image size: 128x161x106 voxels 0.497621x0.497762x0.498787 mm
[reg_aladin_sym] floating image size: 128x161x106 voxels 0.497621x0.497762x0.498787 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [32 41 27]
[reg_aladin_sym] Backward Block number = [32 41 27]
[reg_aladin_sym] Initial forward transformation matrix::
0.9871931 -0.1332686 -0.08768847 15.93332
0.1315825 0.9909959 -0.02476168 -3.324872
0.09019885 0.01290627 0.9958402 0.8702193
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
0.9871931 0.1315825 0.09019886 -15.37026
-0.1332686 0.9909959 0.01290629 5.407114
-0.08768845 -0.02476165 0.9958401 0.4482392
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9893972 -0.1199554 -0.08187769 14.14908
0.1181388 0.9926381 -0.02669907 -3.82015
0.08447762 0.01674306 0.9962847 0.04580342
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9893972 0.1181388 0.0844776 -13.55162
-0.1199553 0.9926381 0.01674306 5.488517
-0.0818777 -0.02669908 0.9962847 1.010866
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin] Registration performed in 0 min 11 sec
[reg_aladin] Have a good day !
Transforming Case2-MRI-landmarks.nii.gz into Case2-MRI-landmarks_linear.nii.gz
Reading affine matrix file: affine_matrix.txt
+0.989 | -0.120 | -0.082 | +14.149
+0.118 | +0.993 | -0.027 | -3.820
+0.084 | +0.017 | +0.996 | +0.046
+0.000 | +0.000 | +0.000 | +1.000
Reading displacements from:
/vol/bitbucket/mt3215/RESECT/RESECT/NIFTI/Case2/output/deeds/zero_displacements.dat
=============================================================
grid step 4
Transforming Case2-MRI_in_US.nii.gz into Case2-MRI_in_US_linear.nii.gz
Reading affine matrix file: affine_matrix.txt
+0.989 | -0.120 | -0.082 | +14.149
+0.118 | +0.993 | -0.027 | -3.820
+0.084 | +0.017 | +0.996 | +0.046
+0.000 | +0.000 | +0.000 | +1.000
Reading displacements from:
/vol/bitbucket/mt3215/RESECT/RESECT/NIFTI/Case2/output/deeds/zero_displacements.dat
=============================================================
grid step 4
Starting registration of Case2-US.nii.gz and Case2-MRI_in_US.nii.gz
=============================================================
Reading affine matrix file: affine_matrix.txt
+0.989 | -0.120 | -0.082 | +14.149
+0.118 | +0.993 | -0.027 | -3.820
+0.084 | +0.017 | +0.996 | +0.046
+0.000 | +0.000 | +0.000 | +1.000
MIND STEPS, 3, 3, 2, 2, 1
==========================================================
Level 0 grid=8 with sizes: 16x20x13 hw=8 quant=5
==========================================================
TMdDSTMdDS
Time: MIND=0.420187, data=1.36371, MST-reg=0.409443, transf.=0.325977
speed=2.30528e+07 dof/s
std(J)=0.73 (J<0)=0e-7 SSD before registration: 7403.73 and after 7403.73
==========================================================
Level 1 grid=7 with sizes: 18x23x15 hw=7 quant=4
==========================================================
TMdDSTMdDS
Time: MIND=0.208236, data=0.861888, MST-reg=0.435103, transf.=0.324669
speed=3.2319e+07 dof/s
std(J)=1.23 (J<0)=0e-7 SSD before registration: 7403.73 and after 6322.38
==========================================================
Level 2 grid=6 with sizes: 21x26x17 hw=6 quant=3
==========================================================
TMdDSTMdDS
Time: MIND=0.414298, data=0.530688, MST-reg=0.394436, transf.=0.325695
speed=4.40861e+07 dof/s
std(J)=1.31 (J<0)=0e-7 SSD before registration: 7403.73 and after 5836.33
==========================================================
Level 3 grid=5 with sizes: 25x32x21 hw=5 quant=2
==========================================================
TMdDSTMdDS
Time: MIND=0.205936, data=0.442802, MST-reg=0.382004, transf.=0.325174
speed=5.42207e+07 dof/s
std(J)=1.31 (J<0)=0e-7 SSD before registration: 7403.73 and after 5713.57
==========================================================
Level 4 grid=4 with sizes: 32x40x26 hw=4 quant=1
==========================================================
TMdDSTMdDS
Time: MIND=0.380978, data=0.616629, MST-reg=0.377375, transf.=0.319653
speed=4.88149e+07 dof/s
std(J)=1.27 (J<0)=0e-7 SSD before registration: 7403.73 and after 5640.4
SSD before registration: 6512.06 and after 5735.76
outputseg /vol/bitbucket/mt3215/RESECT/RESECT/NIFTI/Case2/output/deeds/Case2-deeds_deformed_seg.nii.gz
Finished. Total time: 9.14524 sec. (0 sec. for MIND+data+reg+trans)
('landmark error (vox)', 6.756050569243082)
[reg_aladin]
[reg_aladin] Command line:
[reg_aladin] reg_aladin -ref bucket/RESECT/RESECT/NIFTI/Case3/output/deeds/Case3-US.nii.gz -flo bucket/RESECT/RESECT/NIFTI/Case3/output/deeds/Case3-MRI_in_US.nii.gz -res bucket/RESECT/RESECT/NIFTI/Case3/output/deeds/Case3-MRI_to_US_result_affine.nii.gz -rmask bucket/RESECT/RESECT/NIFTI/Case3/output/deeds/mask_US.nii.gz -fmask bucket/RESECT/RESECT/NIFTI/Case3/output/deeds/mask_US.nii.gz -aff bucket/RESECT/RESECT/NIFTI/Case3/output/deeds/affine_matrix.txt -rigOnly
[reg_aladin]
[reg_aladin] OpenMP is used with 8 thread(s)
[reg_aladin_sym] Parameters
[reg_aladin_sym] Platform: cpu_platform
[reg_aladin_sym] Reference image name: bucket/RESECT/RESECT/NIFTI/Case3/output/deeds/Case3-US.nii.gz
[reg_aladin_sym] 135x126x99 voxels
[reg_aladin_sym] 0.499259x0.496825x0.496969 mm
[reg_aladin_sym] Floating image name: bucket/RESECT/RESECT/NIFTI/Case3/output/deeds/Case3-MRI_in_US.nii.gz
[reg_aladin_sym] 135x126x99 voxels
[reg_aladin_sym] 0.499259x0.496825x0.496969 mm
[reg_aladin_sym] Maximum iteration number: 5
[reg_aladin_sym] (10 during the first level)
[reg_aladin_sym] Percentage of blocks: 50 %
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Current level 1 / 3
[reg_aladin_sym] reference image size: 34x63x50 voxels 1.99704x0.993651x0.993939 mm
[reg_aladin_sym] floating image size: 34x63x50 voxels 1.99704x0.993651x0.993939 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [9 16 13]
[reg_aladin_sym] Backward Block number = [9 16 13]
[reg_aladin_sym] Initial forward transformation matrix::
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9885865 -0.1246995 -0.0845379 8.093358
0.1128102 0.9846452 -0.1332199 11.06226
0.09985229 0.1221627 0.9874744 6.56724
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9885865 0.1128102 0.0998523 -9.904675
-0.1246995 0.9846453 0.1221627 -10.68544
-0.08453789 -0.1332199 0.9874745 -4.327072
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin_sym] Current level 2 / 3
[reg_aladin_sym] reference image size: 68x63x50 voxels 0.998519x0.993651x0.993939 mm
[reg_aladin_sym] floating image size: 68x63x50 voxels 0.998519x0.993651x0.993939 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [17 16 13]
[reg_aladin_sym] Backward Block number = [17 16 13]
[reg_aladin_sym] Initial forward transformation matrix::
0.9885865 -0.1246995 -0.0845379 8.093358
0.1128102 0.9846452 -0.1332199 11.06226
0.09985229 0.1221627 0.9874744 6.56724
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
0.9885865 0.1128102 0.0998523 -9.904675
-0.1246995 0.9846453 0.1221627 -10.68544
-0.08453789 -0.1332199 0.9874745 -4.327072
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9997732 -0.004387152 0.02084278 5.517086
0.005204669 0.9992126 -0.0393315 4.694954
-0.0206538 0.03943114 0.9990088 3.03098
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9997731 0.005204658 -0.02065382 -5.477668
-0.004387165 0.9992127 0.03943106 -4.786569
0.02084276 -0.03933157 0.9990088 -2.958308
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin_sym] Current level 3 / 3
[reg_aladin_sym] reference image size: 135x126x99 voxels 0.499259x0.496825x0.496969 mm
[reg_aladin_sym] floating image size: 135x126x99 voxels 0.499259x0.496825x0.496969 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [34 32 25]
[reg_aladin_sym] Backward Block number = [34 32 25]
[reg_aladin_sym] Initial forward transformation matrix::
0.9997732 -0.004387152 0.02084278 5.517086
0.005204669 0.9992126 -0.0393315 4.694954
-0.0206538 0.03943114 0.9990088 3.03098
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
0.9997731 0.005204658 -0.02065382 -5.477668
-0.004387165 0.9992127 0.03943106 -4.786569
0.02084276 -0.03933157 0.9990088 -2.958308
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9995046 -0.0003766259 0.03146841 5.465987
0.002445781 0.9978338 -0.06574082 4.55029
-0.03137547 0.06578521 0.9973404 2.100185
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9995047 0.00244578 -0.03137549 -5.408514
-0.0003766273 0.9978337 0.06578522 -4.676535
0.0314684 -0.06574081 0.9973404 -1.967465
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin] Registration performed in 0 min 6 sec
[reg_aladin] Have a good day !
Transforming Case3-MRI-landmarks.nii.gz into Case3-MRI-landmarks_linear.nii.gz
Reading affine matrix file: affine_matrix.txt
+1.000 | -0.000 | +0.031 | +5.466
+0.002 | +0.998 | -0.066 | +4.550
-0.031 | +0.066 | +0.997 | +2.100
+0.000 | +0.000 | +0.000 | +1.000
Reading displacements from:
/vol/bitbucket/mt3215/RESECT/RESECT/NIFTI/Case3/output/deeds/zero_displacements.dat
=============================================================
grid step 4
Transforming Case3-MRI_in_US.nii.gz into Case3-MRI_in_US_linear.nii.gz
Reading affine matrix file: affine_matrix.txt
+1.000 | -0.000 | +0.031 | +5.466
+0.002 | +0.998 | -0.066 | +4.550
-0.031 | +0.066 | +0.997 | +2.100
+0.000 | +0.000 | +0.000 | +1.000
Reading displacements from:
/vol/bitbucket/mt3215/RESECT/RESECT/NIFTI/Case3/output/deeds/zero_displacements.dat
=============================================================
grid step 4
Starting registration of Case3-US.nii.gz and Case3-MRI_in_US.nii.gz
=============================================================
Reading affine matrix file: affine_matrix.txt
+1.000 | -0.000 | +0.031 | +5.466
+0.002 | +0.998 | -0.066 | +4.550
-0.031 | +0.066 | +0.997 | +2.100
+0.000 | +0.000 | +0.000 | +1.000
MIND STEPS, 3, 3, 2, 2, 1
==========================================================
Level 0 grid=8 with sizes: 16x15x12 hw=8 quant=5
==========================================================
TMdDSTMdDS
Time: MIND=0.300629, data=0.863536, MST-reg=0.303209, transf.=0.209755
speed=2.42545e+07 dof/s
std(J)=0.83 (J<0)=0e-7 SSD before registration: 3943.83 and after 3943.83
==========================================================
Level 1 grid=7 with sizes: 19x18x14 hw=7 quant=4
==========================================================
TMdDSTMdDS
Time: MIND=0.139815, data=0.656551, MST-reg=0.350945, transf.=0.208496
speed=3.20785e+07 dof/s
std(J)=1.19 (J<0)=0e-7 SSD before registration: 3943.83 and after 3321.2
==========================================================
Level 2 grid=6 with sizes: 22x21x16 hw=6 quant=3
==========================================================
TMdDSTMdDS
Time: MIND=0.271829, data=0.324423, MST-reg=0.304552, transf.=0.20691
speed=5.16403e+07 dof/s
std(J)=1.34 (J<0)=0e-7 SSD before registration: 3943.83 and after 3028.19
==========================================================
Level 3 grid=5 with sizes: 27x25x19 hw=5 quant=2
==========================================================
TMdDSTMdDS
Time: MIND=0.13607, data=0.328422, MST-reg=0.294631, transf.=0.205988
speed=5.4795e+07 dof/s
std(J)=1.36 (J<0)=0e-7 SSD before registration: 3943.83 and after 2937.38
==========================================================
Level 4 grid=4 with sizes: 33x31x24 hw=4 quant=1
==========================================================
TMdDSTMdDS
Time: MIND=0.272843, data=0.403112, MST-reg=0.295369, transf.=0.208371
speed=5.12495e+07 dof/s
std(J)=1.32 (J<0)=0e-7 SSD before registration: 3943.83 and after 3000.07
SSD before registration: 4043.4 and after 3871.21
outputseg /vol/bitbucket/mt3215/RESECT/RESECT/NIFTI/Case3/output/deeds/Case3-deeds_deformed_seg.nii.gz
Finished. Total time: 6.34785 sec. (0 sec. for MIND+data+reg+trans)
('landmark error (vox)', 2.7309359606932557)
[reg_aladin]
[reg_aladin] Command line:
[reg_aladin] reg_aladin -ref bucket/RESECT/RESECT/NIFTI/Case4/output/deeds/Case4-US.nii.gz -flo bucket/RESECT/RESECT/NIFTI/Case4/output/deeds/Case4-MRI_in_US.nii.gz -res bucket/RESECT/RESECT/NIFTI/Case4/output/deeds/Case4-MRI_to_US_result_rigid.nii.gz -rmask bucket/RESECT/RESECT/NIFTI/Case4/output/deeds/mask_US.nii.gz -fmask bucket/RESECT/RESECT/NIFTI/Case4/output/deeds/mask_US.nii.gz -aff bucket/RESECT/RESECT/NIFTI/Case4/output/deeds/affine_matrix.txt -rigOnly
[reg_aladin]
[reg_aladin] OpenMP is used with 8 thread(s)
[reg_aladin_sym] Parameters
[reg_aladin_sym] Platform: cpu_platform
[reg_aladin_sym] Reference image name: bucket/RESECT/RESECT/NIFTI/Case4/output/deeds/Case4-US.nii.gz
[reg_aladin_sym] 144x130x125 voxels
[reg_aladin_sym] 0.498479x0.496454x0.499272 mm
[reg_aladin_sym] Floating image name: bucket/RESECT/RESECT/NIFTI/Case4/output/deeds/Case4-MRI_in_US.nii.gz
[reg_aladin_sym] 144x130x125 voxels
[reg_aladin_sym] 0.498479x0.496454x0.499272 mm
[reg_aladin_sym] Maximum iteration number: 5
[reg_aladin_sym] (10 during the first level)
[reg_aladin_sym] Percentage of blocks: 50 %
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Current level 1 / 3
[reg_aladin_sym] reference image size: 36x33x63 voxels 1.99392x1.98582x0.998544 mm
[reg_aladin_sym] floating image size: 36x33x63 voxels 1.99392x1.98582x0.998544 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [9 9 16]
[reg_aladin_sym] Backward Block number = [9 9 16]
[reg_aladin_sym] Initial forward transformation matrix::
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.999958 0.003105666 -0.00861208 -0.3694931
-0.00336805 0.9995254 -0.0306204 -0.4710127
0.008512896 0.03064811 0.999494 1.832794
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9999581 -0.003368038 0.008512897 0.3522888
0.003105677 0.9995254 0.03064812 0.415765
-0.00861208 -0.03062039 0.999494 -1.849472
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin_sym] Current level 2 / 3
[reg_aladin_sym] reference image size: 72x65x63 voxels 0.996958x0.992908x0.998544 mm
[reg_aladin_sym] floating image size: 72x65x63 voxels 0.996958x0.992908x0.998544 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [18 17 16]
[reg_aladin_sym] Backward Block number = [18 17 16]
[reg_aladin_sym] Initial forward transformation matrix::
0.999958 0.003105666 -0.00861208 -0.3694931
-0.00336805 0.9995254 -0.0306204 -0.4710127
0.008512896 0.03064811 0.999494 1.832794
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
0.9999581 -0.003368038 0.008512897 0.3522888
0.003105677 0.9995254 0.03064812 0.415765
-0.00861208 -0.03062039 0.999494 -1.849472
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.999037 0.02335826 0.03714284 1.887369
-0.02281348 0.9996268 -0.01502455 0.676346
-0.03747991 0.01416275 0.999197 3.593029
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9990369 -0.02281346 -0.03747992 -1.735455
0.02335829 0.9996269 0.01416272 -0.7710665
0.03714282 -0.01502457 0.999197 -3.650084
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin_sym] Current level 3 / 3
[reg_aladin_sym] reference image size: 144x130x125 voxels 0.498479x0.496454x0.499272 mm
[reg_aladin_sym] floating image size: 144x130x125 voxels 0.498479x0.496454x0.499272 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [36 33 32]
[reg_aladin_sym] Backward Block number = [36 33 32]
[reg_aladin_sym] Initial forward transformation matrix::
0.999037 0.02335826 0.03714284 1.887369
-0.02281348 0.9996268 -0.01502455 0.676346
-0.03747991 0.01416275 0.999197 3.593029
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
0.9990369 -0.02281346 -0.03747992 -1.735455
0.02335829 0.9996269 0.01416272 -0.7710665
0.03714282 -0.01502457 0.999197 -3.650084
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9994442 0.02656657 0.02013685 0.3315156
-0.0262888 0.9995573 -0.0139361 0.8433677
-0.02049816 0.01339897 0.9997001 2.608664
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9994442 -0.02628879 -0.02049817 -0.2556873
0.02656658 0.9995573 0.01339898 -0.8867549
0.02013684 -0.01393609 0.9997001 -2.602804
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin] Registration performed in 0 min 9 sec
[reg_aladin] Have a good day !
Transforming Case4-MRI-landmarks.nii.gz into Case4-MRI-landmarks_linear.nii.gz
Reading affine matrix file: affine_matrix.txt
+0.999 | +0.027 | +0.020 | +0.332
-0.026 | +1.000 | -0.014 | +0.843
-0.020 | +0.013 | +1.000 | +2.609
+0.000 | +0.000 | +0.000 | +1.000
Reading displacements from:
/vol/bitbucket/mt3215/RESECT/RESECT/NIFTI/Case4/output/deeds/zero_displacements.dat
=============================================================
grid step 4
Transforming Case4-MRI_in_US.nii.gz into Case4-MRI_in_US_linear.nii.gz
Reading affine matrix file: affine_matrix.txt
+0.999 | +0.027 | +0.020 | +0.332
-0.026 | +1.000 | -0.014 | +0.843
-0.020 | +0.013 | +1.000 | +2.609
+0.000 | +0.000 | +0.000 | +1.000
Reading displacements from:
/vol/bitbucket/mt3215/RESECT/RESECT/NIFTI/Case4/output/deeds/zero_displacements.dat
=============================================================
grid step 4
Starting registration of Case4-US.nii.gz and Case4-MRI_in_US.nii.gz
=============================================================
Reading affine matrix file: affine_matrix.txt
+0.999 | +0.027 | +0.020 | +0.332
-0.026 | +1.000 | -0.014 | +0.843
-0.020 | +0.013 | +1.000 | +2.609
+0.000 | +0.000 | +0.000 | +1.000
MIND STEPS, 3, 3, 2, 2, 1
==========================================================
Level 0 grid=8 with sizes: 18x16x15 hw=8 quant=5
==========================================================
TMdDSTMdDS
Time: MIND=0.426529, data=1.24352, MST-reg=0.455034, transf.=0.294342
speed=2.49909e+07 dof/s
std(J)=0.9 (J<0)=0e-7 SSD before registration: 4433.32 and after 4433.32
==========================================================
Level 1 grid=7 with sizes: 20x18x17 hw=7 quant=4
==========================================================
TMdDSTMdDS
Time: MIND=0.212582, data=0.881523, MST-reg=0.441058, transf.=0.295503
speed=3.12344e+07 dof/s
std(J)=1.08 (J<0)=0e-7 SSD before registration: 4433.32 and after 3840.76
==========================================================
Level 2 grid=6 with sizes: 24x21x20 hw=6 quant=3
==========================================================
TMdDSTMdDS
Time: MIND=0.42175, data=0.539281, MST-reg=0.437321, transf.=0.296595
speed=4.53527e+07 dof/s
std(J)=1.18 (J<0)=0e-7 SSD before registration: 4433.32 and after 3624.72
==========================================================
Level 3 grid=5 with sizes: 28x26x25 hw=5 quant=2
==========================================================
TMdDSTMdDS
Time: MIND=0.209643, data=0.493796, MST-reg=0.40763, transf.=0.296588
speed=5.37464e+07 dof/s
std(J)=1.2 (J<0)=0e-7 SSD before registration: 4433.32 and after 3490.16
==========================================================
Level 4 grid=4 with sizes: 36x32x31 hw=4 quant=1
==========================================================
TMdDSTMdDS
Time: MIND=0.38303, data=0.594391, MST-reg=0.4006, transf.=0.29085
speed=5.23302e+07 dof/s
std(J)=1.15 (J<0)=0e-7 SSD before registration: 4433.32 and after 3511.34
SSD before registration: 4560.09 and after 4607.72
outputseg /vol/bitbucket/mt3215/RESECT/RESECT/NIFTI/Case4/output/deeds/Case4-deeds_deformed_seg.nii.gz
Finished. Total time: 9.10482 sec. (0 sec. for MIND+data+reg+trans)
('landmark error (vox)', 3.4900939188675437)
[reg_aladin]
[reg_aladin] Command line:
[reg_aladin] reg_aladin -ref bucket/RESECT/RESECT/NIFTI/Case5/output/deeds/Case5-US.nii.gz -flo bucket/RESECT/RESECT/NIFTI/Case5/output/deeds/Case5-MRI_in_US.nii.gz -res bucket/RESECT/RESECT/NIFTI/Case5/output/deeds/Case5-MRI_to_US_result_rigid.nii.gz -rmask bucket/RESECT/RESECT/NIFTI/Case5/output/deeds/mask_US.nii.gz -fmask bucket/RESECT/RESECT/NIFTI/Case5/output/deeds/mask_US.nii.gz -aff bucket/RESECT/RESECT/NIFTI/Case5/output/deeds/affine_matrix.txt -rigOnly
[reg_aladin]
[reg_aladin] OpenMP is used with 8 thread(s)
[reg_aladin_sym] Parameters
[reg_aladin_sym] Platform: cpu_platform
[reg_aladin_sym] Reference image name: bucket/RESECT/RESECT/NIFTI/Case5/output/deeds/Case5-US.nii.gz
[reg_aladin_sym] 157x163x135 voxels
[reg_aladin_sym] 0.498447x0.497935x0.498915 mm
[reg_aladin_sym] Floating image name: bucket/RESECT/RESECT/NIFTI/Case5/output/deeds/Case5-MRI_in_US.nii.gz
[reg_aladin_sym] 157x163x135 voxels
[reg_aladin_sym] 0.498447x0.497935x0.498915 mm
[reg_aladin_sym] Maximum iteration number: 5
[reg_aladin_sym] (10 during the first level)
[reg_aladin_sym] Percentage of blocks: 50 %
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Current level 1 / 3
[reg_aladin_sym] reference image size: 40x41x34 voxels 1.99379x1.99174x1.99566 mm
[reg_aladin_sym] floating image size: 40x41x34 voxels 1.99379x1.99174x1.99566 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [10 11 9]
[reg_aladin_sym] Backward Block number = [10 11 9]
[reg_aladin_sym] Initial forward transformation matrix::
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9867853 -0.1245811 -0.1036066 3.120734
0.1344035 0.9864641 0.09393831 7.933566
0.09050122 -0.106622 0.9901723 10.07301
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9867853 0.1344035 0.09050123 -5.057413
-0.1245811 0.986464 -0.106622 -6.363389
-0.1036066 0.09393831 0.9901724 -10.39595
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin_sym] Current level 2 / 3
[reg_aladin_sym] reference image size: 79x82x68 voxels 0.996893x0.995871x0.997831 mm
[reg_aladin_sym] floating image size: 79x82x68 voxels 0.996893x0.995871x0.997831 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [20 21 17]
[reg_aladin_sym] Backward Block number = [20 21 17]
[reg_aladin_sym] Initial forward transformation matrix::
0.9867853 -0.1245811 -0.1036066 3.120734
0.1344035 0.9864641 0.09393831 7.933566
0.09050122 -0.106622 0.9901723 10.07301
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
0.9867853 0.1344035 0.09050123 -5.057413
-0.1245811 0.986464 -0.106622 -6.363389
-0.1036066 0.09393831 0.9901724 -10.39595
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9931796 -0.1026396 -0.05531273 6.107159
0.100902 0.9943373 -0.03334875 3.13273
0.0584224 0.02754015 0.997912 7.626766
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9931796 0.100902 0.05842241 -6.827178
-0.1026396 0.9943373 0.02754013 -2.698196
-0.05531273 -0.03334877 0.997912 -7.168565
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin_sym] Current level 3 / 3
[reg_aladin_sym] reference image size: 157x163x135 voxels 0.498447x0.497935x0.498915 mm
[reg_aladin_sym] floating image size: 157x163x135 voxels 0.498447x0.497935x0.498915 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [40 41 34]
[reg_aladin_sym] Backward Block number = [40 41 34]
[reg_aladin_sym] Initial forward transformation matrix::
0.9931796 -0.1026396 -0.05531273 6.107159
0.100902 0.9943373 -0.03334875 3.13273
0.0584224 0.02754015 0.997912 7.626766
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
0.9931796 0.100902 0.05842241 -6.827178
-0.1026396 0.9943373 0.02754013 -2.698196
-0.05531273 -0.03334877 0.997912 -7.168565
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9950827 -0.09186134 -0.03703997 5.82045
0.08950979 0.994128 -0.06080638 2.642087
0.04240823 0.05719195 0.9974621 7.016271
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9950827 0.08950981 0.04240823 -6.32587
-0.09186131 0.994128 0.05719194 -2.493173
-0.03703997 -0.0608064 0.9974621 -6.622219
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin] Registration performed in 0 min 14 sec
[reg_aladin] Have a good day !
Transforming Case5-MRI-landmarks.nii.gz into Case5-MRI-landmarks_linear.nii.gz
Reading affine matrix file: affine_matrix.txt
+0.995 | -0.092 | -0.037 | +5.820
+0.090 | +0.994 | -0.061 | +2.642
+0.042 | +0.057 | +0.997 | +7.016
+0.000 | +0.000 | +0.000 | +1.000
Reading displacements from:
/vol/bitbucket/mt3215/RESECT/RESECT/NIFTI/Case5/output/deeds/zero_displacements.dat
=============================================================
grid step 4
Transforming Case5-MRI_in_US.nii.gz into Case5-MRI_in_US_linear.nii.gz
Reading affine matrix file: affine_matrix.txt
+0.995 | -0.092 | -0.037 | +5.820
+0.090 | +0.994 | -0.061 | +2.642
+0.042 | +0.057 | +0.997 | +7.016
+0.000 | +0.000 | +0.000 | +1.000
Reading displacements from:
/vol/bitbucket/mt3215/RESECT/RESECT/NIFTI/Case5/output/deeds/zero_displacements.dat
=============================================================
grid step 4
Starting registration of Case5-US.nii.gz and Case5-MRI_in_US.nii.gz
=============================================================
Reading affine matrix file: affine_matrix.txt
+0.995 | -0.092 | -0.037 | +5.820
+0.090 | +0.994 | -0.061 | +2.642
+0.042 | +0.057 | +0.997 | +7.016
+0.000 | +0.000 | +0.000 | +1.000
MIND STEPS, 3, 3, 2, 2, 1
==========================================================
Level 0 grid=8 with sizes: 19x20x16 hw=8 quant=5
==========================================================
TMdDSTMdDS
Time: MIND=0.581846, data=1.78986, MST-reg=0.603896, transf.=0.445515
speed=2.49574e+07 dof/s
std(J)=0.91 (J<0)=0e-7 SSD before registration: 3159.85 and after 3159.85
==========================================================
Level 1 grid=7 with sizes: 22x23x19 hw=7 quant=4
==========================================================
TMdDSTMdDS
Time: MIND=0.286555, data=1.23665, MST-reg=0.677182, transf.=0.452102
speed=3.39081e+07 dof/s
std(J)=1.37 (J<0)=0e-7 SSD before registration: 3159.85 and after 2626.27
==========================================================
Level 2 grid=6 with sizes: 26x27x22 hw=6 quant=3
==========================================================
TMdDSTMdDS
Time: MIND=0.561473, data=0.796895, MST-reg=0.626711, transf.=0.45151
speed=4.76683e+07 dof/s
std(J)=1.47 (J<0)=0e-7 SSD before registration: 3159.85 and after 2347.41
==========================================================
Level 3 grid=5 with sizes: 31x32x27 hw=5 quant=2
==========================================================
TMdDSTMdDS
Time: MIND=0.290723, data=0.679131, MST-reg=0.594433, transf.=0.451551
speed=5.59838e+07 dof/s
std(J)=1.47 (J<0)=0e-7 SSD before registration: 3159.85 and after 2254.79
==========================================================
Level 4 grid=4 with sizes: 39x40x33 hw=4 quant=1
==========================================================
TMdDSTMdDS
Time: MIND=0.559446, data=0.926825, MST-reg=0.579164, transf.=0.451248
speed=4.98396e+07 dof/s
std(J)=1.41 (J<0)=0e-7 SSD before registration: 3159.85 and after 2213.96
SSD before registration: 3142.75 and after 2860.71
outputseg /vol/bitbucket/mt3215/RESECT/RESECT/NIFTI/Case5/output/deeds/Case5-deeds_deformed_seg.nii.gz
Finished. Total time: 13.1604 sec. (0 sec. for MIND+data+reg+trans)
('landmark error (vox)', 3.969310419455153)
[reg_aladin]
[reg_aladin] Command line:
[reg_aladin] reg_aladin -ref bucket/RESECT/RESECT/NIFTI/Case6/output/deeds/Case6-US.nii.gz -flo bucket/RESECT/RESECT/NIFTI/Case6/output/deeds/Case6-MRI_in_US.nii.gz -res bucket/RESECT/RESECT/NIFTI/Case6/output/deeds/Case6-MRI_to_US_result_rigid.nii.gz -rmask bucket/RESECT/RESECT/NIFTI/Case6/output/deeds/mask_US.nii.gz -fmask bucket/RESECT/RESECT/NIFTI/Case6/output/deeds/mask_US.nii.gz -aff bucket/RESECT/RESECT/NIFTI/Case6/output/deeds/affine_matrix.txt -rigOnly
[reg_aladin]
[reg_aladin] OpenMP is used with 8 thread(s)
[reg_aladin_sym] Parameters
[reg_aladin_sym] Platform: cpu_platform
[reg_aladin_sym] Reference image name: bucket/RESECT/RESECT/NIFTI/Case6/output/deeds/Case6-US.nii.gz
[reg_aladin_sym] 118x189x143 voxels
[reg_aladin_sym] 0.498895x0.497866x0.499301 mm
[reg_aladin_sym] Floating image name: bucket/RESECT/RESECT/NIFTI/Case6/output/deeds/Case6-MRI_in_US.nii.gz
[reg_aladin_sym] 118x189x143 voxels
[reg_aladin_sym] 0.498895x0.497866x0.499301 mm
[reg_aladin_sym] Maximum iteration number: 5
[reg_aladin_sym] (10 during the first level)
[reg_aladin_sym] Percentage of blocks: 50 %
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Current level 1 / 3
[reg_aladin_sym] reference image size: 59x48x36 voxels 0.997789x1.99147x1.9972 mm
[reg_aladin_sym] floating image size: 59x48x36 voxels 0.997789x1.99147x1.9972 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [15 12 9]
[reg_aladin_sym] Backward Block number = [15 12 9]
[reg_aladin_sym] Initial forward transformation matrix::
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9980468 0.05089484 0.03622586 3.716575
-0.04926057 0.997787 -0.04466034 -1.165985
-0.03841865 0.04278861 0.9983452 0.9983835
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9980468 -0.04926056 -0.03841867 -3.728397
0.05089484 0.997787 0.04278861 0.9315302
0.03622584 -0.04466035 0.9983452 -1.183441
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin_sym] Current level 2 / 3
[reg_aladin_sym] reference image size: 59x95x72 voxels 0.997789x0.995733x0.998602 mm
[reg_aladin_sym] floating image size: 59x95x72 voxels 0.997789x0.995733x0.998602 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [15 24 18]
[reg_aladin_sym] Backward Block number = [15 24 18]
[reg_aladin_sym] Initial forward transformation matrix::
0.9980468 0.05089484 0.03622586 3.716575
-0.04926057 0.997787 -0.04466034 -1.165985
-0.03841865 0.04278861 0.9983452 0.9983835
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
0.9980468 -0.04926056 -0.03841867 -3.728397
0.05089484 0.997787 0.04278861 0.9315302
0.03622584 -0.04466035 0.9983452 -1.183441
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9974411 0.04013473 0.05916535 4.545492
-0.03911143 0.9990663 -0.01835389 -0.8721041
-0.05984677 0.01599288 0.9980795 1.280884
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9974411 -0.03911142 -0.05984674 -4.491313
0.04013474 0.9990662 0.01599288 0.6683726
0.05916538 -0.01835389 0.9980795 -1.563367
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin_sym] Current level 3 / 3
[reg_aladin_sym] reference image size: 118x189x143 voxels 0.498895x0.497866x0.499301 mm
[reg_aladin_sym] floating image size: 118x189x143 voxels 0.498895x0.497866x0.499301 mm
[reg_aladin_sym] Block size = [4 4 4]
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Forward Block number = [30 48 36]
[reg_aladin_sym] Backward Block number = [30 48 36]
[reg_aladin_sym] Initial forward transformation matrix::
0.9974411 0.04013473 0.05916535 4.545492
-0.03911143 0.9990663 -0.01835389 -0.8721041
-0.05984677 0.01599288 0.9980795 1.280884
0 0 0 1
[reg_aladin_sym] Initial backward transformation matrix::
0.9974411 -0.03911142 -0.05984674 -4.491313
0.04013474 0.9990662 0.01599288 0.6683726
0.05916538 -0.01835389 0.9980795 -1.563367
0 0 0 1
[reg_aladin_sym] * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[reg_aladin_sym] Final forward transformation matrix::
0.9985017 0.03448403 0.04248924 3.230631
-0.03404947 0.9993606 -0.01090922 -0.8812569
-0.04283826 0.009446135 0.9990374 0.7662405
0 0 0 1
[reg_aladin_sym] Final backward transformation matrix::
0.9985016 -0.03404948 -0.04283826 -3.222972
0.03448402 0.9993606 0.009446136 0.7620503
0.04248923 -0.01090922 0.9990374 -0.9123838
0 0 0 1
[reg_aladin_sym] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[reg_aladin] Registration performed in 0 min 11 sec
[reg_aladin] Have a good day !
Transforming Case6-MRI-landmarks.nii.gz into Case6-MRI-landmarks_linear.nii.gz
Reading affine matrix file: affine_matrix.txt
+0.999 | +0.034 | +0.042 | +3.231
-0.034 | +0.999 | -0.011 | -0.881