bcclbackup@bcclbackup-OptiPlex-5080:~/UAY_Imaging_Data/NIFTI/BASELINE/S1057$ run_samseg --input S1057_Sag_CUBE_FLAIR.nii --pallidum-separate --lesion --lesion-mask-pattern 1 --output samsegoutFLAIR3D/ 2024-09-05 15:27:38.456591: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory 2024-09-05 15:27:38.456746: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. WARNING:tensorflow:From /usr/local/freesurfer/7.2.0/python/lib/python3.6/site-packages/tensorflow/python/compat/v2_compat.py:96: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version. Instructions for updating: non-resource variables are not supported in the long term ##---------------------------------------------- Samsegment Options ##---------------------------------------------- output directory: samsegoutFLAIR3D/ input images: S1057_Sag_CUBE_FLAIR.nii modelSpecifications: {'FreeSurferLabels': [0, 165, 258, 16, 24, 8, 47, 15, 259, 3, 42, 7, 46, 41, 2, 63, 54, 18, 53, 44, 17, 31, 5, 85, 60, 28, 14, 26, 12, 51, 62, 58, 4, 30, 43, 52, 11, 49, 13, 50, 10, 72, 29, 99], 'atlasFileName': '/usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz', 'names': ['Unknown', 'Skull', 'Soft_Nonbrain_Tissue', 'Brain-Stem', 'CSF', 'Left-Cerebellum-Cortex', 'Right-Cerebellum-Cortex', '4th-Ventricle', 'Fluid_Inside_Eyes', 'Left-Cerebral-Cortex', 'Right-Cerebral-Cortex', 'Left-Cerebellum-White-Matter', 'Right-Cerebellum-White-Matter', 'Right-Cerebral-White-Matter', 'Left-Cerebral-White-Matter', 'Right-choroid-plexus', 'Right-Amygdala', 'Left-Amygdala', 'Right-Hippocampus', 'Right-Inf-Lat-Vent', 'Left-Hippocampus', 'Left-choroid-plexus', 'Left-Inf-Lat-Vent', 'Optic-Chiasm', 'Right-VentralDC', 'Left-VentralDC', '3rd-Ventricle', 'Left-Accumbens-area', 'Left-Putamen', 'Right-Putamen', 'Right-vessel', 'Right-Accumbens-area', 'Left-Lateral-Ventricle', 'Left-vessel', 'Right-Lateral-Ventricle', 'Right-Pallidum', 'Left-Caudate', 'Right-Thalamus', 'Left-Pallidum', 'Right-Caudate', 'Left-Thalamus', '5th-Ventricle', 'Left-undetermined', 'Lesions'], 'colors': [[0, 0, 0, 0], [255, 165, 0, 255], [128, 128, 128, 255], [119, 159, 176, 255], [60, 60, 60, 255], [230, 148, 34, 255], [230, 148, 34, 255], [42, 204, 164, 255], [128, 0, 128, 255], [205, 62, 78, 255], [205, 62, 78, 255], [220, 248, 164, 255], [220, 248, 164, 255], [0, 225, 0, 255], [245, 245, 245, 255], [0, 200, 221, 255], [103, 255, 255, 255], [103, 255, 255, 255], [220, 216, 20, 255], [196, 58, 250, 255], [220, 216, 20, 255], [0, 200, 200, 255], [196, 58, 250, 255], [234, 169, 30, 255], [165, 42, 42, 255], [165, 42, 42, 255], [204, 182, 142, 255], [255, 165, 0, 255], [236, 13, 176, 255], [236, 13, 176, 255], [160, 32, 240, 255], [255, 165, 0, 255], [120, 18, 134, 255], [160, 32, 240, 255], [120, 18, 134, 255], [13, 48, 255, 255], [122, 186, 220, 255], [0, 118, 14, 255], [12, 48, 255, 255], [122, 186, 220, 255], [0, 118, 14, 255], [120, 190, 150, 255], [135, 206, 235, 255], [255, 0, 0, 255]], 'sharedGMMParameters': [GMMparameter(mergedName='Unknown', numberOfComponents=1, searchStrings=['Unknown', 'Skull', 'undetermined']), GMMparameter(mergedName='GlobalWM', numberOfComponents=1, searchStrings=['White', 'Brain-Stem', 'VentralDC', 'Optic-Chiasm', 'Thalamus']), GMMparameter(mergedName='GlobalGM', numberOfComponents=1, searchStrings=['Cortex', 'Caudate', 'Hippocampus', 'Amygdala', 'Accumbens', 'Thalamus']), GMMparameter(mergedName='GlobalCSF_messy', numberOfComponents=1, searchStrings=['CSF', 'vessel', 'choroid-plexus', 'Fluid']), GMMparameter(mergedName='GlobalCSF_clean', numberOfComponents=1, searchStrings=['Ventricle', 'Inf-Lat-Vent', 'Fluid']), GMMparameter(mergedName='Putamen', numberOfComponents=1, searchStrings=['Putamen']), GMMparameter(mergedName='Pallidum', numberOfComponents=1, searchStrings=['Pallidum']), GMMparameter(mergedName='Lesions', numberOfComponents=1, searchStrings=['Lesions']), GMMparameter(mergedName='Soft', numberOfComponents=3, searchStrings=['Soft'])], 'useDiagonalCovarianceMatrices': True, 'maskingProbabilityThreshold': 0.5, 'maskingDistance': 10.0, 'K': 0.1, 'biasFieldSmoothingKernelSize': 50} optimizationOptions: {'maximumNumberOfDeformationIterations': 20, 'absoluteCostPerVoxelDecreaseStopCriterion': 0.0001, 'verbose': False, 'maximalDeformationStopCriterion': 0.001, 'lineSearchMaximalDeformationIntervalStopCriterion': 0.001, 'maximalDeformationAppliedStopCriterion': 0.0, 'BFGSMaximumMemoryLength': 12, 'multiResolutionSpecification': [{'atlasFileName': '/usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level1.txt.gz', 'targetDownsampledVoxelSpacing': 2.0, 'maximumNumberOfIterations': 100, 'estimateBiasField': True}, {'atlasFileName': '/usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz', 'targetDownsampledVoxelSpacing': 1.0, 'maximumNumberOfIterations': 100, 'estimateBiasField': True}]} Unknown Unknown (100%) Skull (100%) Left-undetermined (100%) GlobalWM Brain-Stem (100%) Left-Cerebellum-White-Matter (100%) Right-Cerebellum-White-Matter (100%) Right-Cerebral-White-Matter (100%) Left-Cerebral-White-Matter (100%) Optic-Chiasm (100%) Right-VentralDC (100%) Left-VentralDC (100%) Right-Thalamus (50%) Left-Thalamus (50%) GlobalGM Left-Cerebellum-Cortex (100%) Right-Cerebellum-Cortex (100%) Left-Cerebral-Cortex (100%) Right-Cerebral-Cortex (100%) Right-Amygdala (100%) Left-Amygdala (100%) Right-Hippocampus (100%) Left-Hippocampus (100%) Left-Accumbens-area (100%) Right-Accumbens-area (100%) Left-Caudate (100%) Right-Thalamus (50%) Right-Caudate (100%) Left-Thalamus (50%) GlobalCSF_messy CSF (100%) Fluid_Inside_Eyes (50%) Right-choroid-plexus (100%) Left-choroid-plexus (100%) Right-vessel (100%) Left-vessel (100%) GlobalCSF_clean 4th-Ventricle (100%) Fluid_Inside_Eyes (50%) Right-Inf-Lat-Vent (100%) Left-Inf-Lat-Vent (100%) 3rd-Ventricle (100%) Left-Lateral-Ventricle (100%) Right-Lateral-Ventricle (100%) 5th-Ventricle (100%) Putamen Left-Putamen (100%) Right-Putamen (100%) Pallidum Right-Pallidum (100%) Left-Pallidum (100%) Lesions Lesions (100%) Soft Soft_Nonbrain_Tissue (100%) Unknown Unknown (100%) Skull (100%) Left-undetermined (100%) GlobalWM Brain-Stem (100%) Left-Cerebellum-White-Matter (100%) Right-Cerebellum-White-Matter (100%) Right-Cerebral-White-Matter (100%) Left-Cerebral-White-Matter (100%) Optic-Chiasm (100%) Right-VentralDC (100%) Left-VentralDC (100%) Right-Thalamus (50%) Left-Thalamus (50%) GlobalGM Left-Cerebellum-Cortex (100%) Right-Cerebellum-Cortex (100%) Left-Cerebral-Cortex (100%) Right-Cerebral-Cortex (100%) Right-Amygdala (100%) Left-Amygdala (100%) Right-Hippocampus (100%) Left-Hippocampus (100%) Left-Accumbens-area (100%) Right-Accumbens-area (100%) Left-Caudate (100%) Right-Thalamus (50%) Right-Caudate (100%) Left-Thalamus (50%) GlobalCSF_messy CSF (100%) Fluid_Inside_Eyes (50%) Right-choroid-plexus (100%) Left-choroid-plexus (100%) Right-vessel (100%) Left-vessel (100%) GlobalCSF_clean 4th-Ventricle (100%) Fluid_Inside_Eyes (50%) Right-Inf-Lat-Vent (100%) Left-Inf-Lat-Vent (100%) 3rd-Ventricle (100%) Left-Lateral-Ventricle (100%) Right-Lateral-Ventricle (100%) 5th-Ventricle (100%) Putamen Left-Putamen (100%) Right-Putamen (100%) Pallidum Right-Pallidum (100%) Left-Pallidum (100%) Lesions Lesions (100%) Soft Soft_Nonbrain_Tissue (100%) Constructing image-to-world transform from header information (S1057_Sag_CUBE_FLAIR.nii) Read image: S1057_Sag_CUBE_FLAIR.nii Constructing image-to-world transform from header information (/usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/template.nii) Read image: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/template.nii performing affine atlas registration image: S1057_Sag_CUBE_FLAIR.nii template: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/template.nii Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE min: 0 max: 7013 robustMin: 0 robustMax: 5515.35 histogram[ 0 ]: 34320 histogram[ 1 ]: 3870 histogram[ 2 ]: 1614 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 0.0859323 cumulativeHistogram[ 1 ]: 0.0956223 cumulativeHistogram[ 2 ]: 0.0996635 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 AFFINE min: 0 max: 7013 robustMin: 0 robustMax: 5515.35 histogram[ 0 ]: 34320 histogram[ 1 ]: 3870 histogram[ 2 ]: 1614 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 0.0859323 cumulativeHistogram[ 1 ]: 0.0956223 cumulativeHistogram[ 2 ]: 0.0996635 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 0 min: 0 max: 7013 robustMin: 0 robustMax: 5515.35 histogram[ 0 ]: 34320 histogram[ 1 ]: 3870 histogram[ 2 ]: 1614 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 0.0859323 cumulativeHistogram[ 1 ]: 0.0956223 cumulativeHistogram[ 2 ]: 0.0996635 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 maximalDeformation=1.0000 minLogLikelihood=-0.5789 maximalDeformation=3.4863 minLogLikelihood=-0.6668 maximalDeformation=0.1941 minLogLikelihood=-0.6672 maximalDeformation=1.6663 minLogLikelihood=-0.6699 maximalDeformation=1.1260 minLogLikelihood=-0.6760 maximalDeformation=4.1538 minLogLikelihood=-0.6963 maximalDeformation=4.4027 minLogLikelihood=-0.7319 maximalDeformation=1.2696 minLogLikelihood=-0.7423 maximalDeformation=2.1395 minLogLikelihood=-0.7497 maximalDeformation=0.9458 minLogLikelihood=-0.7506 maximalDeformation=0.0157 minLogLikelihood=-0.7506 maximalDeformation=0.0000 minLogLikelihood=-0.7506 appliedScaling: 1.0369 Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 0 min: 0 max: 7013 robustMin: 0 robustMax: 5515.35 histogram[ 0 ]: 34320 histogram[ 1 ]: 3870 histogram[ 2 ]: 1614 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 0.0859323 cumulativeHistogram[ 1 ]: 0.0956223 cumulativeHistogram[ 2 ]: 0.0996635 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 maximalDeformation=1.0000 minLogLikelihood=-0.8136 maximalDeformation=0.2475 minLogLikelihood=-0.8154 maximalDeformation=0.3776 minLogLikelihood=-0.8156 maximalDeformation=0.2322 minLogLikelihood=-0.8158 maximalDeformation=0.0000 minLogLikelihood=-0.8158 appliedScaling: 1.0158 Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 0 min: 0 max: 7013 robustMin: 0 robustMax: 5515.35 histogram[ 0 ]: 34320 histogram[ 1 ]: 3870 histogram[ 2 ]: 1614 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 0.0859323 cumulativeHistogram[ 1 ]: 0.0956223 cumulativeHistogram[ 2 ]: 0.0996635 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 maximalDeformation=1.0000 minLogLikelihood=-0.8421 maximalDeformation=0.0000 minLogLikelihood=-0.8421 appliedScaling: 1.0135 INFO: using NIfTI-1 qform writing template transform to samsegoutFLAIR3D/template.lta writing talairach transform to samsegoutFLAIR3D/samseg.talairach.lta atlas registration complete: 0:01:32.599717 INFO: using NIfTI-1 qform Constructing image-to-world transform from header information (S1057_Sag_CUBE_FLAIR.nii) Read image: S1057_Sag_CUBE_FLAIR.nii Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz Transforming points Transforming points [0.5 0.46880001 0.46880001] Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz Transforming points Transforming points Unknown Unknown (100%) Skull (100%) Left-undetermined (100%) GlobalWM Brain-Stem (100%) Left-Cerebellum-White-Matter (100%) Right-Cerebellum-White-Matter (100%) Right-Cerebral-White-Matter (100%) Left-Cerebral-White-Matter (100%) Optic-Chiasm (100%) Right-VentralDC (100%) Left-VentralDC (100%) Right-Thalamus (50%) Left-Thalamus (50%) GlobalGM Left-Cerebellum-Cortex (100%) Right-Cerebellum-Cortex (100%) Left-Cerebral-Cortex (100%) Right-Cerebral-Cortex (100%) Right-Amygdala (100%) Left-Amygdala (100%) Right-Hippocampus (100%) Left-Hippocampus (100%) Left-Accumbens-area (100%) Right-Accumbens-area (100%) Left-Caudate (100%) Right-Thalamus (50%) Right-Caudate (100%) Left-Thalamus (50%) GlobalCSF_messy CSF (100%) Fluid_Inside_Eyes (50%) Right-choroid-plexus (100%) Left-choroid-plexus (100%) Right-vessel (100%) Left-vessel (100%) GlobalCSF_clean 4th-Ventricle (100%) Fluid_Inside_Eyes (50%) Right-Inf-Lat-Vent (100%) Left-Inf-Lat-Vent (100%) 3rd-Ventricle (100%) Left-Lateral-Ventricle (100%) Right-Lateral-Ventricle (100%) 5th-Ventricle (100%) Putamen Left-Putamen (100%) Right-Putamen (100%) Pallidum Right-Pallidum (100%) Left-Pallidum (100%) Lesions Lesions (100%) Soft Soft_Nonbrain_Tissue (100%) ==================== { depth: 1 maximumNumberOfDeformationIterations: 20 absoluteCostPerVoxelDecreaseStopCriterion: 0.0001 verbose: False maximalDeformationStopCriterion: 0.001 lineSearchMaximalDeformationIntervalStopCriterion: 0.001 maximalDeformationAppliedStopCriterion: 0.0 BFGSMaximumMemoryLength: 12 multiResolutionSpecification: { depth: 2 atlasFileName: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level1.txt.gz targetDownsampledVoxelSpacing: 2.0 maximumNumberOfIterations: 100 estimateBiasField: True }, { depth: 2 atlasFileName: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz targetDownsampledVoxelSpacing: 1.0 maximumNumberOfIterations: 100 estimateBiasField: True } } ==================== Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level1.txt.gz Transforming points Transforming points iterationNumber: 0 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=1.0000 minLogLikelihood=487760.8211 maximalDeformation=0.9762 minLogLikelihood=476220.6100 maximalDeformation=0.5677 minLogLikelihood=470266.3308 maximalDeformation=0.3599 minLogLikelihood=467908.8778 maximalDeformation=0.1439 minLogLikelihood=466938.6268 maximalDeformation=0.1081 minLogLikelihood=466269.0216 maximalDeformation=0.1787 minLogLikelihood=465788.4076 maximalDeformation=0.2776 minLogLikelihood=465182.6252 maximalDeformation=0.1687 minLogLikelihood=464754.6647 maximalDeformation=0.0935 minLogLikelihood=464528.8911 maximalDeformation=0.3059 minLogLikelihood=463877.4587 maximalDeformation=0.0774 minLogLikelihood=463745.8676 maximalDeformation=0.0935 minLogLikelihood=463609.6962 maximalDeformation=0.1127 minLogLikelihood=463441.8251 maximalDeformation=0.1619 minLogLikelihood=463187.5921 maximalDeformation=0.1564 minLogLikelihood=462608.9136 maximalDeformation=0.2510 minLogLikelihood=461441.2510 maximalDeformation=0.1309 minLogLikelihood=460995.7756 maximalDeformation=0.3440 minLogLikelihood=459754.9237 maximalDeformation=0.1896 minLogLikelihood=459254.3606 maximalDeformation=0.0000 minLogLikelihood=459254.3606 maximalDeformationApplied: 3.0272 ======================================================= iterationNumber: 1 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.5000 minLogLikelihood=437383.1616 maximalDeformation=0.1307 minLogLikelihood=437045.8520 maximalDeformation=0.3605 minLogLikelihood=435611.2674 maximalDeformation=0.3088 minLogLikelihood=434662.5039 maximalDeformation=0.1808 minLogLikelihood=434415.4526 maximalDeformation=0.1411 minLogLikelihood=434236.2113 maximalDeformation=0.2712 minLogLikelihood=433638.9826 maximalDeformation=0.0496 minLogLikelihood=433578.0158 maximalDeformation=0.0793 minLogLikelihood=433424.2195 maximalDeformation=0.1965 minLogLikelihood=433175.2440 maximalDeformation=0.2956 minLogLikelihood=432856.0983 maximalDeformation=0.1413 minLogLikelihood=432696.5426 maximalDeformation=0.1937 minLogLikelihood=432214.0990 maximalDeformation=0.1511 minLogLikelihood=431852.6707 maximalDeformation=0.0525 minLogLikelihood=431752.5715 maximalDeformation=0.2298 minLogLikelihood=431023.4013 maximalDeformation=0.1273 minLogLikelihood=430681.8437 maximalDeformation=0.1472 minLogLikelihood=430394.8822 maximalDeformation=0.2637 minLogLikelihood=429988.0564 maximalDeformation=0.1224 minLogLikelihood=429879.2509 maximalDeformation=0.0000 minLogLikelihood=429879.2509 maximalDeformationApplied: 1.8855 ======================================================= iterationNumber: 2 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=1.0000 minLogLikelihood=429485.3469 maximalDeformation=0.0633 minLogLikelihood=429293.5979 maximalDeformation=0.5356 minLogLikelihood=427863.0055 maximalDeformation=0.2231 minLogLikelihood=427493.1478 maximalDeformation=0.1106 minLogLikelihood=427228.9901 maximalDeformation=0.1696 minLogLikelihood=426909.9955 maximalDeformation=0.2968 minLogLikelihood=426559.1743 maximalDeformation=0.1200 minLogLikelihood=426462.9219 maximalDeformation=0.1619 minLogLikelihood=426342.3353 maximalDeformation=0.1344 minLogLikelihood=426136.3305 maximalDeformation=0.3552 minLogLikelihood=425793.7715 maximalDeformation=0.2050 minLogLikelihood=425567.9462 maximalDeformation=0.1129 minLogLikelihood=425341.4282 maximalDeformation=0.1888 minLogLikelihood=425084.0704 maximalDeformation=0.1559 minLogLikelihood=424948.3272 maximalDeformation=0.4102 minLogLikelihood=424646.9719 maximalDeformation=0.0572 minLogLikelihood=424610.1244 maximalDeformation=0.0970 minLogLikelihood=424421.0963 maximalDeformation=0.2144 minLogLikelihood=424159.1534 maximalDeformation=0.0482 minLogLikelihood=424082.2629 maximalDeformation=0.0000 minLogLikelihood=424082.2629 maximalDeformationApplied: 1.4028 ======================================================= iterationNumber: 3 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.5000 minLogLikelihood=423816.2146 maximalDeformation=0.0633 minLogLikelihood=423689.6266 maximalDeformation=0.6130 minLogLikelihood=422793.8059 maximalDeformation=0.7534 minLogLikelihood=421710.1016 maximalDeformation=0.1731 minLogLikelihood=421459.4184 maximalDeformation=0.0747 minLogLikelihood=421247.7658 maximalDeformation=0.0589 minLogLikelihood=421086.3120 maximalDeformation=0.3217 minLogLikelihood=420747.1204 maximalDeformation=0.0492 minLogLikelihood=420704.9152 maximalDeformation=0.2670 minLogLikelihood=420520.9044 maximalDeformation=0.7148 minLogLikelihood=420263.7893 maximalDeformation=0.0960 minLogLikelihood=420214.5483 maximalDeformation=0.2352 minLogLikelihood=420050.2930 maximalDeformation=0.2876 minLogLikelihood=419983.8283 maximalDeformation=0.0988 minLogLikelihood=419929.1065 maximalDeformation=0.1108 minLogLikelihood=419813.1630 maximalDeformation=0.1972 minLogLikelihood=419481.6663 maximalDeformation=0.2505 minLogLikelihood=418995.3215 maximalDeformation=0.2058 minLogLikelihood=418774.8188 maximalDeformation=0.1331 minLogLikelihood=418679.3197 maximalDeformation=0.0000 minLogLikelihood=418679.3197 maximalDeformationApplied: 1.4935 ======================================================= iterationNumber: 4 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.5000 minLogLikelihood=418385.4377 maximalDeformation=0.0805 minLogLikelihood=418220.6030 maximalDeformation=0.3849 minLogLikelihood=417678.0416 maximalDeformation=0.5103 minLogLikelihood=417429.6501 maximalDeformation=0.1978 minLogLikelihood=417267.7499 maximalDeformation=0.1711 minLogLikelihood=417047.7369 maximalDeformation=0.1814 minLogLikelihood=416766.6636 maximalDeformation=0.3090 minLogLikelihood=416461.1292 maximalDeformation=0.3210 minLogLikelihood=416173.6343 maximalDeformation=0.0365 minLogLikelihood=416107.6149 maximalDeformation=0.2478 minLogLikelihood=415750.4449 maximalDeformation=0.0766 minLogLikelihood=415702.1366 maximalDeformation=0.0834 minLogLikelihood=415631.5104 maximalDeformation=0.1191 minLogLikelihood=415593.5907 maximalDeformation=0.1502 minLogLikelihood=415510.3529 maximalDeformation=0.1266 minLogLikelihood=415444.8180 maximalDeformation=0.3470 minLogLikelihood=415381.7858 maximalDeformation=0.1906 minLogLikelihood=415186.5679 maximalDeformation=0.1927 minLogLikelihood=414938.8852 maximalDeformation=0.2468 minLogLikelihood=414706.7117 maximalDeformation=0.0000 minLogLikelihood=414706.7117 maximalDeformationApplied: 1.2804 ======================================================= iterationNumber: 5 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.3405 minLogLikelihood=414596.5322 maximalDeformation=0.2156 minLogLikelihood=414459.3559 maximalDeformation=0.2791 minLogLikelihood=414290.5647 maximalDeformation=0.1679 minLogLikelihood=414236.3766 maximalDeformation=0.0523 minLogLikelihood=414202.7623 maximalDeformation=0.2734 minLogLikelihood=414067.8248 maximalDeformation=0.2025 minLogLikelihood=413954.7262 maximalDeformation=0.1614 minLogLikelihood=413834.7182 maximalDeformation=0.1135 minLogLikelihood=413743.7527 maximalDeformation=0.3210 minLogLikelihood=413592.6721 maximalDeformation=0.3475 minLogLikelihood=413544.7875 maximalDeformation=0.1249 minLogLikelihood=413486.9818 maximalDeformation=0.1001 minLogLikelihood=413387.3469 maximalDeformation=0.4614 minLogLikelihood=413186.5453 maximalDeformation=0.4658 minLogLikelihood=413082.8317 maximalDeformation=0.3932 minLogLikelihood=413023.1863 maximalDeformation=0.1496 minLogLikelihood=412936.5447 maximalDeformation=0.1601 minLogLikelihood=412807.5402 maximalDeformation=0.3295 minLogLikelihood=412648.1827 maximalDeformation=0.1788 minLogLikelihood=412555.3541 maximalDeformation=0.0000 minLogLikelihood=412555.3541 maximalDeformationApplied: 2.3418 ======================================================= iterationNumber: 6 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.2500 minLogLikelihood=412408.5730 maximalDeformation=0.2148 minLogLikelihood=412351.1862 maximalDeformation=0.1769 minLogLikelihood=412312.0016 maximalDeformation=0.1484 minLogLikelihood=412271.3874 maximalDeformation=0.1204 minLogLikelihood=412238.2119 maximalDeformation=0.1451 minLogLikelihood=412201.6717 maximalDeformation=0.1135 minLogLikelihood=412164.0188 maximalDeformation=0.1779 minLogLikelihood=412121.5760 maximalDeformation=0.1984 minLogLikelihood=412089.9524 maximalDeformation=0.0487 minLogLikelihood=412083.4933 maximalDeformation=0.0682 minLogLikelihood=412077.9257 maximalDeformation=0.0356 minLogLikelihood=412068.0856 maximalDeformation=0.1960 minLogLikelihood=412041.2762 maximalDeformation=0.0890 minLogLikelihood=412018.2356 maximalDeformation=0.0697 minLogLikelihood=411999.4764 maximalDeformation=0.1257 minLogLikelihood=411962.5834 maximalDeformation=0.1275 minLogLikelihood=411924.9119 maximalDeformation=0.1555 minLogLikelihood=411882.5776 maximalDeformation=0.1318 minLogLikelihood=411840.3936 maximalDeformation=0.1565 minLogLikelihood=411796.1060 maximalDeformation=0.0000 minLogLikelihood=411796.1060 maximalDeformationApplied: 1.1636 ======================================================= iterationNumber: 7 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.1651 minLogLikelihood=411729.2051 maximalDeformation=0.1178 minLogLikelihood=411710.1246 maximalDeformation=0.1608 minLogLikelihood=411702.9037 maximalDeformation=0.0402 minLogLikelihood=411692.9220 maximalDeformation=0.1950 minLogLikelihood=411674.5195 maximalDeformation=0.0469 minLogLikelihood=411661.1313 maximalDeformation=0.0677 minLogLikelihood=411648.5093 maximalDeformation=0.1204 minLogLikelihood=411637.2475 maximalDeformation=0.0492 minLogLikelihood=411623.9512 maximalDeformation=0.0709 minLogLikelihood=411608.5834 maximalDeformation=0.0860 minLogLikelihood=411596.0492 maximalDeformation=0.0514 minLogLikelihood=411582.8994 maximalDeformation=0.0888 minLogLikelihood=411568.5826 maximalDeformation=0.0637 minLogLikelihood=411554.2075 maximalDeformation=0.0840 minLogLikelihood=411538.0531 maximalDeformation=0.0816 minLogLikelihood=411522.2470 maximalDeformation=0.0576 minLogLikelihood=411506.0895 maximalDeformation=0.0553 minLogLikelihood=411489.2754 maximalDeformation=0.0656 minLogLikelihood=411473.0263 maximalDeformation=0.0810 minLogLikelihood=411456.3293 maximalDeformation=0.0000 minLogLikelihood=411456.3293 maximalDeformationApplied: 0.6020 ======================================================= iterationNumber: 8 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.1081 minLogLikelihood=411417.9299 maximalDeformation=0.0929 minLogLikelihood=411408.8825 maximalDeformation=0.0714 minLogLikelihood=411401.7367 maximalDeformation=0.0442 minLogLikelihood=411395.2762 maximalDeformation=0.0376 minLogLikelihood=411388.9994 maximalDeformation=0.0363 minLogLikelihood=411383.2295 maximalDeformation=0.0383 minLogLikelihood=411377.0741 maximalDeformation=0.0554 minLogLikelihood=411371.4612 maximalDeformation=0.0425 minLogLikelihood=411365.7748 maximalDeformation=0.0408 minLogLikelihood=411359.9325 maximalDeformation=0.0486 minLogLikelihood=411354.0217 maximalDeformation=0.0624 minLogLikelihood=411347.9155 maximalDeformation=0.0545 minLogLikelihood=411341.2892 maximalDeformation=0.0491 minLogLikelihood=411334.4433 maximalDeformation=0.0521 minLogLikelihood=411328.2082 maximalDeformation=0.0605 minLogLikelihood=411322.0353 maximalDeformation=0.0624 minLogLikelihood=411315.4930 maximalDeformation=0.0575 minLogLikelihood=411308.9974 maximalDeformation=0.0631 minLogLikelihood=411302.8574 maximalDeformation=0.0631 minLogLikelihood=411295.8920 maximalDeformation=0.0000 minLogLikelihood=411295.8920 maximalDeformationApplied: 0.5223 ======================================================= iterationNumber: 9 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.0379 minLogLikelihood=411271.1260 maximalDeformation=0.0155 minLogLikelihood=411267.7869 maximalDeformation=0.0228 minLogLikelihood=411264.7696 maximalDeformation=0.0315 minLogLikelihood=411262.3193 maximalDeformation=0.0271 minLogLikelihood=411259.6950 maximalDeformation=0.0321 minLogLikelihood=411257.1141 maximalDeformation=0.0225 minLogLikelihood=411254.8560 maximalDeformation=0.0330 minLogLikelihood=411252.5234 maximalDeformation=0.0394 minLogLikelihood=411250.3347 maximalDeformation=0.0408 minLogLikelihood=411248.0638 maximalDeformation=0.0485 minLogLikelihood=411245.5178 maximalDeformation=0.0437 minLogLikelihood=411243.2071 maximalDeformation=0.0402 minLogLikelihood=411241.1640 maximalDeformation=0.0355 minLogLikelihood=411238.8039 maximalDeformation=0.0379 minLogLikelihood=411236.5061 maximalDeformation=0.0300 minLogLikelihood=411234.3587 maximalDeformation=0.0291 minLogLikelihood=411232.0604 maximalDeformation=0.0321 minLogLikelihood=411229.6415 maximalDeformation=0.0268 minLogLikelihood=411227.1567 maximalDeformation=0.0320 minLogLikelihood=411224.2547 maximalDeformation=0.0000 minLogLikelihood=411224.2547 maximalDeformationApplied: 0.5466 ======================================================= iterationNumber: 10 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.0451 minLogLikelihood=411206.7496 maximalDeformation=0.0154 minLogLikelihood=411204.2311 maximalDeformation=0.0285 minLogLikelihood=411202.8034 maximalDeformation=0.0126 minLogLikelihood=411201.5631 maximalDeformation=0.0238 minLogLikelihood=411199.9379 maximalDeformation=0.0178 minLogLikelihood=411198.7037 maximalDeformation=0.0200 minLogLikelihood=411197.4349 maximalDeformation=0.0280 minLogLikelihood=411196.2600 maximalDeformation=0.0121 minLogLikelihood=411195.2208 maximalDeformation=0.0163 minLogLikelihood=411194.0952 maximalDeformation=0.0212 minLogLikelihood=411192.9618 maximalDeformation=0.0210 minLogLikelihood=411191.9011 maximalDeformation=0.0183 minLogLikelihood=411190.5365 maximalDeformation=0.0190 minLogLikelihood=411189.2539 maximalDeformation=0.0164 minLogLikelihood=411188.0619 maximalDeformation=0.0220 minLogLikelihood=411186.6861 maximalDeformation=0.0257 minLogLikelihood=411185.2415 maximalDeformation=0.0288 minLogLikelihood=411183.8831 maximalDeformation=0.0173 minLogLikelihood=411182.3530 maximalDeformation=0.0217 minLogLikelihood=411180.6087 maximalDeformation=0.0000 minLogLikelihood=411180.6087 maximalDeformationApplied: 0.2251 ======================================================= Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level1.txt.gz Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 1 [BRACKETING] Found a really good solution -- no need for zooming: 1 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 6.01057 ----------------------- [BRACKETING] Hit a really bad solution -- ready for zooming: 8.96169 [ZOOMING] Zooming with low=0 and high=8.96169 bisected: 4.48084 interpolated: 2.13939 [ZOOMING] Found a good solution: 2.13939 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 0.517428 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 0.263854 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 0.0649843 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 0.0617439 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 0.0290226 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 0.00602553 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 0.00297477 ----------------------- Optimizer: maximalDeformation is too small; stopping iterationNumber: 0 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=1.0000 minLogLikelihood=3191258.8972 maximalDeformation=2.0802 minLogLikelihood=3177494.4489 maximalDeformation=1.1575 minLogLikelihood=3169871.1665 maximalDeformation=0.9523 minLogLikelihood=3163356.8677 maximalDeformation=0.1354 minLogLikelihood=3162784.1023 maximalDeformation=0.4236 minLogLikelihood=3161976.2433 maximalDeformation=0.3454 minLogLikelihood=3160276.4239 maximalDeformation=0.5508 minLogLikelihood=3156786.1448 maximalDeformation=0.2447 minLogLikelihood=3155332.6358 maximalDeformation=0.1943 minLogLikelihood=3154628.6828 maximalDeformation=0.4608 minLogLikelihood=3153468.7020 maximalDeformation=0.3950 minLogLikelihood=3152902.0281 maximalDeformation=0.1085 minLogLikelihood=3152323.8761 maximalDeformation=0.3688 minLogLikelihood=3150234.3723 maximalDeformation=0.4148 minLogLikelihood=3148141.9831 maximalDeformation=0.5366 minLogLikelihood=3145881.7202 maximalDeformation=0.2088 minLogLikelihood=3145180.1965 maximalDeformation=0.2790 minLogLikelihood=3144263.2286 maximalDeformation=0.8878 minLogLikelihood=3142908.5640 maximalDeformation=0.8606 minLogLikelihood=3141056.1781 maximalDeformation=0.0000 minLogLikelihood=3141056.1781 maximalDeformationApplied: 3.6294 ======================================================= iterationNumber: 1 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=1.0000 minLogLikelihood=3137304.9178 maximalDeformation=0.1466 minLogLikelihood=3136268.0158 maximalDeformation=0.7885 minLogLikelihood=3133144.1994 maximalDeformation=0.7408 minLogLikelihood=3131630.4438 maximalDeformation=0.3204 minLogLikelihood=3131211.4906 maximalDeformation=0.3780 minLogLikelihood=3130578.3211 maximalDeformation=0.5497 minLogLikelihood=3129636.6883 maximalDeformation=0.6186 minLogLikelihood=3128753.9846 maximalDeformation=0.4155 minLogLikelihood=3127915.2398 maximalDeformation=0.2406 minLogLikelihood=3127506.6487 maximalDeformation=0.2863 minLogLikelihood=3127052.4602 maximalDeformation=0.2072 minLogLikelihood=3126657.5798 maximalDeformation=0.3761 minLogLikelihood=3125790.4898 maximalDeformation=0.4125 minLogLikelihood=3125223.8293 maximalDeformation=0.2092 minLogLikelihood=3125094.4761 maximalDeformation=0.1766 minLogLikelihood=3124919.2144 maximalDeformation=0.2114 minLogLikelihood=3124761.8475 maximalDeformation=0.1540 minLogLikelihood=3124673.9424 maximalDeformation=0.1894 minLogLikelihood=3124504.0995 maximalDeformation=0.2054 minLogLikelihood=3124296.7829 maximalDeformation=0.0000 minLogLikelihood=3124296.7829 maximalDeformationApplied: 3.5816 ======================================================= iterationNumber: 2 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.5000 minLogLikelihood=3123571.2323 maximalDeformation=0.6767 minLogLikelihood=3123017.6494 maximalDeformation=0.5944 minLogLikelihood=3122739.9995 maximalDeformation=0.2113 minLogLikelihood=3122308.8339 maximalDeformation=0.7058 minLogLikelihood=3121436.6497 maximalDeformation=0.6405 minLogLikelihood=3120783.6299 maximalDeformation=0.6296 minLogLikelihood=3120325.7735 maximalDeformation=0.6020 minLogLikelihood=3119896.9142 maximalDeformation=0.2774 minLogLikelihood=3119594.0554 maximalDeformation=0.3806 minLogLikelihood=3119259.8877 maximalDeformation=0.2749 minLogLikelihood=3118914.1460 maximalDeformation=0.6837 minLogLikelihood=3118276.7155 maximalDeformation=0.2637 minLogLikelihood=3117904.4439 maximalDeformation=0.2284 minLogLikelihood=3117572.8877 maximalDeformation=0.5776 minLogLikelihood=3117166.6732 maximalDeformation=0.2299 minLogLikelihood=3116870.8550 maximalDeformation=0.1684 minLogLikelihood=3116435.1232 maximalDeformation=0.1852 minLogLikelihood=3116186.0283 maximalDeformation=0.4487 minLogLikelihood=3115982.2204 maximalDeformation=0.1988 minLogLikelihood=3115838.3690 maximalDeformation=0.0000 minLogLikelihood=3115838.3690 maximalDeformationApplied: 3.6704 ======================================================= iterationNumber: 3 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.5000 minLogLikelihood=3115268.0681 maximalDeformation=0.2145 minLogLikelihood=3115033.7589 maximalDeformation=0.3491 minLogLikelihood=3114687.2610 maximalDeformation=0.3464 minLogLikelihood=3114637.1986 maximalDeformation=0.2728 minLogLikelihood=3114541.9949 maximalDeformation=0.1978 minLogLikelihood=3114407.2809 maximalDeformation=0.1931 minLogLikelihood=3114277.9597 maximalDeformation=0.4342 minLogLikelihood=3114065.7698 maximalDeformation=0.2221 minLogLikelihood=3113975.7684 maximalDeformation=0.1055 minLogLikelihood=3113900.2275 maximalDeformation=0.2654 minLogLikelihood=3113713.9698 maximalDeformation=0.1369 minLogLikelihood=3113701.4209 maximalDeformation=0.0771 minLogLikelihood=3113636.3478 maximalDeformation=0.0891 minLogLikelihood=3113562.4513 maximalDeformation=0.0280 minLogLikelihood=3113542.5279 maximalDeformation=0.1406 minLogLikelihood=3113443.5370 maximalDeformation=0.2327 minLogLikelihood=3113295.6260 maximalDeformation=0.4446 minLogLikelihood=3113147.7236 maximalDeformation=0.2453 minLogLikelihood=3113000.2887 maximalDeformation=0.3255 minLogLikelihood=3112834.3057 maximalDeformation=0.0000 minLogLikelihood=3112834.3057 maximalDeformationApplied: 1.5937 ======================================================= iterationNumber: 4 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.5000 minLogLikelihood=3112659.3334 maximalDeformation=0.2011 minLogLikelihood=3112493.0290 maximalDeformation=0.2059 minLogLikelihood=3112434.0016 maximalDeformation=0.0907 minLogLikelihood=3112375.8925 maximalDeformation=0.3501 minLogLikelihood=3112242.8614 maximalDeformation=0.2444 minLogLikelihood=3112153.2373 maximalDeformation=0.1668 minLogLikelihood=3112095.7756 maximalDeformation=0.0985 minLogLikelihood=3112077.6029 maximalDeformation=0.0388 minLogLikelihood=3112064.6492 maximalDeformation=0.0813 minLogLikelihood=3111999.5148 maximalDeformation=0.2023 minLogLikelihood=3111879.8500 maximalDeformation=0.1181 minLogLikelihood=3111785.5543 maximalDeformation=0.1301 minLogLikelihood=3111757.6652 maximalDeformation=0.1991 minLogLikelihood=3111751.2417 maximalDeformation=0.1446 minLogLikelihood=3111705.6381 maximalDeformation=0.1461 minLogLikelihood=3111663.3387 maximalDeformation=0.0702 minLogLikelihood=3111589.4379 maximalDeformation=0.3293 minLogLikelihood=3111426.2040 maximalDeformation=0.1425 minLogLikelihood=3111376.8334 maximalDeformation=0.0828 minLogLikelihood=3111303.4027 maximalDeformation=0.0000 minLogLikelihood=3111303.4027 maximalDeformationApplied: 1.3024 ======================================================= iterationNumber: 5 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.2500 minLogLikelihood=3111108.4797 maximalDeformation=0.1536 minLogLikelihood=3111069.6696 maximalDeformation=0.0179 minLogLikelihood=3111051.4279 maximalDeformation=0.2106 minLogLikelihood=3110917.7387 maximalDeformation=0.1766 minLogLikelihood=3110902.1565 maximalDeformation=0.0583 minLogLikelihood=3110873.0198 maximalDeformation=0.1229 minLogLikelihood=3110807.1611 maximalDeformation=0.1314 minLogLikelihood=3110739.2114 maximalDeformation=0.2347 minLogLikelihood=3110639.7628 maximalDeformation=0.1068 minLogLikelihood=3110632.2565 maximalDeformation=0.0488 minLogLikelihood=3110607.7197 maximalDeformation=0.1456 minLogLikelihood=3110553.5475 maximalDeformation=0.2179 minLogLikelihood=3110472.4514 maximalDeformation=0.1394 minLogLikelihood=3110397.9559 maximalDeformation=0.2966 minLogLikelihood=3110314.2397 maximalDeformation=0.2080 minLogLikelihood=3110304.2834 maximalDeformation=0.1629 minLogLikelihood=3110258.2039 maximalDeformation=0.1521 minLogLikelihood=3110244.4400 maximalDeformation=0.1131 minLogLikelihood=3110199.0020 maximalDeformation=0.2267 minLogLikelihood=3110127.7764 maximalDeformation=0.0000 minLogLikelihood=3110127.7764 maximalDeformationApplied: 1.5361 ======================================================= iterationNumber: 6 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.5000 minLogLikelihood=3109993.2560 maximalDeformation=0.1576 minLogLikelihood=3109940.9171 maximalDeformation=0.0483 minLogLikelihood=3109923.1777 maximalDeformation=0.1154 minLogLikelihood=3109876.7110 maximalDeformation=0.1890 minLogLikelihood=3109824.4576 maximalDeformation=0.2290 minLogLikelihood=3109775.0931 maximalDeformation=0.1807 minLogLikelihood=3109726.7785 maximalDeformation=0.1654 minLogLikelihood=3109672.7121 maximalDeformation=0.1616 minLogLikelihood=3109618.1083 maximalDeformation=0.1303 minLogLikelihood=3109574.4608 maximalDeformation=0.1395 minLogLikelihood=3109524.1158 maximalDeformation=0.1679 minLogLikelihood=3109494.6175 maximalDeformation=0.1299 minLogLikelihood=3109439.0515 maximalDeformation=0.1991 minLogLikelihood=3109378.5180 maximalDeformation=0.1291 minLogLikelihood=3109301.2397 maximalDeformation=0.3839 minLogLikelihood=3109235.6991 maximalDeformation=0.2015 minLogLikelihood=3109163.2505 maximalDeformation=0.3144 minLogLikelihood=3109079.0845 maximalDeformation=0.2903 minLogLikelihood=3108989.7683 maximalDeformation=0.3138 minLogLikelihood=3108883.0639 maximalDeformation=0.0000 minLogLikelihood=3108883.0639 maximalDeformationApplied: 1.1775 ======================================================= iterationNumber: 7 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.3852 minLogLikelihood=3108713.7134 maximalDeformation=0.2587 minLogLikelihood=3108668.8345 maximalDeformation=0.0769 minLogLikelihood=3108634.3241 maximalDeformation=0.1394 minLogLikelihood=3108582.6502 maximalDeformation=0.3901 minLogLikelihood=3108579.4047 maximalDeformation=0.2091 minLogLikelihood=3108536.7488 maximalDeformation=0.1001 minLogLikelihood=3108491.9165 maximalDeformation=0.1132 minLogLikelihood=3108462.9347 maximalDeformation=0.1417 minLogLikelihood=3108430.3698 maximalDeformation=0.2230 minLogLikelihood=3108390.3486 maximalDeformation=0.2769 minLogLikelihood=3108367.7471 maximalDeformation=0.0960 minLogLikelihood=3108319.0995 maximalDeformation=0.1956 minLogLikelihood=3108278.3467 maximalDeformation=0.1117 minLogLikelihood=3108239.7979 maximalDeformation=0.1346 minLogLikelihood=3108207.3399 maximalDeformation=0.0998 minLogLikelihood=3108175.2863 maximalDeformation=0.1294 minLogLikelihood=3108132.3222 maximalDeformation=0.1506 minLogLikelihood=3108088.9028 maximalDeformation=0.1699 minLogLikelihood=3108045.2976 maximalDeformation=0.1360 minLogLikelihood=3107986.9590 maximalDeformation=0.0000 minLogLikelihood=3107986.9590 maximalDeformationApplied: 1.2561 ======================================================= iterationNumber: 8 EM converged! 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 maximalDeformation=0.2500 minLogLikelihood=3107900.7547 maximalDeformation=0.1288 minLogLikelihood=3107875.5487 maximalDeformation=0.0371 minLogLikelihood=3107867.1768 maximalDeformation=0.0794 minLogLikelihood=3107844.1223 maximalDeformation=0.1844 minLogLikelihood=3107814.7388 maximalDeformation=0.3107 minLogLikelihood=3107790.8001 maximalDeformation=0.0995 minLogLikelihood=3107771.6532 maximalDeformation=0.1183 minLogLikelihood=3107751.7797 maximalDeformation=0.0656 minLogLikelihood=3107737.2511 maximalDeformation=0.1437 minLogLikelihood=3107719.5705 maximalDeformation=0.1220 minLogLikelihood=3107704.0209 maximalDeformation=0.0997 minLogLikelihood=3107688.4977 maximalDeformation=0.0582 minLogLikelihood=3107673.3067 maximalDeformation=0.0909 minLogLikelihood=3107661.4634 maximalDeformation=0.0533 minLogLikelihood=3107645.1513 maximalDeformation=0.0933 minLogLikelihood=3107628.4661 maximalDeformation=0.0521 minLogLikelihood=3107615.0482 maximalDeformation=0.0766 minLogLikelihood=3107598.7065 maximalDeformation=0.1057 minLogLikelihood=3107579.7704 maximalDeformation=0.1083 minLogLikelihood=3107557.3650 maximalDeformation=0.0000 minLogLikelihood=3107557.3650 maximalDeformationApplied: 0.9869 ======================================================= Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz ^[[B^[[B^[[A^[[B^[[B^[[A^[[A^[[B^[[A^[[B^[[A^[[A^[[B^[[B^[[A^[[A^[[B^[[B^[[B [2]+ Killed run_samseg --input S1057_Sag_CUBE_FLAIR.nii --pallidum-separate --lesion --lesion-mask-pattern 1 --output samsegoutFLAIR3D/ Killed