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For more details, please visit https://support.apple.com/kb/HT208050. doc-imac:~ clarklab$ cd /Volumes/Clark_Lab_NAS/HP2 doc-imac:HP2 clarklab$ csh csh.FreeSurfer_MiDeFace_HP20008 -------- freesurfer-darwin-macOS-7.3.2-20220804-6354275 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/7.3.2 FSFAST_HOME /Applications/freesurfer/7.3.2/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.3.2/subjects MNI_DIR /Applications/freesurfer/7.3.2/mni FSL_DIR /Users/clarklab/fsl *************************************************** HP20008 Thu May 18 14:08:50 EDT 2023 Beginning MiDeFace ======================= Thu May 18 14:08:50 EDT 2023 setenv SUBJECTS_DIR /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data cd /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files /Applications/freesurfer/7.3.2/bin/mideface --i T2_SPACE.nii --o T2_mideface_zeroes.nii --odir qa --pics --code HP20008 -rwxr-xr-x 1 root wheel 27366 Aug 4 2022 /Applications/freesurfer/7.3.2/bin/mideface freesurfer-darwin-macOS-7.3.2-20220804-6354275 $Id$ Darwin doc-imac.anbg.mssm.edu 21.6.0 Darwin Kernel Version 21.6.0: Thu Mar 9 20:08:59 PST 2023; root:xnu-8020.240.18.700.8~1/RELEASE_X86_64 x86_64 pid 93387 UseXvfb 1 samseg --i /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii --o /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg --threads 1 --block-coordinate-descent --options /Applications/freesurfer/7.3.2/average/mideface-atlas/samseg-options.json /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files Thu May 18 14:08:51 EDT 2023 setenv SUBJECTS_DIR /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data cd /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files /Applications/freesurfer/7.3.2/bin/samseg --i /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii --o /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg --threads 1 --block-coordinate-descent --options /Applications/freesurfer/7.3.2/average/mideface-atlas/samseg-options.json freesurfer-darwin-macOS-7.3.2-20220804-6354275 samseg 7.3.2 Darwin doc-imac.anbg.mssm.edu 21.6.0 Darwin Kernel Version 21.6.0: Thu Mar 9 20:08:59 PST 2023; root:xnu-8020.240.18.700.8~1/RELEASE_X86_64 x86_64 Using Block Coordinate Descent fs_time run_samseg -o /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg --threads 1 --save-warp --options /Applications/freesurfer/7.3.2/average/mideface-atlas/samseg-options.json -i /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii Constructing image-to-world transform from header information (/Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii) Read image: /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii Constructing image-to-world transform from header information (/Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii) Read image: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE min: 0 max: 801 robustMin: 0 robustMax: 687.029 histogram[ 0 ]: 92818 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 0.261453 cumulativeHistogram[ 1 ]: 0.261453 cumulativeHistogram[ 2 ]: 0.261453 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 AFFINE min: 0 max: 801 robustMin: 0 robustMax: 687.029 histogram[ 0 ]: 92818 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 0.261453 cumulativeHistogram[ 1 ]: 0.261453 cumulativeHistogram[ 2 ]: 0.261453 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 0 min: 0 max: 801 robustMin: 0 robustMax: 687.029 histogram[ 0 ]: 92818 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 0.261453 cumulativeHistogram[ 1 ]: 0.261453 cumulativeHistogram[ 2 ]: 0.261453 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 0 min: 0 max: 801 robustMin: 0 robustMax: 687.029 histogram[ 0 ]: 92818 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 0.261453 cumulativeHistogram[ 1 ]: 0.261453 cumulativeHistogram[ 2 ]: 0.261453 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 0 min: 0 max: 801 robustMin: 0 robustMax: 687.029 histogram[ 0 ]: 92818 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 0.261453 cumulativeHistogram[ 1 ]: 0.261453 cumulativeHistogram[ 2 ]: 0.261453 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 Constructing image-to-world transform from header information (/Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii) Read image: /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz Transforming points Transforming points 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 1 0.398942 SLIDING 1 0.398942 SLIDING Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 1 [BRACKETING] Hit a really bad solution -- ready for zooming: 1 [ZOOMING] Zooming with low=0 and high=1 bisected: 0.5 bisected: 0.25 bisected: 0.125 interpolated: 1.2403e-11 Too small for current range [0 0.125]; using something forcibly bigger instead: 0.0125 interpolated: 1.22363e-11 Too small for current range [0 0.0125]; using something forcibly bigger instead: 0.00125 [ZOOMING] Zooming interval size too low; returning best: 0 ----------------------- Optimizer: maximalDeformation is too small; stopping 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 1 0.398942 SLIDING Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Constructing image-to-world transform from header information (/Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii) Read image: /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Read mesh collection: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz ##---------------------------------------------- Samsegment Options ##---------------------------------------------- output directory: /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg input images: /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.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, 77, 4, 30, 43, 52, 11, 49, 13, 50, 10, 80, 72], 'atlasFileName': '/Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/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', 'WM-hypointensities', 'Left-Lateral-Ventricle', 'Left-vessel', 'Right-Lateral-Ventricle', 'Right-Pallidum', 'Left-Caudate', 'Right-Thalamus', 'Left-Pallidum', 'Right-Caudate', 'Left-Thalamus', 'non-WM-hypointensities', '5th-Ventricle'], '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], [200, 70, 255, 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], [164, 108, 226, 255], [120, 190, 150, 255]], 'sharedGMMParameters': [GMMparameter(mergedName='Unknown', numberOfComponents=1, searchStrings=['Unknown', 'Skull']), GMMparameter(mergedName='GlobalWM', numberOfComponents=1, searchStrings=['White', 'Brain-Stem', 'VentralDC', 'Optic-Chiasm', 'Thalamus', 'Pallidum']), GMMparameter(mergedName='GlobalGM', numberOfComponents=1, searchStrings=['Cortex', 'Caudate', 'Hippocampus', 'Amygdala', 'Accumbens', 'hypointensities', '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='Soft', numberOfComponents=3, searchStrings=['Soft'])], 'useDiagonalCovarianceMatrices': True, 'maskingProbabilityThreshold': 0.5, 'maskingDistance': 10.0, 'K': 0.1, 'biasFieldSmoothingKernelSize': 50, 'whiteMatterAndCortexSmoothingSigma': 0} optimizationOptions: {'maximumNumberOfDeformationIterations': 1, 'absoluteCostPerVoxelDecreaseStopCriterion': 0.01, 'verbose': False, 'maximalDeformationStopCriterion': 0.01, 'lineSearchMaximalDeformationIntervalStopCriterion': 0.01, 'maximalDeformationAppliedStopCriterion': 0.0, 'BFGSMaximumMemoryLength': 12, 'multiResolutionSpecification': [{'atlasFileName': '/Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz', 'targetDownsampledVoxelSpacing': 2.0, 'maximumNumberOfIterations': 50, 'estimateBiasField': True}, {'atlasFileName': '/Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz', 'targetDownsampledVoxelSpacing': 1.0, 'maximumNumberOfIterations': 2, 'estimateBiasField': True}]} performing affine atlas registration image: /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii template: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii maximalDeformation=1.0000 minLogLikelihood=-0.6296 maximalDeformation=4.3170 minLogLikelihood=-0.7299 maximalDeformation=1.4603 minLogLikelihood=-0.7627 maximalDeformation=1.7593 minLogLikelihood=-0.8112 maximalDeformation=1.3975 minLogLikelihood=-0.8147 maximalDeformation=0.5921 minLogLikelihood=-0.8190 maximalDeformation=0.1803 minLogLikelihood=-0.8193 maximalDeformation=0.5480 minLogLikelihood=-0.8197 maximalDeformation=0.2110 minLogLikelihood=-0.8200 maximalDeformation=0.0000 minLogLikelihood=-0.8200 appliedScaling: 1.0396 maximalDeformation=1.0000 minLogLikelihood=-0.8619 maximalDeformation=0.3183 minLogLikelihood=-0.8635 maximalDeformation=0.1541 minLogLikelihood=-0.8640 maximalDeformation=0.1304 minLogLikelihood=-0.8641 maximalDeformation=0.0000 minLogLikelihood=-0.8641 appliedScaling: 1.0135 maximalDeformation=0.2422 minLogLikelihood=-0.8670 maximalDeformation=0.1273 minLogLikelihood=-0.8673 maximalDeformation=0.0000 minLogLikelihood=-0.8673 appliedScaling: 1.0029 writing template transform to /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg/template.lta writing talairach transform to /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg/samseg.talairach.lta atlas registration complete: 0:01:16.153826 [0.80000001 1. 1. ] Unknown Unknown (100%) Skull (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-Pallidum (100%) Right-Thalamus (50%) Left-Pallidum (100%) 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%) WM-hypointensities (100%) Left-Caudate (100%) Right-Thalamus (50%) Right-Caudate (100%) Left-Thalamus (50%) non-WM-hypointensities (100%) 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%) Soft Soft_Nonbrain_Tissue (100%) ==================== { depth: 1 maximumNumberOfDeformationIterations: 1 absoluteCostPerVoxelDecreaseStopCriterion: 0.01 verbose: False maximalDeformationStopCriterion: 0.01 lineSearchMaximalDeformationIntervalStopCriterion: 0.01 maximalDeformationAppliedStopCriterion: 0.0 BFGSMaximumMemoryLength: 12 multiResolutionSpecification: { depth: 2 atlasFileName: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz targetDownsampledVoxelSpacing: 2.0 maximumNumberOfIterations: 50 estimateBiasField: True }, { depth: 2 atlasFileName: /Applications/freesurfer/7.3.2/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz targetDownsampledVoxelSpacing: 1.0 maximumNumberOfIterations: 2 estimateBiasField: True } } ==================== iterationNumber: 0 EM converged! blockNumber 0 efficiency: 123.2635 % relative size: 22.4057 % setup time: 0.7393 sec blockNumber 1 efficiency: 128.7404 % relative size: 19.5106 % setup time: 0.3520 sec blockNumber 2 efficiency: 134.5473 % relative size: 19.8730 % setup time: 0.3560 sec blockNumber 3 efficiency: 124.3133 % relative size: 22.8241 % setup time: 0.3613 sec blockNumber 4 efficiency: 128.2308 % relative size: 21.4979 % setup time: 0.3611 sec blockNumber 5 efficiency: 130.3563 % relative size: 21.8640 % setup time: 0.3598 sec Total time spent: 0.0030 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.0000 ======================================================= iterationNumber: 1 EM converged! ProbabilisticAtlas reusing warm optimizers!! Total time spent: 0.0032 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.0000 ======================================================= iterationNumber: 2 EM converged! ProbabilisticAtlas reusing warm optimizers!! Total time spent: 0.0032 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.0000 ======================================================= iterationNumber: 0 EM converged! blockNumber 0 efficiency: 123.6818 % relative size: 20.0209 % setup time: 1.6803 sec blockNumber 1 efficiency: 119.2911 % relative size: 21.3268 % setup time: 0.8321 sec blockNumber 2 efficiency: 119.5228 % relative size: 21.1033 % setup time: 0.8133 sec blockNumber 3 efficiency: 124.9611 % relative size: 19.1179 % setup time: 0.7918 sec blockNumber 4 efficiency: 120.6353 % relative size: 19.6161 % setup time: 0.7893 sec blockNumber 5 efficiency: 121.6696 % relative size: 20.3414 % setup time: 0.7899 sec Total time spent: 0.0063 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.0000 ======================================================= iterationNumber: 1 EM converged! ProbabilisticAtlas reusing warm optimizers!! Total time spent: 0.0058 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.0000 ======================================================= using default intracranial structures to compute sbtiv measure Saving the template warp run_samseg complete: 0:03:51.969135 GCAMwrite run_samseg complete Thu May 18 14:12:48 EDT 2023 lta_convert --inlta /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg/samseg.talairach.lta --outmni /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg/samseg.talairach.xfm 7.3.2 --inlta: /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg/samseg.talairach.lta input LTA transform. --outmni: /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg/samseg.talairach.xfm output MNI/XFM matrix. LTA read, type : 1 1.00232 -0.00171 -0.01024 0.11147; 0.00062 1.02822 0.18915 -30.77016; 0.01145 -0.13297 1.10383 29.40451; 0.00000 -0.00000 -0.00000 1.00000; lta_convert successful. mri_segstats --ctab-default --seg /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg/seg.mgz --sum /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg/seg.stats Using defalt ctab /Applications/freesurfer/7.3.2/FreeSurferColorLUT.txt 7.3.2 cwd cmdline mri_segstats --ctab-default --seg /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg/seg.mgz --sum /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg/seg.stats sysname Darwin hostname doc-imac.anbg.mssm.edu machine x86_64 user clarklab whitesurfname white UseRobust 0 Loading /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg/seg.mgz Voxel Volume is 0.8 mm^3 Generating list of segmentation ids Found 1436 segmentations Computing statistics for each segmentation Reporting on 44 segmentations Using PrintSegStat mri_segstats done Started at Thu May 18 14:08:51 EDT 2023 Ended at Thu May 18 14:12:59 EDT 2023 Samseg-Run-Time-Min 4.13 Samseg-Run-Time-Hours 0.07 samseg Done mri_binarize --i /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg/seg.mgz --match 2 3 7 8 16 24 41 42 46 47 165 259 4 5 10 11 12 13 17 18 26 28 30 31 14 15 16 77 85 43 44 49 50 51 52 53 54 58 60 62 63 --o /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/seg.bin.dil.mgz --dilate 1 7.3.2 cwd /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files cmdline mri_binarize --i /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg/seg.mgz --match 2 3 7 8 16 24 41 42 46 47 165 259 4 5 10 11 12 13 17 18 26 28 30 31 14 15 16 77 85 43 44 49 50 51 52 53 54 58 60 62 63 --o /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/seg.bin.dil.mgz --dilate 1 sysname Darwin hostname doc-imac.anbg.mssm.edu machine x86_64 user clarklab input /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg/seg.mgz frame 0 nErode3d 0 nErode2d 0 output /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/seg.bin.dil.mgz Binarizing based on matching values nMatch 41 0 2 1 3 2 7 3 8 4 16 5 24 6 41 7 42 8 46 9 47 10 165 11 259 12 4 13 5 14 10 15 11 16 12 17 13 18 17 19 18 20 26 21 28 22 30 23 31 24 14 25 15 26 16 27 77 28 85 29 43 30 44 31 49 32 50 33 51 34 52 35 53 36 54 37 58 38 60 39 62 40 63 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 2536253 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 2902317 voxels in final mask Writing output to /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/seg.bin.dil.mgz Count: 2902317 2321853.634598 12582912 23.065543 mri_binarize done mri_concatenate_lta /Applications/freesurfer/7.3.2/average/mideface-atlas/reg.samseg-default.lta /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/samseg/template.lta /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/atlas2input.lta Read individual LTAs Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2... Writing combined LTA to file /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/atlas2input.lta... mri_concatenate_lta successful. lta_convert --subject defacing-atlas --invert --inlta /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/atlas2input.lta --outlta /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/input2atlas.lta 7.3.2 --s: defacing-atlas subject name --invert: will invert transform. --inlta: /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/atlas2input.lta input LTA transform. --outlta: /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/input2atlas.lta output LTA. LTA read, type : 1 0.95349 0.00561 0.01919 -1.26266; -0.00030 0.93510 -0.11943 32.21196; -0.02016 0.08128 0.82160 -16.58488; -0.00000 0.00000 -0.00000 1.00000; setting subject to defacing-atlas Writing LTA to file /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/input2atlas.lta... lta_convert successful. mris_apply_reg --lta /Applications/freesurfer/7.3.2/average/mideface-atlas/average.head.dec44.us7.remesh3.ripple.surf /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/atlas2input.lta /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/template.surf Reading in /Applications/freesurfer/7.3.2/average/mideface-atlas/average.head.dec44.us7.remesh3.ripple.surf Reading in /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/atlas2input.lta Changing type to REGISTER_DAT MRISltaMultiply(): applying matrix -0.95349 -0.01920 0.00561 2.65421; -0.02016 0.82160 -0.08128 -1.34135; 0.00030 0.11943 0.93510 -0.59179; -0.00000 -0.00000 -0.00000 1.00000; ----------------------------------- Determinant of linear transform is negative, so reversing face order Writing surf to /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/template.surf mris_apply_reg done mkheadsurf -i /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii -o /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.mgz -surf /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.surf -rescale -no-inflate -fill-holes-islands -mc -no-curv INFO: log file is /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/mkheadsurf.log -------------------------------- Thu May 18 14:13:06 EDT 2023 /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files mri_seghead --invol /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii --outvol /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.mgz --fill 1 --thresh1 20 --thresh2 20 --nhitsmin 2 --rescale --fill-holes-islands -------------------------------- input volume: /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii output volume: /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.mgz threshold1: 20 threshold2: 20 nhitsmin: 2 fill value: 1 Loading input volume Changing type, rescale = 1 MRIchangeType: Building histogram 0 892 1000, flo=0, fhi=255, dest_type=0 Filling Columns Filling Rows Filling Slices Merging nhits = 3193229 Removing islands MRIremoveVolumeIslands() thresh=0.5, nKeep=1, nclusters = 4314 Removing Volume Holes MRIremoveVolumeHoles() thresh=0.5, nKeep=1 MRIremoveVolumeIslands() thresh=0.5, nKeep=1, nclusters = 1 Filling axial Slice Holes ostr RAS slicedir 6 slicediruse 3 slicedim 192 256 1 MRIremoveSliceHodes() removed 35831 voxels Filling sag Slice Holes ostr RAS slicedir 4 slicediruse 1 slicedim 1 256 256 MRIremoveSliceHodes() removed 62817 voxels Filling cor Slice Holes slicedir 2 slicediruse 2 slicedim 192 1 256 MRIremoveSliceHodes() removed 60795 voxels Counting N Head Voxels = 3327616 N Back Voxels = 9255296 Avg. Back Intensity = 13.465048 Max. Back Intensity = 671.000000 Writing output Done -------------------------------- Thu May 18 14:13:35 EDT 2023 /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files mri_mc /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.mgz 1 /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.surf -------------------------------- preprocessing...done starting generation of surface... slice nb 10... slice nb 20... slice nb 30... slice nb 40... slice nb 50... slice nb 60... slice nb 70... slice nb 80... slice nb 90... slice nb 100... slice nb 110... slice nb 120... slice nb 130... slice nb 140... slice nb 150... slice nb 160... slice nb 170... slice nb 180... slice nb 190... slice nb 200... slice nb 210... slice nb 220... slice nb 230... constructing final surface... (surface with 907856 faces and 453256 vertices)...done computing the maximum edge length...1.414214 mm reversing orientation of faces... checking orientation of surface... 0.000 % of the vertices (0 vertices) exhibit an orientation change counting number of connected components... 453256 voxel in cpt #1: X=-672 [v=453256,e=1361784,f=907856] located at (4.588478, -9.686043, 9.754057) For the whole surface: X=-672 [v=453256,e=1361784,f=907856] One single component has been found nothing to do writing out surface...done -------------------------------- Thu May 18 14:13:42 EDT 2023 /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files mris_smooth -n 10 -nw /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.surf /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.surf -------------------------------- smoothing for 10 iterations smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... Started at: Thu May 18 14:13:06 EDT 2023 Ended at: Thu May 18 14:13:52 EDT 2023 mkheadsurf done mri_defacer --i /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii --ts /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/template.surf --min /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/min.surf --max /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/max.surf --m /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/face.mask.mgz --o /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_mideface_zeroes.nii --hm /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.mgz --distdat /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/dist.samples --stats /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/stats.dat --w /Applications/freesurfer/7.3.2/average/mideface-atlas/mideface.watermark.dec44.us7.remesh3.label 5 --l /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.lower.dec44.us7.remesh3.label --l /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.upper.no-eyes.no-nose.dec44.us7.remesh3.label --l /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.nose.dec44.us7.remesh3.label --l /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.eyes.dec44.us7.remesh3.label --l /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.ear.left.dec44.us7.remesh3.label 2 3 --l /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.ear.right.dec44.us7.remesh3.label 2 3 --xmask /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/seg.bin.dil.mgz 7.3.2 cd /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files mri_defacer --i /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii --ts /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/template.surf --min /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/min.surf --max /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/max.surf --m /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/face.mask.mgz --o /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_mideface_zeroes.nii --hm /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.mgz --distdat /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/dist.samples --stats /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/stats.dat --w /Applications/freesurfer/7.3.2/average/mideface-atlas/mideface.watermark.dec44.us7.remesh3.label 5 --l /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.lower.dec44.us7.remesh3.label --l /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.upper.no-eyes.no-nose.dec44.us7.remesh3.label --l /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.nose.dec44.us7.remesh3.label --l /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.eyes.dec44.us7.remesh3.label --l /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.ear.left.dec44.us7.remesh3.label 2 3 --l /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.ear.right.dec44.us7.remesh3.label 2 3 --xmask /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/seg.bin.dil.mgz sysname Darwin hostname doc-imac.anbg.mssm.edu machine x86_64 user clarklab Applying watermark d=5 Applying watermark 2207 DeltaDist = 0.266667, dL = 0.0888889 DistInMin 2 DistInMax 100 DistInFrac 0.9 DistOutMin 2 DistOutMax 100 DistOutFrac 1 DeltaDist 0.266667 dL 0.0888889 Pad 5 5 5 FillType 1 FillConstIn 0 FillConstOut 0 DoRipple 0 =============================================== Label 0 /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.lower.dec44.us7.remesh3.label 2 20 MiDeface::DistanceBounds() DeltaDist=0.266667 Raw DistIn = 20, DistOut = 2.13333 PostMinCheck DistIn = 20, DistOut = 2.13333 MiDeface::SegFace() =============================================== Label 1 /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.upper.no-eyes.no-nose.dec44.us7.remesh3.label 2 20 MiDeface::DistanceBounds() DeltaDist=0.266667 Raw DistIn = 20, DistOut = 5.86667 PostMinCheck DistIn = 20, DistOut = 5.86667 MiDeface::SegFace() =============================================== Label 2 /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.nose.dec44.us7.remesh3.label 2 20 MiDeface::DistanceBounds() DeltaDist=0.266667 Raw DistIn = 20, DistOut = 0 DistOut=0 < DistOutMin=2, resetting PostMinCheck DistIn = 20, DistOut = 2 MiDeface::SegFace() =============================================== Label 3 /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.eyes.dec44.us7.remesh3.label 2 20 MiDeface::DistanceBounds() DeltaDist=0.266667 Raw DistIn = 20, DistOut = 1.06667 DistOut=1.06667 < DistOutMin=2, resetting PostMinCheck DistIn = 20, DistOut = 2 MiDeface::SegFace() =============================================== Label 4 /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.ear.left.dec44.us7.remesh3.label 2 3 MiDeface::DistanceBounds() DeltaDist=0.266667 Raw DistIn = 3.2, DistOut = 0 DistOut=0 < DistOutMin=2, resetting PostMinCheck DistIn = 3.2, DistOut = 2 MiDeface::SegFace() =============================================== Label 5 /Applications/freesurfer/7.3.2/average/mideface-atlas/average.face.ear.right.dec44.us7.remesh3.label 2 3 MiDeface::DistanceBounds() DeltaDist=0.266667 Raw DistIn = 3.2, DistOut = 1.33333 DistOut=1.33333 < DistOutMin=2, resetting PostMinCheck DistIn = 3.2, DistOut = 2 MiDeface::SegFace() =============================================== MiDeface::FaceIntensityStats() Mode2 2 2 7650 nface1vox 39990 gmean 81.1021 gstddev 51.42 min 0 max 431 nface2vox 162059 gmean 30.2994 gstddev 22.0091 min 0 max 294 mode 2 gmeanratio 2.67669 40.5511 MiDeface::Deface() nface1vox 39990 gmean1 81.1021 gstddev1 51.42 min1 0 max1 431 nface2vox 162059 gmean2 30.2994 gstddev2 22.0091 mode2 2 min2 0 max2 294 gmeanratio 2.67669 40.5511 nxmask 110748 Embedding code mideface-freesurfer into output mri_defacer done mri_convert --ctab /Applications/freesurfer/7.3.2/average/mideface-atlas/deface.ctab /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/face.mask.mgz /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/face.mask.mgz mri_convert --ctab /Applications/freesurfer/7.3.2/average/mideface-atlas/deface.ctab /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/face.mask.mgz /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/face.mask.mgz reading from /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/face.mask.mgz... TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, -9.83477e-07, 9.83477e-07) j_ras = (9.83477e-07, 1, 2.98028e-08) k_ras = (-9.83477e-07, -2.98018e-08, 1) embedding color lookup table writing to /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/face.mask.mgz... mri_vol2surf --vol2surf /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/face.mask.mgz /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.surf 0 0 0 regheader novsm 0 /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/facemask-on-headsurf.mgz projtype 0, projdist 0, interp 0 mri_vol2surf --volsurf done mkheadsurf -i /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_mideface_zeroes.nii -o /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.defaced.mgz -surf /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.defaced.surf -rescale -no-inflate -fill-holes-islands -mc -no-curv INFO: log file is /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/mkheadsurf.log -------------------------------- Thu May 18 14:14:27 EDT 2023 /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files mri_seghead --invol /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_mideface_zeroes.nii --outvol /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.defaced.mgz --fill 1 --thresh1 20 --thresh2 20 --nhitsmin 2 --rescale --fill-holes-islands -------------------------------- input volume: /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_mideface_zeroes.nii output volume: /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.defaced.mgz threshold1: 20 threshold2: 20 nhitsmin: 2 fill value: 1 Loading input volume Changing type, rescale = 1 MRIchangeType: Building histogram 0 892 1000, flo=0, fhi=255, dest_type=0 Filling Columns Filling Rows Filling Slices Merging nhits = 3710987 Removing islands MRIremoveVolumeIslands() thresh=0.5, nKeep=1, nclusters = 3234 Removing Volume Holes MRIremoveVolumeHoles() thresh=0.5, nKeep=1 MRIremoveVolumeIslands() thresh=0.5, nKeep=1, nclusters = 1 Filling axial Slice Holes ostr RAS slicedir 6 slicediruse 3 slicedim 192 256 1 MRIremoveSliceHodes() removed 79325 voxels Filling sag Slice Holes ostr RAS slicedir 4 slicediruse 1 slicedim 1 256 256 MRIremoveSliceHodes() removed 77838 voxels Filling cor Slice Holes slicedir 2 slicediruse 2 slicedim 192 1 256 MRIremoveSliceHodes() removed 52972 voxels Counting N Head Voxels = 3905452 N Back Voxels = 8677460 Avg. Back Intensity = 12.008756 Max. Back Intensity = 671.000000 Writing output Done -------------------------------- Thu May 18 14:14:54 EDT 2023 /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files mri_mc /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.defaced.mgz 1 /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.defaced.surf -------------------------------- preprocessing...done starting generation of surface... slice nb 10... slice nb 20... slice nb 30... slice nb 40... slice nb 50... slice nb 60... slice nb 70... slice nb 80... slice nb 90... slice nb 100... slice nb 110... slice nb 120... slice nb 130... slice nb 140... slice nb 150... slice nb 160... slice nb 170... slice nb 180... slice nb 190... slice nb 200... slice nb 210... slice nb 220... slice nb 230... constructing final surface... (surface with 929588 faces and 464168 vertices)...done computing the maximum edge length...1.414214 mm reversing orientation of faces... checking orientation of surface... 0.000 % of the vertices (0 vertices) exhibit an orientation change counting number of connected components... 464168 voxel in cpt #1: X=-626 [v=464168,e=1394382,f=929588] located at (0.635410, -14.677386, 5.592774) For the whole surface: X=-626 [v=464168,e=1394382,f=929588] One single component has been found nothing to do writing out surface...done -------------------------------- Thu May 18 14:15:01 EDT 2023 /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files mris_smooth -n 10 -nw /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.defaced.surf /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.defaced.surf -------------------------------- smoothing for 10 iterations smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... Started at: Thu May 18 14:14:27 EDT 2023 Ended at: Thu May 18 14:15:12 EDT 2023 mkheadsurf done freeview -f /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.surf:affinexfm=/Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/input2atlas.lta --hide-3d-slices -viewport 3d -cam Azimuth -90 -ss /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/HP20008.face-before.png --quit this pid 93908 setting display to 50 [1] 93920 pid 93920 Starting command freeview -f /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.surf:affinexfm=/Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/input2atlas.lta --hide-3d-slices -viewport 3d -cam Azimuth -90 -ss /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/HP20008.face-before.png --quit Reading surf xfm LTA /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/input2atlas.lta Changing type to REGISTER_DAT MRISltaMultiply(): applying matrix -1.04824 -0.02509 0.00411 2.75105; -0.02537 1.20135 0.10457 1.74064; 0.00357 -0.15343 1.05605 0.40968; -0.00000 -0.00000 0.00000 1.00000; ----------------------------------- ----------------------------------- 00; NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/input2atlas.lta Determinant of linear transform is negative, so reversing face order Determinant of linear transform is negative, so reversing face order 008/nii_files/qa/input2atlas.lta Program exited normally freeview -f /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.defaced.surf:affinexfm=/Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/input2atlas.lta --hide-3d-slices -viewport 3d -cam Azimuth -90 -ss /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/HP20008.face-after.png --quit this pid 93931 setting display to 50 [1] 93943 pid 93943 Starting command freeview -f /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.defaced.surf:affinexfm=/Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/input2atlas.lta --hide-3d-slices -viewport 3d -cam Azimuth -90 -ss /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/HP20008.face-after.png --quit Reading surf xfm LTA /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/input2atlas.lta Changing type to REGISTER_DAT MRISltaMultiply(): applying matrix -1.04824 -0.02509 0.00411 2.75105; -0.02537 1.20135 0.10457 1.74064; 0.00357 -0.15343 1.05605 0.40968; -0.00000 -0.00000 0.00000 1.00000; ----------------------------------- ----------------------------------- 00; NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/input2atlas.lta Determinant of linear transform is negative, so reversing face order Determinant of linear transform is negative, so reversing face order 008/nii_files/qa/input2atlas.lta Program exited normally [1] + Done Xvfb :50 fsvglrun freeview /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_SPACE.nii /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/T2_mideface_zeroes.nii --hide-3d-slices -viewport 3d -f /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.surf:edgecolor=yellow -f /Volumes/Clark_Lab_NAS/HP2/HP2_all_MRI_data/HP20008/nii_files/qa/head.defaced.surf:edgecolor=red:visible=0 Started at Thu May 18 14:08:50 EDT 2023 Ended at Thu May 18 14:15:31 EDT 2023 Midefacer-Run-Time-Sec 401 Midefacer-Run-Time-Min 8.02 Midefacer-Run-Time-Hours 0.11 midefacer Done ======================= HP20008 Thu May 18 14:15:31 EDT 2023 Completed MiDeFace *************************************************** doc-imac:HP2 clarklab$