External Email - Use Caution
Patrick,
I notice that you are running this on Frontera at TACC. I believe
that TACC uses the Intel compilers as their default. I would guess
that FreeSurfer is compiled with GCC, not Intel.
You might try unloading the Intel compilers and loading the GCC
compiler module instead.
You might also want to send something to the mailing list for support
at TACC (used to be XSEDE, but its name changed last year, I think).
For a segfault like this, the system administrators are probably best
positioned to answer. If you can give them instructions for running
it themselves, that is the best situation.
I hope this make sense and is of some help.
On Thu, May 18, 2023 at 3:26 PM Patrick Sadil <psad...@jh.edu> wrote:
>
> External Email - Use Caution
>
> Thanks for the responses!
>
> Yes -- the same input volume will sometimes succeed and sometimes fail
> depending upon the platform.
>
> Here is an example of the mri_info for one such volume
>
> $ mri_info volume.nii.gz
> niiRead(): detected input as 64 bit double, reading in as 32 bit float
> Volume information for volume.nii.gz
> type: nii
> dimensions: 193 x 229 x 193
> voxel sizes: 1.000000, 1.000000, 1.000000
> type: FLOAT (3)
> fov: 193.000
> dof: 1
> xstart: -96.5, xend: 96.5
> ystart: -114.5, yend: 114.5
> zstart: -96.5, zend: 96.5
> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
> degrees
> nframes: 1
> PhEncDir: UNKNOWN
> FieldStrength: 0.000000
> ras xform present
> xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r =
> -0.5000
> : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a =
> -18.5000
> : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s =
> 18.5000
> Orientation : LPS
> Primary Slice Direction: axial
>
> voxel to ras transform:
> -1.0000 0.0000 0.0000 96.0000
> 0.0000 -1.0000 0.0000 96.0000
> 0.0000 0.0000 1.0000 -78.0000
> 0.0000 0.0000 0.0000 1.0000
>
> voxel-to-ras determinant 1
>
> ras to voxel transform:
> -1.0000 0.0000 0.0000 96.0000
> 0.0000 -1.0000 0.0000 96.0000
> 0.0000 0.0000 1.0000 78.0000
> 0.0000 0.0000 0.0000 1.0000
>
>
> Thanks for the information about memory swapping. Here's a log of the memory
> usage as reported by `free` every 5 seconds during a failing run on the HPC
> (FS 7.3.2, no containers)
>
> date time total used free shared
> buff/cache available
> 2023-05-17 17:32:04 191515 4753 186381 10
> 379 184648
> 2023-05-17 17:32:09 191515 4760 186369 10
> 385 184638
> 2023-05-17 17:32:14 191515 4774 186346 10
> 393 184620
> 2023-05-17 17:32:19 191515 4779 186334 10
> 401 184612
> 2023-05-17 17:32:24 191515 4792 186311 10
> 411 184593
> 2023-05-17 17:32:29 191515 5251 185817 10
> 446 184117
> 2023-05-17 17:32:34 191515 5250 185817 10
> 447 184117
> 2023-05-17 17:32:39 191515 5253 185814 10
> 447 184114
> 2023-05-17 17:32:44 191515 5254 185813 10
> 447 184113
> 2023-05-17 17:32:50 191515 5180 185887 10
> 447 184188
> 2023-05-17 17:32:55 191515 5179 185888 10
> 447 184189
> 2023-05-17 17:33:00 191515 5178 185889 10
> 447 184189
> 2023-05-17 17:33:05 191515 5180 185887 10
> 447 184188
> 2023-05-17 17:33:10 191515 5180 185887 10
> 447 184187
> 2023-05-17 17:33:15 191515 5181 185886 10
> 447 184187
> 2023-05-17 17:33:20 191515 5180 185887 10
> 447 184188
> 2023-05-17 17:33:25 191515 5179 185888 10
> 447 184188
> 2023-05-17 17:33:30 191515 5180 185886 10
> 447 184187
> 2023-05-17 17:33:35 191515 5181 185886 10
> 447 184187
> 2023-05-17 17:33:40 191515 5180 185887 10
> 447 184187
> 2023-05-17 17:33:45 191515 5181 185886 10
> 447 184186
> 2023-05-17 17:33:50 191515 5181 185886 10
> 447 184186
> 2023-05-17 17:33:55 191515 5181 185886 10
> 447 184186
> 2023-05-17 17:34:00 191515 5136 185925 10
> 453 184229
> 2023-05-17 17:34:05 191515 5157 185875 10
> 482 184193
> 2023-05-17 17:34:10 191515 5411 185621 10
> 482 183939
> 2023-05-17 17:34:15 191515 5344 185676 10
> 494 184001
> 2023-05-17 17:34:20 191515 5348 185667 10
> 498 183994
>
> I think this indicates that the system should has plenty of memory.
>
> FWIW, here is the terminal output produced during the logged run (error is
> always at the same place)
>
> $ mideface --i volume.nii.gz --o defaced.nii.gz
> Wed May 17 17:31:59 CDT 2023
>
> setenv SUBJECTS_DIR /work2/08266/psadil/freesurfer/subjects
> cd /[...redacted...]/jobs/release
> /work2/08266/psadil/freesurfer/bin/mideface --i volume.nii.gz --o
> defaced.nii.gz
> -rwx------ 1 psadil G-821866 27366 Aug 3 2022
> /work2/08266/psadil/freesurfer/bin/mideface
>
> freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275
> $Id$
> Linux c103-211.frontera.tacc.utexas.edu 3.10.0-1160.45.1.el7.x86_64 #1 SMP
> Wed Oct 13 17:20:51 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
> pid 205539
> UseXvfb 1
> samseg --i /[...redacted...]/jobs/release/volume.nii.gz --o
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg --threads 1
> --block-coordinate-descent --options
> /work2/08266/psadil/freesurfer/average/mideface-atlas/samseg-options.json
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg
> /[...redacted...]/jobs/release
> /[...redacted...]/jobs/release
> Wed May 17 17:32:00 CDT 2023
>
> setenv SUBJECTS_DIR /work2/08266/psadil/freesurfer/subjects
> cd /[...redacted...]/jobs/release
> /work2/08266/psadil/freesurfer/bin/samseg --i
> /[...redacted...]/jobs/release/volume.nii.gz --o
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg --threads 1
> --block-coordinate-descent --options
> /work2/08266/psadil/freesurfer/average/mideface-atlas/samseg-options.json
>
> freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275
> samseg 7.3.2
> Linux c103-211.frontera.tacc.utexas.edu 3.10.0-1160.45.1.el7.x86_64 #1 SMP
> Wed Oct 13 17:20:51 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
> Using Block Coordinate Descent
> fs_time run_samseg -o
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg --threads 1
> --save-warp --options
> /work2/08266/psadil/freesurfer/average/mideface-atlas/samseg-options.json -i
> /[...redacted...]/jobs/release/volume.nii.gz
> Constructing image-to-world transform from header information
> (/[...redacted...]/jobs/release/volume.nii.gz)
> Read image: /[...redacted...]/jobs/release/volume.nii.gz
> Constructing image-to-world transform from header information
> (/work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii)
> Read image:
> /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii
> Read mesh collection:
> /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz
> Transforming points
> Transforming points
> AFFINE
> min: -48.627
> max: 1250.65
> robustMin: -1.51633
> robustMax: 1096.98
> histogram[ 0 ]: 1
> histogram[ 1 ]: 0
> histogram[ 2 ]: 0
> histogram[ 3997 ]: 0
> histogram[ 3998 ]: 0
> histogram[ 3999 ]: 1
> cumulativeHistogram[ 0 ]: 3.07385e-06
> cumulativeHistogram[ 1 ]: 3.07385e-06
> cumulativeHistogram[ 2 ]: 3.07385e-06
> cumulativeHistogram[ 3997 ]: 0.999997
> cumulativeHistogram[ 3998 ]: 0.999997
> cumulativeHistogram[ 3999 ]: 1
> AFFINE
> min: -48.627
> max: 1250.65
> robustMin: -1.51633
> robustMax: 1096.98
> histogram[ 0 ]: 1
> histogram[ 1 ]: 0
> histogram[ 2 ]: 0
> histogram[ 3997 ]: 0
> histogram[ 3998 ]: 0
> histogram[ 3999 ]: 1
> cumulativeHistogram[ 0 ]: 3.07385e-06
> cumulativeHistogram[ 1 ]: 3.07385e-06
> cumulativeHistogram[ 2 ]: 3.07385e-06
> cumulativeHistogram[ 3997 ]: 0.999997
> cumulativeHistogram[ 3998 ]: 0.999997
> cumulativeHistogram[ 3999 ]: 1
> Read mesh collection:
> /work2/08266/psadil/freesurfer/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: -48.627
> max: 1250.65
> robustMin: -1.51633
> robustMax: 1096.98
> histogram[ 0 ]: 1
> histogram[ 1 ]: 0
> histogram[ 2 ]: 0
> histogram[ 3997 ]: 0
> histogram[ 3998 ]: 0
> histogram[ 3999 ]: 1
> cumulativeHistogram[ 0 ]: 3.07385e-06
> cumulativeHistogram[ 1 ]: 3.07385e-06
> cumulativeHistogram[ 2 ]: 3.07385e-06
> cumulativeHistogram[ 3997 ]: 0.999997
> cumulativeHistogram[ 3998 ]: 0.999997
> cumulativeHistogram[ 3999 ]: 1
> Read mesh collection:
> /work2/08266/psadil/freesurfer/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: -48.627
> max: 1250.65
> robustMin: -1.51633
> robustMax: 1096.98
> histogram[ 0 ]: 1
> histogram[ 1 ]: 0
> histogram[ 2 ]: 0
> histogram[ 3997 ]: 0
> histogram[ 3998 ]: 0
> histogram[ 3999 ]: 1
> cumulativeHistogram[ 0 ]: 3.07385e-06
> cumulativeHistogram[ 1 ]: 3.07385e-06
> cumulativeHistogram[ 2 ]: 3.07385e-06
> cumulativeHistogram[ 3997 ]: 0.999997
> cumulativeHistogram[ 3998 ]: 0.999997
> cumulativeHistogram[ 3999 ]: 1
> Read mesh collection:
> /work2/08266/psadil/freesurfer/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: -48.627
> max: 1250.65
> robustMin: -1.51633
> robustMax: 1096.98
> histogram[ 0 ]: 1
> histogram[ 1 ]: 0
> histogram[ 2 ]: 0
> histogram[ 3997 ]: 0
> histogram[ 3998 ]: 0
> histogram[ 3999 ]: 1
> cumulativeHistogram[ 0 ]: 3.07385e-06
> cumulativeHistogram[ 1 ]: 3.07385e-06
> cumulativeHistogram[ 2 ]: 3.07385e-06
> cumulativeHistogram[ 3997 ]: 0.999997
> cumulativeHistogram[ 3998 ]: 0.999997
> cumulativeHistogram[ 3999 ]: 1
> Constructing image-to-world transform from header information
> (/[...redacted...]/jobs/release/volume.nii.gz)
> Read image: /[...redacted...]/jobs/release/volume.nii.gz
> Read mesh collection:
> /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
> Transforming points
> Transforming points
> ##----------------------------------------------
> Samsegment Options
> ##----------------------------------------------
> output directory:
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg
> input images: /[...redacted...]/jobs/release/volume.nii.gz
> 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':
> '/work2/08266/psadil/freesurfer/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, 22
0, 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':
> '/work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz',
> 'targetDownsampledVoxelSpacing': 2.0, 'maximumNumberOfIterations': 50,
> 'estimateBiasField': True}, {'atlasFileName':
> '/work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz',
> 'targetDownsampledVoxelSpacing': 1.0, 'maximumNumberOfIterations': 2,
> 'estimateBiasField': True}]}
> performing affine atlas registration
> image: /[...redacted...]/jobs/release/volume.nii.gz
> template:
> /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii
> maximalDeformation=1.0000 minLogLikelihood=-0.7440
> maximalDeformation=1.0371 minLogLikelihood=-0.7600
> maximalDeformation=0.8439 minLogLikelihood=-0.7668
> maximalDeformation=8.9885 minLogLikelihood=-0.8230
> maximalDeformation=2.1805 minLogLikelihood=-0.8250
> maximalDeformation=1.8946 minLogLikelihood=-0.8368
> maximalDeformation=3.3974 minLogLikelihood=-0.8455
> maximalDeformation=0.0787 minLogLikelihood=-0.8459
> maximalDeformation=0.0193 minLogLikelihood=-0.8459
> maximalDeformation=0.0000 minLogLikelihood=-0.8459
> appliedScaling: 1.0158
> maximalDeformation=1.0000 minLogLikelihood=-0.8630
> maximalDeformation=0.2734 minLogLikelihood=-0.8636
> maximalDeformation=0.2836 minLogLikelihood=-0.8638
> maximalDeformation=0.1536 minLogLikelihood=-0.8640
> maximalDeformation=0.5760 minLogLikelihood=-0.8641
> maximalDeformation=0.3851 minLogLikelihood=-0.8642
> maximalDeformation=0.0000 minLogLikelihood=-0.8642
> appliedScaling: 1.0047
> maximalDeformation=1.0000 minLogLikelihood=-0.8699
> maximalDeformation=0.0000 minLogLikelihood=-0.8699
> appliedScaling: 1.0017
> writing template transform to
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/template.lta
> writing talairach transform to
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/samseg.talairach.lta
> atlas registration complete: 0:01:34.254165
> [1. 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%)
> ====================
> Read mesh collection:
> /work2/08266/psadil/freesurfer/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:
> /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
> Transforming points
> Transforming points
> Read mesh collection:
> /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz
> Read mesh collection:
> /work2/08266/psadil/freesurfer/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:
> /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
> Transforming points
> Transforming points
> Read mesh collection:
> /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
> Read mesh collection:
> /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
> Constructing image-to-world transform from header information
> (/[...redacted...]/jobs/release/volume.nii.gz)
> Read image: /[...redacted...]/jobs/release/volume.nii.gz
> Read mesh collection:
> /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
> Transforming points
> Transforming points
> Read mesh collection:
> /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
> Read mesh collection:
> /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
> niiRead(): detected input as 64 bit double, reading in as 32 bit float
> Read mesh collection:
> /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
> {
> depth: 1
> maximumNumberOfDeformationIterations: 1
> absoluteCostPerVoxelDecreaseStopCriterion: 0.01
> verbose: False
> maximalDeformationStopCriterion: 0.01
> lineSearchMaximalDeformationIntervalStopCriterion: 0.01
> maximalDeformationAppliedStopCriterion: 0.0
> BFGSMaximumMemoryLength: 12
> multiResolutionSpecification: {
> depth: 2
> atlasFileName:
> /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz
> targetDownsampledVoxelSpacing: 2.0
> maximumNumberOfIterations: 50
> estimateBiasField: True
> }, {
> depth: 2
> atlasFileName:
> /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
> targetDownsampledVoxelSpacing: 1.0
> maximumNumberOfIterations: 2
> estimateBiasField: True
> }
> }
> ====================
> iterationNumber: 0
> EM converged!
> blockNumber 0
> efficiency: 127.8986 %
> relative size: 19.7796 %
> setup time: 0.6695 sec
> blockNumber 1
> efficiency: 129.5280 %
> relative size: 20.8106 %
> setup time: 0.4791 sec
> blockNumber 2
> efficiency: 124.7648 %
> relative size: 23.2798 %
> setup time: 0.4969 sec
> blockNumber 3
> efficiency: 127.9526 %
> relative size: 20.9638 %
> setup time: 0.4770 sec
> blockNumber 4
> efficiency: 124.4211 %
> relative size: 23.4852 %
> setup time: 0.4918 sec
> blockNumber 5
> efficiency: 127.3941 %
> relative size: 18.5357 %
> setup time: 0.4698 sec
> Total time spent: 0.0033 sec
> maximalDeformation=0.0000
> maximalDeformationApplied: 0.0000
> =======================================================
> iterationNumber: 1
> EM converged!
> ProbabilisticAtlas reusing warm optimizers!!
> Total time spent: 0.0034 sec
> maximalDeformation=0.0000
> maximalDeformationApplied: 0.0000
> =======================================================
> iterationNumber: 2
> EM converged!
> ProbabilisticAtlas reusing warm optimizers!!
> Total time spent: 0.0034 sec
> maximalDeformation=0.0000
> maximalDeformationApplied: 0.0000
> =======================================================
> iterationNumber: 0
> EM converged!
> blockNumber 0
> efficiency: 118.7363 %
> relative size: 20.8927 %
> setup time: 1.6169 sec
> blockNumber 1
> efficiency: 121.0767 %
> relative size: 20.8433 %
> setup time: 1.0427 sec
> blockNumber 2
> efficiency: 123.9971 %
> relative size: 18.9659 %
> setup time: 1.0240 sec
> blockNumber 3
> efficiency: 118.9662 %
> relative size: 20.6564 %
> setup time: 1.0509 sec
> blockNumber 4
> efficiency: 117.7030 %
> relative size: 19.9348 %
> setup time: 1.0399 sec
> blockNumber 5
> efficiency: 122.6568 %
> relative size: 19.1271 %
> setup time: 1.0273 sec
> Total time spent: 0.0124 sec
> maximalDeformation=0.0000
> maximalDeformationApplied: 0.0000
> =======================================================
> iterationNumber: 1
> EM converged!
> ProbabilisticAtlas reusing warm optimizers!!
> Total time spent: 0.0089 sec
> maximalDeformation=0.0000
> maximalDeformationApplied: 0.0000
> =======================================================
> using default intracranial structures to compute sbtiv measure
> Saving the template warp
> run_samseg complete: 0:04:08.072359
> GCAMwrite
> @#@FSTIME 2023:05:17:17:32:00 run_samseg N 9 e 276.60 S 6.87 U 226.42 P 84%
> M 5448744 F 4116 R 1612330 W 0 c 42 w 14636 I 267688 O 323136 L 0.01 1.32 2.98
> @#@FSLOADPOST 2023:05:17:17:36:36 run_samseg N 9 0.96 1.06 2.44
> run_samseg complete
> Wed May 17 17:36:36 CDT 2023
> lta_convert --inlta
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/samseg.talairach.lta
> --outmni
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/samseg.talairach.xfm
> 7.3.2
>
> --inlta:
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/samseg.talairach.lta
> input LTA transform.
> --outmni:
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/samseg.talairach.xfm
> output MNI/XFM matrix.
> LTA read, type : 1
> 1.02236 0.01245 0.12949 0.58992;
> -0.00437 1.08080 -0.00870 2.62878;
> -0.15613 0.06510 1.14175 12.21557;
> 0.00000 0.00000 0.00000 1.00000;
> lta_convert successful.
> mri_segstats --ctab-default --seg
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz --sum
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.stats
> Using defalt ctab /work2/08266/psadil/freesurfer/FreeSurferColorLUT.txt
>
> 7.3.2
> cwd
> cmdline mri_segstats --ctab-default --seg
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz --sum
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.stats
> sysname Linux
> hostname c103-211.frontera.tacc.utexas.edu
> machine x86_64
> user psadil
> whitesurfname white
> UseRobust 0
> Loading /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz
> Voxel Volume is 1 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 Wed May 17 17:31:59 CDT 2023
> Ended at Wed May 17 17:36:40 CDT 2023
> Samseg-Run-Time-Min 4.68
> Samseg-Run-Time-Hours 0.08
>
> samseg Done
> @#@FSTIME 2023:05:17:17:31:59 samseg N 9 e 280.79 S 6.97 U 230.29 P 84% M
> 5448744 F 4122 R 1647009 W 0 c 108 w 15165 I 283968 O 323472 L 0.01 1.32 2.98
> @#@FSLOADPOST 2023:05:17:17:36:40 samseg N 9 0.96 1.06 2.43
> mri_binarize --i
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/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
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg.bin.dil.mgz
> --dilate 1
>
> 7.3.2
> cwd /[...redacted...]/jobs/release
> cmdline mri_binarize --i
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/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
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg.bin.dil.mgz
> --dilate 1
> sysname Linux
> hostname c103-211.frontera.tacc.utexas.edu
> machine x86_64
> user psadil
>
> input
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz
> frame 0
> nErode3d 0
> nErode2d 0
> output
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/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
> Starting parallel 1
> Found 1843081 values in range
> Dilating 1 voxels in 3d
> Counting number of voxels in first frame
> Found 2059752 voxels in final mask
> Writing output to
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg.bin.dil.mgz
> Count: 2059752 2059752.000000 8530021 24.147092
> mri_binarize done
> mri_concatenate_lta
> /work2/08266/psadil/freesurfer/average/mideface-atlas/reg.samseg-default.lta
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/template.lta
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/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
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input.lta...
> mri_concatenate_lta successful.
> lta_convert --subject defacing-atlas --invert --inlta
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input.lta
> --outlta
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/input2atlas.lta
> 7.3.2
>
> --s: defacing-atlas subject name
> --invert: will invert transform.
> --inlta:
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input.lta input
> LTA transform.
> --outlta:
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/input2atlas.lta output
> LTA.
> LTA read, type : 1
> 0.92032 0.00244 -0.09021 -0.96096;
> 0.00139 0.90319 0.03621 -3.20219;
> 0.11587 -0.08143 0.79401 -4.69215;
> -0.00000 -0.00000 -0.00000 1.00000;
> setting subject to defacing-atlas
> Writing LTA to file
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/input2atlas.lta...
> lta_convert successful.
> mris_apply_reg --lta
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.head.dec44.us7.remesh3.ripple.surf
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input.lta
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/template.surf
> Reading in
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.head.dec44.us7.remesh3.ripple.surf
> Reading in
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input.lta
> Changing type to REGISTER_DAT
> MRISltaMultiply(): applying matrix
> 0.92032 -0.09021 -0.00244 1.39829;
> 0.11587 0.79401 0.08143 -47.35222;
> 0.00139 0.03621 -0.90319 7.85163;
> -0.00000 -0.00000 0.00000 1.00000;
> -----------------------------------
> Determinant of linear transform is negative, so reversing face order
> Writing surf to
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/template.surf
> mris_apply_reg done
> mkheadsurf -i /[...redacted...]/jobs/release/volume.nii.gz -o
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.mgz -surf
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.surf -rescale
> -no-inflate -fill-holes-islands -mc -no-curv
> INFO: log file is
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/mkheadsurf.log
> --------------------------------
> Wed May 17 17:36:46 CDT 2023
> /[...redacted...]/jobs/release
> mri_seghead --invol /[...redacted...]/jobs/release/volume.nii.gz --outvol
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.mgz --fill 1
> --thresh1 20 --thresh2 20 --nhitsmin 2 --rescale --fill-holes-islands
> --------------------------------
> input volume: /[...redacted...]/jobs/release/volume.nii.gz
> output volume: /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.mgz
> threshold1: 20
> threshold2: 20
> nhitsmin: 2
> fill value: 1
> Loading input volume
> niiRead(): detected input as 64 bit double, reading in as 32 bit float
> Changing type, rescale = 1
> MRIchangeType: Building histogram -68.7235 1307.2 1000, flo=0, fhi=255,
> dest_type=0
> Filling Columns
> Filling Rows
> Filling Slices
> Merging
> nhits = 2945860
> Removing islands
> MRIremoveVolumeIslands() thresh=0.5, nKeep=1, nclusters = 687
> Removing Volume Holes
> MRIremoveVolumeHoles() thresh=0.5, nKeep=1
> MRIremoveVolumeIslands() thresh=0.5, nKeep=1, nclusters = 1
> Filling axial Slice Holes
> ostr LPS
> slicedir 6 slicediruse 3
> slicedim 193 229 1
> MRIremoveSliceHodes() removed 16112 voxels
> Filling sag Slice Holes
> ostr LPS
> slicedir 4 slicediruse 1
> slicedim 1 229 193
> MRIremoveSliceHodes() removed 2775 voxels
> Filling cor Slice Holes
> slicedir 2 slicediruse 2
> slicedim 193 1 193
> MRIremoveSliceHodes() removed 822 voxels
> Counting
> N Head Voxels = 2964151
> N Back Voxels = 5565870
> Avg. Back Intensity = 13.248070
> Max. Back Intensity = 1151.476440
> Writing output
> Done
> --------------------------------
> Wed May 17 17:36:58 CDT 2023
> /[...redacted...]/jobs/release
> mri_mc /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.mgz 1
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/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...
> constructing final surface...
> (surface with 354632 faces and 177302 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...
> 177302 voxel in cpt #1: X=-14 [v=177302,e=531948,f=354632] located at
> (2.291599, -29.413504, -3.787194)
> For the whole surface: X=-14 [v=177302,e=531948,f=354632]
> One single component has been found
> nothing to do
> writing out surface...done
> --------------------------------
> Wed May 17 17:37:01 CDT 2023
> /[...redacted...]/jobs/release
> mris_smooth -n 10 -nw
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.surf
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.surf
> --------------------------------
> smoothing for 10 iterations
> smoothing surface tessellation for 10 iterations...
> smoothing complete - recomputing first and second fundamental forms...
>
> Started at: Wed May 17 17:36:46 CDT 2023
> Ended at: Wed May 17 17:37:05 CDT 2023
> mkheadsurf done
> @#@FSTIME 2023:05:17:17:36:46 mkheadsurf N 11 e 18.35 S 0.59 U 17.37 P 97% M
> 434560 F 3 R 278026 W 0 c 49 w 584 I 21736 O 25328 L 0.97 1.06 2.42
> @#@FSLOADPOST 2023:05:17:17:37:05 mkheadsurf N 11 0.97 1.05 2.39
> mri_defacer --i /[...redacted...]/jobs/release/volume.nii.gz --ts
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/template.surf --min
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/min.surf --max
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/max.surf --m
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/face.mask.mgz --o
> /[...redacted...]/jobs/release/defaced.nii.gz --hm
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.mgz --distdat
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/dist.samples --stats
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/stats.dat --w
> /work2/08266/psadil/freesurfer/average/mideface-atlas/mideface.watermark.dec44.us7.remesh3.label
> 5 --l
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.lower.dec44.us7.remesh3.label
> --l
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.upper.no-eyes.no-nose.dec44.us7.remesh3.label
> --l
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.nose.dec44.us7.remesh3.label
> --l
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.eyes.dec44.us7.remesh3.label
> --l
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.left.dec44.us7.remesh3.label
> 2 3 --l
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.right.dec44.us7.remesh3.label
> 2 3 --xmask
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg.bin.dil.mgz
>
> 7.3.2
> cd /[...redacted...]/jobs/release
> mri_defacer --i /[...redacted...]/jobs/release/volume.nii.gz --ts
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/template.surf --min
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/min.surf --max
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/max.surf --m
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/face.mask.mgz --o
> /[...redacted...]/jobs/release/defaced.nii.gz --hm
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.mgz --distdat
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/dist.samples --stats
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/stats.dat --w
> /work2/08266/psadil/freesurfer/average/mideface-atlas/mideface.watermark.dec44.us7.remesh3.label
> 5 --l
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.lower.dec44.us7.remesh3.label
> --l
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.upper.no-eyes.no-nose.dec44.us7.remesh3.label
> --l
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.nose.dec44.us7.remesh3.label
> --l
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.eyes.dec44.us7.remesh3.label
> --l
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.left.dec44.us7.remesh3.label
> 2 3 --l
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.right.dec44.us7.remesh3.label
> 2 3 --xmask
> /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg.bin.dil.mgz
> sysname Linux
> hostname c103-211.frontera.tacc.utexas.edu
> machine x86_64
> user psadil
> niiRead(): detected input as 64 bit double, reading in as 32 bit float
> Applying watermark d=5
> Applying watermark 2207
> DeltaDist = 0.333333, dL = 0.111111
> DistInMin 2
> DistInMax 100
> DistInFrac 0.9
> DistOutMin 2
> DistOutMax 100
> DistOutFrac 1
> DeltaDist 0.333333
> dL 0.111111
> Pad 5 5 5
> FillType 1
> FillConstIn 0
> FillConstOut 0
> DoRipple 0
>
> ===============================================
> Label 0
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.lower.dec44.us7.remesh3.label
> 2 20
> MiDeface::DistanceBounds() DeltaDist=0.333333
> Raw DistIn = 0, DistOut = 0
> DistIn=0 < DistInMin=2, resetting
> DistOut=0 < DistOutMin=2, resetting
> PostMinCheck DistIn = 2, DistOut = 2
>
> MiDeface::SegFace()
> ===============================================
> Label 1
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.upper.no-eyes.no-nose.dec44.us7.remesh3.label
> 2 20
> MiDeface::DistanceBounds() DeltaDist=0.333333
> Raw DistIn = 1, DistOut = 9.33333
> DistIn=1 < DistInMin=2, resetting
> PostMinCheck DistIn = 2, DistOut = 9.33333
>
> MiDeface::SegFace()
> ===============================================
> Label 2
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.nose.dec44.us7.remesh3.label
> 2 20
> MiDeface::DistanceBounds() DeltaDist=0.333333
> Raw DistIn = 2.66667, DistOut = 2.66667
> PostMinCheck DistIn = 2.66667, DistOut = 2.66667
>
> MiDeface::SegFace()
> ===============================================
> Label 3
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.eyes.dec44.us7.remesh3.label
> 2 20
> MiDeface::DistanceBounds() DeltaDist=0.333333
> Raw DistIn = 7, DistOut = 6.66667
> PostMinCheck DistIn = 7, DistOut = 6.66667
>
> MiDeface::SegFace()
> ===============================================
> Label 4
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.left.dec44.us7.remesh3.label
> 2 3
> MiDeface::DistanceBounds() DeltaDist=0.333333
> Raw DistIn = 3, DistOut = 2
> PostMinCheck DistIn = 3, DistOut = 2
>
> MiDeface::SegFace()
> ===============================================
> Label 5
> /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.right.dec44.us7.remesh3.label
> 2 3
> MiDeface::DistanceBounds() DeltaDist=0.333333
> Raw DistIn = 3, DistOut = 5.33333
> PostMinCheck DistIn = 3, DistOut = 5.33333
>
> MiDeface::SegFace()
> *** Error in `mri_defacer': double free or corruption (!prev):
> 0x000000000f9e1090 ***
> ======= Backtrace: =========
> /lib64/libc.so.6(+0x81329)[0x2b0d12670329]
> mri_defacer[0x4aaa0e]
> mri_defacer[0x423bd5]
> mri_defacer[0x4163d8]
> /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b0d12611555]
> mri_defacer[0x419327]
> ======= Memory map: ========
> 00400000-006f7000 r-xp 00000000 3d8:ad14e 144121710017324715
> /work2/08266/psadil/freesurfer/bin/mri_defacer
> 008f6000-008fe000 r--p 002f6000 3d8:ad14e 144121710017324715
> /work2/08266/psadil/freesurfer/bin/mri_defacer
> 008fe000-00928000 rw-p 002fe000 3d8:ad14e 144121710017324715
> /work2/08266/psadil/freesurfer/bin/mri_defacer
> 00928000-011c1000 rw-p 00000000 00:00 0
> 026c1000-13727000 rw-p 00000000 00:00 0
> [heap]
> 2b0d11411000-2b0d11433000 r-xp 00000000 fd:00 402880897
> /usr/lib64/ld-2.17.so
> 2b0d11433000-2b0d11437000 rw-p 00000000 00:00 0
> 2b0d11454000-2b0d11456000 rw-p 00000000 00:00 0
> 2b0d11456000-2b0d1145e000 r--p 00000000 fd:00 278039021
> /opt/apps/gcc/8.3.0/lib64/libgomp.so.1.0.0
> 2b0d1145e000-2b0d1147c000 r-xp 00008000 fd:00 278039021
> /opt/apps/gcc/8.3.0/lib64/libgomp.so.1.0.0
> 2b0d1147c000-2b0d11484000 r--p 00026000 fd:00 278039021
> /opt/apps/gcc/8.3.0/lib64/libgomp.so.1.0.0
> 2b0d11484000-2b0d11485000 r--p 0002d000 fd:00 278039021
> /opt/apps/gcc/8.3.0/lib64/libgomp.so.1.0.0
> 2b0d11485000-2b0d11486000 rw-p 0002e000 fd:00 278039021
> /opt/apps/gcc/8.3.0/lib64/libgomp.so.1.0.0
> 2b0d11486000-2b0d11487000 rw-p 00000000 00:00 0
> 2b0d11487000-2b0d11518000 r--p 00000000 fd:00 278039063
> /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25
> 2b0d11518000-2b0d115c4000 r-xp 00091000 fd:00 278039063
> /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25
> 2b0d115c4000-2b0d11602000 r--p 0013d000 fd:00 278039063
> /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25
> 2b0d11602000-2b0d11603000 ---p 0017b000 fd:00 278039063
> /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25
> 2b0d11603000-2b0d1160d000 r--p 0017b000 fd:00 278039063
> /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25
> 2b0d1160d000-2b0d1160f000 rw-p 00185000 fd:00 278039063
> /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25
> 2b0d1160f000-2b0d11613000 rw-p 00000000 00:00 0
> 2b0d11613000-2b0d11616000 r--p 00000000 fd:00 278039010
> /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1
> 2b0d11616000-2b0d11627000 r-xp 00003000 fd:00 278039010
> /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1
> 2b0d11627000-2b0d1162a000 r--p 00014000 fd:00 278039010
> /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1
> 2b0d1162a000-2b0d1162b000 ---p 00017000 fd:00 278039010
> /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1
> 2b0d1162b000-2b0d1162c000 r--p 00017000 fd:00 278039010
> /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1
> 2b0d1162c000-2b0d1162d000 rw-p 00018000 fd:00 278039010
> /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1
> 2b0d1162d000-2b0d11632000 rw-p 00000000 00:00 0
> 2b0d11632000-2b0d11633000 r--p 00021000 fd:00 402880897
> /usr/lib64/ld-2.17.so
> 2b0d11633000-2b0d11634000 rw-p 00022000 fd:00 402880897
> /usr/lib64/ld-2.17.so
> 2b0d11634000-2b0d11635000 rw-p 00000000 00:00 0
> 2b0d11635000-2b0d11675000 r-xp 00000000 fd:00 269642820
> /opt/apps/xalt/2.10.34/lib64/libxalt_init.so
> 2b0d11675000-2b0d11875000 ---p 00040000 fd:00 269642820
> /opt/apps/xalt/2.10.34/lib64/libxalt_init.so
> 2b0d11875000-2b0d11876000 r--p 00040000 fd:00 269642820
> /opt/apps/xalt/2.10.34/lib64/libxalt_init.so
> 2b0d11876000-2b0d11877000 rw-p 00041000 fd:00 269642820
> /opt/apps/xalt/2.10.34/lib64/libxalt_init.so
> 2b0d11877000-2b0d11878000 rw-p 00000000 00:00 0
> 2b0d11878000-2b0d1188d000 r-xp 00000000 fd:00 404656596
> /usr/lib64/libz.so.1.2.7
> 2b0d1188d000-2b0d11a8c000 ---p 00015000 fd:00 404656596
> /usr/lib64/libz.so.1.2.7
> 2b0d11a8c000-2b0d11a8d000 r--p 00014000 fd:00 404656596
> /usr/lib64/libz.so.1.2.7
> 2b0d11a8d000-2b0d11a8e000 rw-p 00015000 fd:00 404656596
> /usr/lib64/libz.so.1.2.7
> 2b0d11a8e000-2b0d11aa5000 r-xp 00000000 fd:00 402965799
> /usr/lib64/libpthread-2.17.so
> 2b0d11aa5000-2b0d11ca4000 ---p 00017000 fd:00 402965799
> /usr/lib64/libpthread-2.17.so
> 2b0d11ca4000-2b0d11ca5000 r--p 00016000 fd:00 402965799
> /usr/lib64/libpthread-2.17.so
> 2b0d11ca5000-2b0d11ca6000 rw-p 00017000 fd:00 402965799
> /usr/lib64/libpthread-2.17.so
> 2b0d11ca6000-2b0d11caa000 rw-p 00000000 00:00 0
> 2b0d11caa000-2b0d11cac000 r-xp 00000000 fd:00 402880903
> /usr/lib64/libdl-2.17.so
> 2b0d11cac000-2b0d11eac000 ---p 00002000 fd:00 402880903
> /usr/lib64/libdl-2.17.so
> 2b0d11eac000-2b0d11ead000 r--p 00002000 fd:00 402880903
> /usr/lib64/libdl-2.17.so
> 2b0d11ead000-2b0d11eae000 rw-p 00003000 fd:00 402880903
> /usr/lib64/libdl-2.17.so
> 2b0d11eae000-2b0d11faf000 r-xp 00000000 fd:00 402880909
> /usr/lib64/libm-2.17.so
> 2b0d11faf000-2b0d121ae000 ---p 00101000 fd:00 402880909
> /usr/lib64/libm-2.17.so
> 2b0d121ae000-2b0d121af000 r--p 00100000 fd:00 402880909
> /usr/lib64/libm-2.17.so
> 2b0d121af000-2b0d121b0000 rw-p 00101000 fd:00 402880909
> /usr/lib64/libm-2.17.so
> 2b0d121b0000-2b0d121b8000 r-xp 00000000 fd:00 402704011
> /usr/lib64/libcrypt-2.17.so
> 2b0d121b8000-2b0d123b7000 ---p 00008000 fd:00 402704011
> /usr/lib64/libcrypt-2.17.so
> 2b0d123b7000-2b0d123b8000 r--p 00007000 fd:00 402704011
> /usr/lib64/libcrypt-2.17.so
> 2b0d123b8000-2b0d123b9000 rw-p 00008000 fd:00 402704011
> /usr/lib64/libcrypt-2.17.so
> 2b0d123b9000-2b0d123e7000 rw-p 00000000 00:00 0
> 2b0d123e7000-2b0d123ee000 r-xp 00000000 fd:00 403139684
> /usr/lib64/librt-2.17.so
> 2b0d123ee000-2b0d125ed000 ---p 00007000 fd:00 403139684
> /usr/lib64/librt-2.17.so
> 2b0d125ed000-2b0d125ee000 r--p 00006000 fd:00 403139684
> /usr/lib64/librt-2.17.so
> 2b0d125ee000-2b0d125ef000 rw-p 00007000 fd:00 403139684
> /usr/lib64/librt-2.17.so
> 2b0d125ef000-2b0d127b3000 r-xp 00000000 fd:00 402704007
> /usr/lib64/libc-2.17.so
> 2b0d127b3000-2b0d129b2000 ---p 001c4000 fd:00 402704007
> /usr/lib64/libc-2.17.so
> 2b0d129b2000-2b0d129b6000 r--p 001c3000 fd:00 402704007
> /usr/lib64/libc-2.17.so===============================================
>
> MiDeface::FaceIntensityStats()
> Mode2 12 12 4352
> @#@FSTIME 2023:05:17:17:37:05 mri_defacer N 39 e 12.40 S 0.44 U 11.68 P 97%
> M 801792 F 1 R 283367 W 0 c 2 w 129 I 10144 O 1392 L 0.97 1.05 2.39
> @#@FSLOADPOST 2023:05:17:17:37:17 mri_defacer N 39 0.98 1.05 2.38
> ERROR:
>
>
> Patrick Sadil, PhD (he/him/his)
> Research Associate
> psadil.github.io/psadil
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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