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, 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': '/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
From: fsbuild <fsbuild@contbay.com>
Sent: Wednesday, May 17, 2023 6:12 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Patrick Sadil <psadil1@jh.edu>
Subject: Re: [Freesurfer] Uncaught exceptions when processing some images with MiDeFace
 
While I do no know and have not looked at the source code in question, if you lookup that error online, one explanation is memory corruption is happening by writing beyond the end of allocated memory, e.g., by using free(g) incorrectly.

However the code is written, an issue with memory allocation might be exacerbated depending upon how memory management is done on the platform.  Memory management on MacOS is extremely aggressive about swapping out to disk well before physical RAM is in danger of being underrun.   Or it is virtually impossible to run out of physical RAM on macOS though things may slow down to a crawl and/or thrash.   It might be informative to know if you are hitting memory limits in the cluster and in the container (where it crashes) - but for some reason not on MacOS.  Similarly, it would be interesting to know if the memory error occurs when run on a stand alone linux workstation.

- R.

On May 17, 2023, at 16:27, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

        External Email - Use Caution        

So the same input volume will sometimes succeed and sometimes fail depending upon the platform? 

On 5/17/2023 12:05 PM, Patrick Sadil wrote:
        External Email - Use Caution        
Hello,
     I am trying to process several images with MiDeFace but running into issues with memory and uncaught exceptions.

Of 50 images, about half are processed successfully. On the other half MiDeFace fails consistently. However, whether the images fail seems to depend on the platform. Here's what I've tried
  • Fails
    • freesurfer-linux-centos7_x86_64-7.4.0.tar.gz install on HPC, CentOS Linux release 7.9.2009 (Core)
    • freesurfer-linux-centos7_x86_64-7.3.2.tar.gz install on HPC, CentOS Linux release 7.9.2009 (Core)
    • Apptainer image from docker://freesurfer/freesurfer:7.3.2, (this is built on CentOS:7) run on HPC
    • Docker image from docker://freesurfer/freesurfer:7.3.2, (this is built on CentOS:7) Apple M1 Pro; 13.3.1
    • Custom docker image (below), built and run on Apple M1 Pro; 13.3.1
  • Succeeds
    • freesurfer-darwin-macOS-7.4.0.pkg, installed and run on Apple M1 Pro; 13.3.1

So, I'm not sure whether this is a bug or something that I need to configure differently.

############

Example apptainer command

$ apptainer exec -e -B $(pwd):/data docker://freesurfer/freesurfer:7.3.2 mideface --i /data/volume.nii.gz --o /data/defaced.nii.gz --odir /data/qa

Example docker command

> docker run --rm -it -v $(pwd):/data freesurfer/freesurfer:7.3.2 mideface --i /data/volume.nii.gz --o /data/defaced.nii.gz --odir /data/qa


Example "bare" command

> mideface --i volume.nii.gz --o defaced.nii.gz --odir qa

############

On the CentOS runs, the error is

MiDeface::SegFace()
*** Error in `mri_defacer': double free or corruption (!prev): 0x000000000e4d64f0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x4001f6b329]
mri_defacer[0x4b0ebe]
mri_defacer[0x422c15]
mri_defacer[0x415308]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x4001f0c555]
mri_defacer[0x418367]
======= Memory map: ========
400000-700000 r-xp 00000000 fe:01 4223092                                /usr/local/freesurfer/bin/mri_defacer
700000-900000 ---p 00000000 00:00 0                                      
900000-908000 r--p 00300000 fe:01 4223092                                /usr/local/freesurfer/bin/mri_defacer
908000-932000 rw-p 00308000 fe:01 4223092                                /usr/local/freesurfer/bin/mri_defacer
932000-13ee1000 rw-p 00000000 00:00 0                                    
4000000000-4000001000 ---p 00000000 00:00 0                              
4000001000-4000801000 rw-p 00000000 00:00 0                              [stack]
4000801000-4000823000 r-xp 00000000 fe:01 2527596                        /usr/lib64/ld-2.17.so
4000823000-4000a22000 ---p 00000000 00:00 0                              
4000a22000-4000a23000 r--p 00021000 fe:01 2527596                        /usr/lib64/ld-2.17.so
4000a23000-4000a24000 rw-p 00022000 fe:01 2527596                        /usr/lib64/ld-2.17.so
4000a24000-4000a27000 rw-p 00000000 00:00 0                              
4000a2b000-4000a2c000 rw-p 00000000 00:00 0                              
4000a2c000-4000a41000 r-xp 00000000 fe:01 2527648                        /usr/lib64/libz.so.1.2.7
4000a41000-4000c40000 ---p 00015000 fe:01 2527648                        /usr/lib64/libz.so.1.2.7
4000c40000-4000c41000 r--p 00014000 fe:01 2527648                        /usr/lib64/libz.so.1..2.7
4000c41000-4000c42000 rw-p 00015000 fe:01 2527648                        /usr/lib64/libz.so.1.2.7
4000c42000-4000c59000 r-xp 00000000 fe:01 2527629                        /usr/lib64/libpthread-2.17.so
4000c59000-4000e58000 ---p 00017000 fe:01 2527629                        /usr/lib64/libpthread-2.17.so
4000e58000-4000e59000 r--p 00016000 fe:01 2527629                        /usr/lib64/libpthread-2.17.so
4000e59000-4000e5a000 rw-p 00017000 fe:01 2527629                        /usr/lib64/libpthread-2.17.so
4000e5a000-4000e5e000 rw-p 00000000 00:00 0                              
4000e5e000-4000e60000 r-xp 00000000 fe:01 2527609                        /usr/lib64/libdl-2.17.so
4000e60000-4001060000 ---p 00002000 fe:01 2527609                        /usr/lib64/libdl-2..17.so
4001060000-4001061000 r--p 00002000 fe:01 2527609                        /usr/lib64/libdl-2.17.so
4001061000-4001062000 rw-p 00003000 fe:01 2527609                        /usr/lib64/libdl-2.17.so
4001062000-4001063000 rw-p 00000000 00:00 0                              
4001063000-4001164000 r-xp 00000000 fe:01 2527611                        /usr/lib64/libm-2.17.so
4001164000-4001363000 ---p 00101000 fe:01 2527611                        /usr/lib64/libm-2.17.so
4001363000-4001364000 r--p 00100000 fe:01 2527611                        /usr/lib64/libm-2..17.so
4001364000-4001365000 rw-p 00101000 fe:01 2527611                        /usr/lib64/libm-2.17.so
4001365000-400138a000 r-xp 00000000 fe:01 2527938                        /usr/lib64/libgomp.so.1.0.0
400138a000-4001589000 ---p 00025000 fe:01 2527938                        /usr/lib64/libgomp.so.1.0.0
4001589000-400158a000 r--p 00024000 fe:01 2527938                        /usr/lib64/libgomp.so.1.0.0
400158a000-400158b000 rw-p 00025000 fe:01 2527938                        /usr/lib64/libgomp.so.1.0..0
400158b000-4001593000 r-xp 00000000 fe:01 2527607                        /usr/lib64/libcrypt-2.17.so
4001593000-4001792000 ---p 00008000 fe:01 2527607                        /usr/lib64/libcrypt-2.17.so
4001792000-4001793000 r--p 00007000 fe:01 2527607                        /usr/lib64/libcrypt-2.17.so
4001793000-4001794000 rw-p 00008000 fe:01 2527607                        /usr/lib64/libcrypt-2.17.so
4001794000-40017c3000 rw-p 00000000 00:00 0                              
40017c3000-40017ca000 r-xp 00000000 fe:01 2527633                        /usr/lib64/librt-2.17.so
40017ca000-40019c9000 ---p 00007000 fe:01 2527633                        /usr/lib64/librt-2.17.so
40019c9000-40019ca000 r--p 00006000 fe:01 2527633                        /usr/lib64/librt-2.17.so
40019ca000-40019cb000 rw-p 00007000 fe:01 2527633                        /usr/lib64/librt-2.17.so
40019cb000-4001ab4000 r-xp 00000000 fe:01 2123191                        /usr/lib64/libstdc++.so.6.0.19
4001ab4000-4001cb4000 ---p 000e9000 fe:01 2123191                        /usr/lib64/libstdc++.so.6.0.19
4001cb4000-4001cbc000 r--p 000e9000 fe:01 2123191                        /usr/lib64/libstdc++.so.6.0.19
4001cbc000-4001cbe000 rw-p 000f1000 fe:01 2123191                        /usr/lib64/libstdc++.so.6..0.19
4001cbe000-4001cd3000 rw-p 00000000 00:00 0                              
4001cd3000-4001ce8000 r-xp 00000000 fe:01 2123006                        /usr/lib64/libgcc_s-4.8.5-20150702.so.1
4001ce8000-4001ee7000 ---p 00015000 fe:01 2123006                        /usr/lib64/libgcc_s-4.8.5-20150702.so.1
4001ee7000-4001ee8000 r--p 00014000 fe:01 2123006                        /usr/lib64/libgcc_s-4.8.5-20150702.so.1
4001ee8000-4001ee9000 rw-p 00015000 fe:01 2123006                        /usr/lib64/libgcc_s-4.8.5-20150702.so.1
4001ee9000-4001eea000 rw-p 00000000 00:00 0                              
4001eea000-40020ae000 r-xp 00000000 fe:01 2527603                        /usr/lib64/libc-2.17.so
40020ae000-40022ad000 ---p 001c4000 fe:01 2527603                        /usr/lib64/libc-2.17.so
40022ad000-40022b1000 r--p 001c3000 fe:01 2527603                        /usr/lib64/libc-2.17.so
40022b1000-40022b3000 rw-p 001c7000 fe:01 2527603                        /usr/lib64/libc-2.17.so
40022b3000-40022b8000 rw-p 00000000 00:00 0                              
40022b8000-40022ba000 r-xp 00000000 fe:01 2527589                        /usr/lib64/libfreebl3.so
40022ba000-40024b9000 ---p 00002000 fe:01 2527589                        /usr/lib64/libfreebl3.so
40024b9000-40024ba000 r--p 00001000 fe:01 2527589                        /usr/lib64/libfreebl3.so
40024ba000-40024bb000 rw-p 00002000 fe:01 2527589                        /usr/lib64/libfreebl3.so
40024bb000-40024c0000 rw-p 00000000 00:00 0                              
40024c1000-40024c2000 rw-p 00000000 00:00 0                              
40024c7000-40024d3000 r-xp 00000000 fe:01 2527621                        /usr/lib64/libnss_files-2.17.so
40024d3000-40026d2000 ---p 0000c000 fe:01 2527621                        /usr/lib64/libnss_files-2.17.so
40026d2000-40026d3000 r--p 0000b000 fe:01 2527621                        /usr/lib64/libnss_files-2.17.so
40026d3000-40026d4000 rw-p 0000c000 fe:01 2527621                        /usr/lib64/libnss_files-2.17.so
40026d4000-40026da000 rw-p 00000000 00:00 0                              
40026dc000-4004767000 rw-p 00000000 00:00 0                              
400476a000-400c2f1000 rw-p 00000000 00:00 0                              
400db9d000-400e3c0000 rw-p 00000000 00:00 0                              
400e3c1000-401044c000 rw-p 00000000 00:00 0                              
401044d000-40215ba000 rw-p 00000000 00:00 0                              
40215bd000-4023648000 rw-p 00000000 00:00 0                              
4023649000-4023ec1000 rw-p 00000000 00:00 0                              
4023eca000-4023ecb000 rw-p 00000000 00:00 0                              
4024000000-4024021000 rw-p 00000000 00:00 0                              
4024021000-4028000000 ---p 00000000 00:00 0                              
ffffffffff600000-ffffffffff601000 --xp 00000000 00:00 0                  [vsyscall]
===============================================

MiDeface::FaceIntensityStats()
Mode2 12 12  4362
qemu: uncaught target signal 6 (Aborted) - core dumped
Abort
ERROR:

############

With a docker image using Ubuntu base, the error is 

MiDeface::SegFace()
qemu: uncaught target signal 11 (Segmentation fault) - core dumped
Segmentation fault
ERROR:


############
# model: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://github.com/freesurfer/freesurfer/blob/dev/Dockerfile
# Dockerfile

FROM ubuntu:22.04

COPY freesurfer_ubuntu22-7.4.0_amd64.deb /tmp/fs.deb

# install
RUN apt-get update \
    && apt-get install -y /tmp/fs.deb \
    && rm -rf /var/lib/apt/lists/* \
    && rm /tmp/fs.deb

COPY license /usr/local/freesurfer/7.4.0/.license

# setup fs env
ENV OS Linux
ENV FREESURFER_HOME /usr/local/freesurfer/7.4.0
ENV PATH ${FREESURFER_HOME}/bin:${FREESURFER_HOME}/fsfast/bin:${FREESURFER_HOME}/tktools:{$FREESURFER_HOME}/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
ENV FREESURFER ${FREESURFER_HOME}
ENV SUBJECTS_DIR ${FREESURFER_HOME}/subjects
ENV LOCAL_DIR ${FREESURFER_HOME}/local
ENV FSFAST_HOME ${FREESURFER_HOME}/fsfast
ENV FMRI_ANALYSIS_DIR ${FREESURFER_HOME}/fsfast
ENV FUNCTIONALS_DIR ${FREESURFER_HOME}/sessions
ENV FS_LICENSE ${FREESURFER_HOME}/.license

# set default fs options
ENV FS_OVERRIDE 0
ENV FIX_VERTEX_AREA ""
ENV FSF_OUTPUT_FORMAT nii.gz

# mni env requirements
ENV MINC_BIN_DIR ${FREESURFER_HOME}/mni/bin
ENV MINC_LIB_DIR ${FREESURFER_HOME}/mni/lib
ENV MNI_DIR ${FREESURFER_HOME}/mni
ENV MNI_DATAPATH ${FREESURFER_HOME}/mni/data
ENV MNI_PERL5LIB ${FREESURFER_HOME}/mni/share/perl5
ENV PERL5LIB ${FREESURFER_HOME}/mni/share/perl5


Thanks!
Patrick Sadil, PhD (he/him/his)
Research Associate

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