Re: [Freesurfer] Uncaught exceptions when processing some images with MiDeFace - Freesurfer

24 May 2023


      External Email - Use Caution
If I understand your previous emails correctly, the failure cannot be reproduced on a stand alone machine running a standard version of linux or Mac OS. &nbsp; Given that circumstance, even if we had your data to run the command with, we can’t reproduce the cluster run time environment. &nbsp;I also don’t see you mentioning a core dump file which could help trace back an issue.
Depending upon the version of samseg called in the script, there are comments reporting it can require 14G RAM (or maybe more).. &nbsp; I would consult with the cluster admins to see if they can run your job with some kind of memory/resource profiling to incrementally log resource usage happening in real-time as the job progresses. &nbsp;Then at the point (timestamp) of failure there might be some useful information from that and/or the system logs that can show if something is going on with memory and/or other resources.
- R.
On May 24, 2023, at 09:46, Patrick Sadil &lt;psadil1@jh.edu&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;I am definitely confused -- especially since the failures depend on the image (as I said at the start, about half of the images can be processed with MiDeFace just fine).I don't see how this could be an issue with compilers. One of the platforms that I tried was the official freesurfer container run on the HPC setup (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://hub.docker.com/r/freesurfer/freesurfer; tag: 7.3.2). That HPC system is CentOS (yes, this is the Frontera system at TACC)$ lsb_release -aLSB Version:      :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarchDistributor ID:   CentOSDescription:      CentOS Linux release 7.9.2009 (Core)Release:    7.9.2009Codename:   CoreJust to be explicit, MiDeFace was run with$ apptainer exec -e -B $(pwd):$(pwd) --env "FS_LICENSE=$(pwd)/license" --env "FS_TIME_ALLOW=0" docker://freesurfer/freesurfer:7.3.2 mideface --i volume.nii.gz --o defaced.nii.gzand ended with[...]MiDeface::SegFace()===============================================Label 5 /usr/local/freesurfer/average/mideface-atlas/average.face.ear.right.dec44.us7.remesh3.label 2 3MiDeface::DistanceBounds() DeltaDist=0.333333Raw DistIn = 3, DistOut = 5.33333PostMinCheck DistIn = 3, DistOut = 5.33333MiDeface::SegFace()double free or corruption (!prev)AbortERROR:Patrick Sadil, PhD (he/him/his)Research Associatepsadil.github.io/psadilFrom:&nbsp;fsbuild &lt;fsbuild@contbay.com&gt;Sent:&nbsp;Thursday, May 18, 2023 9:22 PMTo:&nbsp;freesurfer@nmr.mgh.harvard.edu &lt;freesurfer@nmr.mgh.harvard.edu&gt;Cc:&nbsp;Patrick Sadil &lt;psadil1@jh.edu&gt;Subject:&nbsp;Re: [Freesurfer] Uncaught exceptions when processing some images with MiDeFace&nbsp;It does not make sense that it runs fine on a stand alone machine with no virtualization/container and not on the cluster.A reliable way to setup freesurfer on a linux system is to use the .rpm or .deb package installers.&nbsp; Since that requires sudo, some users host a VM for this since it contains a built in X-server allowing freeview to work out of the box. &nbsp; A linux VM with freesurfer installed runs on any machine with an Intel processor where the host OS is Windows, MacOS, or Linux.&nbsp; Similarly it works to install Freesurfer with sudo privs in a docker CentOS7, 8, Ubuntu 18, 20, 22 container (e.g., hosted from a linux server) and run the entire recon-all pipeline in the container. &nbsp; We don't support running freesurfer Intel MacOS binaries on Apple silicon hardware thru a container/virtualization.Clusters may use modules or a tool like spack to setup the run time environment and system library dependenices for a given application.&nbsp; I tested running a recon-all a while back on the XSEDE cluster under CentOS8 using an older freesurfer 7.X release and it worked fine.&nbsp; But if the runtime dependencies are not correct, then maybe you could get a segfault.&nbsp;&nbsp; Freesurfer is compiled with gcc on linux, so it might not work if the cluster runtime environment somehow included libraries specific to the install of the icc compilers/toolschain instead of the gcc environment.- R.On 5/18/23 15:38, Bennet Fauber (bennet@umich.edu) wrote:        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 &lt;psadil1@jh.edu&gt; 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 2023-05-17 17:32:04 2023-05-17 17:32:09 2023-05-17 17:32:14 2023-05-17 17:32:19 2023-05-17 17:32:24 2023-05-17 17:32:29 2023-05-17 17:32:34 2023-05-17 17:32:39 2023-05-17 17:32:44 2023-05-17 17:32:50 2023-05-17 17:32:55 2023-05-17 17:33:00 2023-05-17 17:33:05 2023-05-17 17:33:10 2023-05-17 17:33:15 2023-05-17 17:33:20 2023-05-17 17:33:25 2023-05-17 17:33:30 2023-05-17 17:33:35 2023-05-17 17:33:40 2023-05-17 17:33:45 2023-05-17 17:33:50 2023-05-17 17:33:55 2023-05-17 17:34:00 2023-05-17 17:34:05 2023-05-17 17:34:10 2023-05-17 17:34:15 2023-05-17 17:34:20

total        used        free      shared  buff/cache   available 191515        4753      186381          10         379      184648 191515        4760      186369          10         385      184638 191515        4774      186346          10         393      184620 191515        4779      186334          10         401      184612 191515        4792      186311          10         411      184593 191515        5251      185817          10         446      184117 191515        5250      185817          10         447      184117 191515        5253      185814          10         447      184114 191515        5254      185813          10         447      184113 191515        5180      185887          10         447      184188 191515        5179      185888          10         447      184189 191515        5178      185889          10         447      184189 191515        5180      185887          10         447      184188 191515        5180      185887          10         447      184187 191515        5181      185886          10         447      184187 191515        5180      185887          10         447      184188 191515        5179      185888          10         447      184188 191515        5180      185886          10         447      184187 191515        5181      185886          10         447      184187 191515        5180      185887          10         447      184187 191515        5181      185886          10         447      184186 191515        5181      185886          10         447      184186 191515        5181      185886          10         447      184186 191515        5136      185925          10         453      184229 191515        5157      185875          10         482      184193 191515        5411      185621          10         482      183939 191515        5344      185676          10         494      184001 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 &lt; DistInMin=2, resetting
DistOut=0 &lt; 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 &lt; 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
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