Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

FSL not installed in setup
by Lauren Stephens 18 May '23

18 May '23

External Email - Use Caution Hi Freesurfers, I am trying to run tracula and was running the command bedpostx_datacheck and the terminal said: -------- freesurfer-darwin-macOS-7.3.2-20220804-6354275 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/7.3.2 FSFAST_HOME /Applications/freesurfer/7.3.2/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.3.2/subjects MNI_DIR /Applications/freesurfer/7.3.2/mni SLE-PBS-h4tkn18vq6x3:~ timothydurazzo$ bedpostx_datacheck -bash: bedpostx_datacheck: command not found SLE-PBS-h4tkn18vq6x3:~ timothydurazzo$ I see that FSL (FSL_DIR) is not in the freesurfer environment at the top, how can we add that in order to get bedpostx_datacheck to run properly? Thank you, Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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Re: [Freesurfer] Uncaught exceptions when processing some images with MiDeFace
by Patrick Sadil 18 May '23

18 May '23

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

2 1

MiDeFace
by Hermann, Jacob 18 May '23

18 May '23

External Email - Use Caution We have successfully run MiDeFace on our neuroimaging files and it seems like a great option for our purposes (user friendly, easy to implement). However, we have noticed that there are some facial features (nose and mouth) that do not get obstructed on most of our participants who are from a primarily African American sample. We are wondering if other groups are experiencing this too as we are unsure if this is related to our population. If there was any way that we could adjust any settings to obscure these features that would be great, but it appears as though the algorithm could be improved to further obscure some parts of the face.

2 2

seeking help with -bedp error in TRACULA (FS 7.2.0)
by Harriott, Emily M 18 May '23

18 May '23

External Email - Use Caution Dear FreeSurfer experts, I hope this email finds you all well. I am trying to run TRACULA (FreeSurfer version 7.2.0) on our university cluster computing system and am getting stuck on the bedpostx command. The staff at our computing cluster think that it might be an issue with a slurm script created along with the -bedp command (“it is an issue with the slurm command formed inside (with srun command)”), but are not sure and were unable to help beyond that as they are not experienced in FreeSurfer. I am hoping a FreeSurfer expert here might be able to help me figure out how to fix this error. I run these commands without errors: recon-all -i /fs0/users/harrioem/DWI_practice/rawdata/RC3001_v1/T1.nii -s RC3001_v1 -sd /fs0/users/harrioem/DWI_practice/subjects -all segmentThalamicNuclei.sh RC3001_v1 trac-all -prep -c /fs0/users/harrioem/DWI_practice/subjects/RC3001_v1/dmrirc.file When I try to run: trac-all -bedp -c /fs0/users/harrioem/DWI_practice/subjects/RC3001_v1/dmrirc.file I get this error: (base) [harrioem@cutting subjects]$ trac-all -bedp -c /fs0/users/harrioem/DWI_practice/subjects/RC3001_v1/dmrirc.file INFO: SUBJECTS_DIR is /fs0/users/harrioem/DWI_practice/subjects INFO: Diffusion root is /fs0/users/harrioem/DWI_practice/subjects Actual FREESURFER_HOME /cvmfs/oasis.opensciencegrid.org/accre/mirror/common/easybuild/software/FreeSurfer/7.2.0 ln -sf ../dlabel/diff/aparc+aseg_mask.bbr.nii.gz /fs0/users/harrioem/DWI_practice/subjects/RC3001_v1/dmri/nodif_brain_mask.nii.gz WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 -model 1 /fs0/users/harrioem/DWI_practice/subjects/RC3001_v1/dmri subjectdir is /fs0/users/harrioem/DWI_practice/subjects/RC3001_v1/dmri Making bedpostx directory structure Queuing preprocessing stages srun: error: Invalid --mail-type specification Queuing parallel processing stage ----- Bedpostx Monitor ----- srun: error: invalid partition specified: normal srun: error: Unable to allocate resources: Invalid partition name specified Queuing post processing stage srun: error: invalid partition specified: normal srun: error: Unable to allocate resources: Invalid partition name specified I have attached the dmrirc.file and the trac-all log hoping they might help. The dmrirc.file only contains 3 tracts for ease of testing but will eventually (once everything works!) contain them all. Any assistance anyone might be able to provide would be so greatly appreciated. Thank you so very much! Emily Harriott PhD student, Vanderbilt University

1 0

Help Needed with Thalamic NucleiDTI Module and Freeview Display
by 胡馨月 18 May '23

18 May '23

External Email - Use Caution Dear FreeSurfer Experts, I hope you are doing well. I have encountered an issue while using the Thalamic NucleiDTI module in FreeSurfer and would appreciate your guidance. I am attempting to segment the thalamus using the module, but the Pc, VM, and Pt nuclei are missing in the segmentation results. Could you please advise me on resolving this issue? Additionally, I would like instructions on how to display the Thalamic NucleiDTI module results in Freeview. Please guide me on the steps to visualize the results accurately in Freeview. Thank you for your support. I look forward to your response. Best regards, Xinyue Hu West China Hospital of Sichuan University

2 1

Re: [Freesurfer] Uncaught exceptions when processing some images with MiDeFace
by Patrick Sadil 18 May '23

18 May '23

1 0

Password to uncompress VM freesurfer
by Albert Juncà 18 May '23

18 May '23

External Email - Use Caution Hi, As per instructions I'm requesting the password to uncompress the freesurfer VM. Thanks.

1 0

Re: [Freesurfer] Uncaught exceptions when processing some images with MiDeFace
by fsbuild 17 May '23

17 May '23

External Email - Use Caution 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(a)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 triedFailsfreesurfer-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 HPCDocker image from docker://freesurfer/freesurfer:7.3.2, (this is built on CentOS:7) Apple M1 Pro; 13.3.1Custom docker image (below), built and run on Apple M1 Pro; 13.3.1Succeedsfreesurfer-darwin-macOS-7.4.0.pkg, installed and run on Apple M1 Pro; 13.3.1So, 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/qaExample 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/qaExample "bare" command> mideface --i volume.nii.gz --o defaced.nii.gz --odir qa############On the CentOS runs, the error isMiDeface::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_defacer700000-900000 ---p 00000000 00:00 0                                      900000-908000 r--p 00300000 fe:01 4223092                                /usr/local/freesurfer/bin/mri_defacer908000-932000 rw-p 00308000 fe:01 4223092                                /usr/local/freesurfer/bin/mri_defacer932000-13ee1000 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.so4000823000-4000a22000 ---p 00000000 00:00 0                              4000a22000-4000a23000 r--p 00021000 fe:01 2527596                        /usr/lib64/ld-2.17.so4000a23000-4000a24000 rw-p 00022000 fe:01 2527596                        /usr/lib64/ld-2.17.so4000a24000-4000a27000 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.1.2.74000a41000-4000c40000 ---p 00015000 fe:01 2527648                        /usr/lib64/libz.so.1.2.74000c40000-4000c41000 r--p 00014000 fe:01 2527648                        /usr/lib64/libz.so.1.2..74000c41000-4000c42000 rw-p 00015000 fe:01 2527648                        /usr/lib64/libz..so.1.2.74000c42000-4000c59000 r-xp 00000000 fe:01 2527629                        /usr/lib64/libpthread-2.17.so4000c59000-4000e58000 ---p 00017000 fe:01 2527629                        /usr/lib64/libpthread-2.17.so4000e58000-4000e59000 r--p 00016000 fe:01 2527629                        /usr/lib64/libpthread-2.17.so4000e59000-4000e5a000 rw-p 00017000 fe:01 2527629                        /usr/lib64/libpthread-2.17.so4000e5a000-4000e5e000 rw-p 00000000 00:00 0                              4000e5e000-4000e60000 r-xp 00000000 fe:01 2527609                        /usr/lib64/libdl-2.17.so4000e60000-4001060000 ---p 00002000 fe:01 2527609                        /usr/lib64/libdl-2.17.so4001060000-4001061000 r--p 00002000 fe:01 2527609                        /usr/lib64/libdl-2.17.so4001061000-4001062000 rw-p 00003000 fe:01 2527609                        /usr/lib64/libdl-2.17.so4001062000-4001063000 rw-p 00000000 00:00 0                              4001063000-4001164000 r-xp 00000000 fe:01 2527611                        /usr/lib64/libm-2.17.so4001164000-4001363000 ---p 00101000 fe:01 2527611                        /usr/lib64/libm-2.17.so4001363000-4001364000 r--p 00100000 fe:01 2527611                        /usr/lib64/libm-2.17.so4001364000-4001365000 rw-p 00101000 fe:01 2527611                        /usr/lib64/libm-2.17.so4001365000-400138a000 r-xp 00000000 fe:01 2527938                        /usr/lib64/libgomp.so.1.0.0400138a000-4001589000 ---p 00025000 fe:01 2527938                        /usr/lib64/libgomp.so.1.0.04001589000-400158a000 r--p 00024000 fe:01 2527938                        /usr/lib64/libgomp.so.1.0.0400158a000-400158b000 rw-p 00025000 fe:01 2527938                        /usr/lib64/libgomp.so.1.0.0400158b000-4001593000 r-xp 00000000 fe:01 2527607                        /usr/lib64/libcrypt-2.17.so4001593000-4001792000 ---p 00008000 fe:01 2527607                        /usr/lib64/libcrypt-2.17.so4001792000-4001793000 r--p 00007000 fe:01 2527607                        /usr/lib64/libcrypt-2.17.so4001793000-4001794000 rw-p 00008000 fe:01 2527607                        /usr/lib64/libcrypt-2.17.so4001794000-40017c3000 rw-p 00000000 00:00 0                              40017c3000-40017ca000 r-xp 00000000 fe:01 2527633                        /usr/lib64/librt-2.17.so40017ca000-40019c9000 ---p 00007000 fe:01 2527633                        /usr/lib64/librt-2.17.so40019c9000-40019ca000 r--p 00006000 fe:01 2527633                        /usr/lib64/librt-2.17.so40019ca000-40019cb000 rw-p 00007000 fe:01 2527633                        /usr/lib64/librt-2.17.so40019cb000-4001ab4000 r-xp 00000000 fe:01 2123191                        /usr/lib64/libstdc++.so.6.0.194001ab4000-4001cb4000 ---p 000e9000 fe:01 2123191                        /usr/lib64/libstdc++.so.6.0.194001cb4000-4001cbc000 r--p 000e9000 fe:01 2123191                        /usr/lib64/libstdc++.so.6.0.194001cbc000-4001cbe000 rw-p 000f1000 fe:01 2123191                        /usr/lib64/libstdc++.so.6.0.194001cbe000-4001cd3000 rw-p 00000000 00:00 0                              4001cd3000-4001ce8000 r-xp 00000000 fe:01 2123006                        /usr/lib64/libgcc_s-4.8.5-20150702.so.14001ce8000-4001ee7000 ---p 00015000 fe:01 2123006                        /usr/lib64/libgcc_s-4.8.5-20150702..so.14001ee7000-4001ee8000 r--p 00014000 fe:01 2123006                        /usr/lib64/libgcc_s-4.8.5-20150702.so.14001ee8000-4001ee9000 rw-p 00015000 fe:01 2123006                        /usr/lib64/libgcc_s-4.8.5-20150702.so.14001ee9000-4001eea000 rw-p 00000000 00:00 0                              4001eea000-40020ae000 r-xp 00000000 fe:01 2527603                        /usr/lib64/libc-2.17.so40020ae000-40022ad000 ---p 001c4000 fe:01 2527603                        /usr/lib64/libc-2.17.so40022ad000-40022b1000 r--p 001c3000 fe:01 2527603                        /usr/lib64/libc-2.17.so40022b1000-40022b3000 rw-p 001c7000 fe:01 2527603                        /usr/lib64/libc-2.17.so40022b3000-40022b8000 rw-p 00000000 00:00 0                              40022b8000-40022ba000 r-xp 00000000 fe:01 2527589                        /usr/lib64/libfreebl3.so40022ba000-40024b9000 ---p 00002000 fe:01 2527589                        /usr/lib64/libfreebl3.so40024b9000-40024ba000 r--p 00001000 fe:01 2527589                        /usr/lib64/libfreebl3.so40024ba000-40024bb000 rw-p 00002000 fe:01 2527589                        /usr/lib64/libfreebl3.so40024bb000-40024c0000 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.so40024d3000-40026d2000 ---p 0000c000 fe:01 2527621                        /usr/lib64/libnss_files-2.17.so40026d2000-40026d3000 r--p 0000b000 fe:01 2527621                        /usr/lib64/libnss_files-2.17.so40026d3000-40026d4000 rw-p 0000c000 fe:01 2527621                        /usr/lib64/libnss_files-2.17.so40026d4000-40026da000 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  4362qemu: uncaught target signal 6 (Aborted) - core dumpedAbortERROR:############With a docker image using Ubuntu base, the error is MiDeface::SegFace()qemu: uncaught target signal 11 (Segmentation fault) - core dumpedSegmentation faultERROR:############# model: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://github.com/freesurfer/freesurfer/blob/dev/Dockerfile# DockerfileFROM ubuntu:22.04COPY freesurfer_ubuntu22-7.4.0_amd64.deb /tmp/fs.deb# installRUN apt-get update \    && apt-get install -y /tmp/fs.deb \    && rm -rf /var/lib/apt/lists/* \    && rm /tmp/fs..debCOPY license /usr/local/freesurfer/7.4.0/.license# setup fs envENV OS LinuxENV FREESURFER_HOME /usr/local/freesurfer/7.4.0ENV 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:/binENV FREESURFER ${FREESURFER_HOME}ENV SUBJECTS_DIR ${FREESURFER_HOME}/subjectsENV LOCAL_DIR ${FREESURFER_HOME}/localENV FSFAST_HOME ${FREESURFER_HOME}/fsfastENV FMRI_ANALYSIS_DIR ${FREESURFER_HOME}/fsfastENV FUNCTIONALS_DIR ${FREESURFER_HOME}/sessionsENV FS_LICENSE ${FREESURFER_HOME}/.license# set default fs optionsENV FS_OVERRIDE 0ENV FIX_VERTEX_AREA ""ENV FSF_OUTPUT_FORMAT nii.gz# mni env requirementsENV MINC_BIN_DIR ${FREESURFER_HOME}/mni/binENV MINC_LIB_DIR ${FREESURFER_HOME}/mni/libENV MNI_DIR ${FREESURFER_HOME}/mniENV MNI_DATAPATH ${FREESURFER_HOME}/mni/dataENV MNI_PERL5LIB ${FREESURFER_HOME}/mni/share/perl5ENV PERL5LIB ${FREESURFER_HOME}/mni/share/perl5Thanks!Patrick Sadil, PhD (he/him/his)Research Associatepsadil.github.io/psadil_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1laBDOs68qgMCwS6DLNr5FqHfBCv5WY81hMckdEareZx45… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Re: [Freesurfer] recon-all
by fsbuild 17 May '23

17 May '23

External Email - Use Caution I think your SUBJECTS_DIR environment variable is still set to the default spath to ubject data that is set by default in the 7.2.0 release.  It is not intended that you add your own subjects in the freesurfer distribution as those are examples (and you don’t have write permission there on purpose). I would try manually setting (override) SUBJECTS_DIR in your environment to point to a path that is not under /usr/local, e.g., in your home drectory.  The akira subject data needs to live under a path set in SUBJECTS_DIR where you have both read/write permission. - R. On May 17, 2023, at 16:27, Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote:        External Email - Use Caution        can't read that. can you cut-and-paste into the email?On 5/17/2023 1:29 PM, mahmoodasdfzjy wrote:        External Email - Use Caution        SorryI have a problem when I want to recon-all my T1-MPRAGE data.I face with this probmlem that attached it.Can you help me?<storage_emulated_0_DCIM_Camera_%DB%B2%DB%B0%DB%B2%DB%B3%DB%B0%DB%B5%DB%B1%DB%B7_%DB%B2%DB%B1%DB%B5%DB%B9%DB%B2%DB%B5_jpg_1684344578234.jpeg>ارسال شده از دستگاه Galaxy من_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/10Ij9n2Z5PYSrTFqoz6-gzphOQum4VEDByrvSWKsyQTPci… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

recon-all
by mahmoodasdfzjy 17 May '23

17 May '23

External Email - Use Caution SorryI have a problem when I want to recon-all my T1-MPRAGE data.I face with this probmlem that attached it.Can you help me?ارسال شده از دستگاه Galaxy من

2 1

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