Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

Re: [Freesurfer] Uncaught exceptions when processing some images with MiDeFace
by fsbuild 24 May '23

24 May '23

External Email - Use Caution 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.  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.   A linux VM with freesurfer installed runs on any machine with an Intel processor where the host OS is Windows, MacOS, or Linux.  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.   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.  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.  But if the runtime dependencies are not correct, then maybe you could get a segfault.   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(a)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 <psadil1(a)jh.edu> wrote: External Email - Use Caution Thanks for the responses! Yes -- the same input volume will sometimes succeed and sometimes fail depending upon the platform. Here is an example of the mri_info for one such volume $ mri_info volume.nii.gz niiRead(): detected input as 64 bit double, reading in as 32 bit float Volume information for volume.nii.gz type: nii dimensions: 193 x 229 x 193 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 193.000 dof: 1 xstart: -96.5, xend: 96.5 ystart: -114.5, yend: 114.5 zstart: -96.5, zend: 96.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -0.5000 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = -18.5000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.5000 Orientation : LPS Primary Slice Direction: axial voxel to ras transform: -1.0000 0.0000 0.0000 96.0000 0.0000 -1.0000 0.0000 96.0000 0.0000 0.0000 1.0000 -78.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: -1.0000 0.0000 0.0000 96.0000 0.0000 -1.0000 0.0000 96.0000 0.0000 0.0000 1.0000 78.0000 0.0000 0.0000 0.0000 1.0000 Thanks for the information about memory swapping. Here's a log of the memory usage as reported by `free` every 5 seconds during a failing run on the HPC (FS 7.3.2, no containers) date time total used free shared buff/cache available 2023-05-17 17:32:04 191515 4753 186381 10 379 184648 2023-05-17 17:32:09 191515 4760 186369 10 385 184638 2023-05-17 17:32:14 191515 4774 186346 10 393 184620 2023-05-17 17:32:19 191515 4779 186334 10 401 184612 2023-05-17 17:32:24 191515 4792 186311 10 411 184593 2023-05-17 17:32:29 191515 5251 185817 10 446 184117 2023-05-17 17:32:34 191515 5250 185817 10 447 184117 2023-05-17 17:32:39 191515 5253 185814 10 447 184114 2023-05-17 17:32:44 191515 5254 185813 10 447 184113 2023-05-17 17:32:50 191515 5180 185887 10 447 184188 2023-05-17 17:32:55 191515 5179 185888 10 447 184189 2023-05-17 17:33:00 191515 5178 185889 10 447 184189 2023-05-17 17:33:05 191515 5180 185887 10 447 184188 2023-05-17 17:33:10 191515 5180 185887 10 447 184187 2023-05-17 17:33:15 191515 5181 185886 10 447 184187 2023-05-17 17:33:20 191515 5180 185887 10 447 184188 2023-05-17 17:33:25 191515 5179 185888 10 447 184188 2023-05-17 17:33:30 191515 5180 185886 10 447 184187 2023-05-17 17:33:35 191515 5181 185886 10 447 184187 2023-05-17 17:33:40 191515 5180 185887 10 447 184187 2023-05-17 17:33:45 191515 5181 185886 10 447 184186 2023-05-17 17:33:50 191515 5181 185886 10 447 184186 2023-05-17 17:33:55 191515 5181 185886 10 447 184186 2023-05-17 17:34:00 191515 5136 185925 10 453 184229 2023-05-17 17:34:05 191515 5157 185875 10 482 184193 2023-05-17 17:34:10 191515 5411 185621 10 482 183939 2023-05-17 17:34:15 191515 5344 185676 10 494 184001 2023-05-17 17:34:20 191515 5348 185667 10 498 183994 I think this indicates that the system should has plenty of memory. FWIW, here is the terminal output produced during the logged run (error is always at the same place) $ mideface --i volume.nii.gz --o defaced.nii.gz Wed May 17 17:31:59 CDT 2023 setenv SUBJECTS_DIR /work2/08266/psadil/freesurfer/subjects cd /[...redacted...]/jobs/release /work2/08266/psadil/freesurfer/bin/mideface --i volume.nii.gz --o defaced.nii.gz -rwx------ 1 psadil G-821866 27366 Aug 3 2022 /work2/08266/psadil/freesurfer/bin/mideface freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275 $Id$ Linux c103-211.frontera.tacc.utexas.edu 3.10.0-1160.45.1.el7.x86_64 #1 SMP Wed Oct 13 17:20:51 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux pid 205539 UseXvfb 1 samseg --i /[...redacted...]/jobs/release/volume.nii.gz --o /[...redacted....]/jobs/release/tmpdir.midefacer.205539/samseg --threads 1 --block-coordinate-descent --options /work2/08266/psadil/freesurfer/average/mideface-atlas/samseg-options.json /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg /[...redacted....]/jobs/release /[...redacted...]/jobs/release Wed May 17 17:32:00 CDT 2023 setenv SUBJECTS_DIR /work2/08266/psadil/freesurfer/subjects cd /[...redacted...]/jobs/release /work2/08266/psadil/freesurfer/bin/samseg --i /[...redacted...]/jobs/release/volume.nii.gz --o /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg --threads 1 --block-coordinate-descent --options /work2/08266/psadil/freesurfer/average/mideface-atlas/samseg-options.json freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275 samseg 7.3.2 Linux c103-211.frontera.tacc.utexas.edu 3.10.0-1160.45.1.el7.x86_64 #1 SMP Wed Oct 13 17:20:51 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Using Block Coordinate Descent fs_time run_samseg -o /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg --threads 1 --save-warp --options /work2/08266/psadil/freesurfer/average/mideface-atlas/samseg-options.json -i /[...redacted...]/jobs/release/volume.nii.gz Constructing image-to-world transform from header information (/[...redacted...]/jobs/release/volume.nii.gz) Read image: /[...redacted...]/jobs/release/volume.nii.gz Constructing image-to-world transform from header information (/work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii) Read image: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE min: -48.627 max: 1250.65 robustMin: -1.51633 robustMax: 1096.98 histogram[ 0 ]: 1 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 3.07385e-06 cumulativeHistogram[ 1 ]: 3.07385e-06 cumulativeHistogram[ 2 ]: 3.07385e-06 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 AFFINE min: -48.627 max: 1250.65 robustMin: -1.51633 robustMax: 1096.98 histogram[ 0 ]: 1 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 3.07385e-06 cumulativeHistogram[ 1 ]: 3.07385e-06 cumulativeHistogram[ 2 ]: 3.07385e-06 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 0 min: -48.627 max: 1250.65 robustMin: -1.51633 robustMax: 1096.98 histogram[ 0 ]: 1 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 3.07385e-06 cumulativeHistogram[ 1 ]: 3.07385e-06 cumulativeHistogram[ 2 ]: 3.07385e-06 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 0 min: -48.627 max: 1250.65 robustMin: -1.51633 robustMax: 1096.98 histogram[ 0 ]: 1 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 3.07385e-06 cumulativeHistogram[ 1 ]: 3.07385e-06 cumulativeHistogram[ 2 ]: 3.07385e-06 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 0 min: -48.627 max: 1250.65 robustMin: -1.51633 robustMax: 1096.98 histogram[ 0 ]: 1 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 3.07385e-06 cumulativeHistogram[ 1 ]: 3.07385e-06 cumulativeHistogram[ 2 ]: 3.07385e-06 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 Constructing image-to-world transform from header information (/[...redacted...]/jobs/release/volume.nii.gz) Read image: /[...redacted...]/jobs/release/volume.nii.gz Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points ##---------------------------------------------- Samsegment Options ##---------------------------------------------- output directory: /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg input images: /[...redacted...]/jobs/release/volume.nii.gz modelSpecifications: {'FreeSurferLabels': [0, 165, 258, 16, 24, 8, 47, 15, 259, 3, 42, 7, 46, 41, 2, 63, 54, 18, 53, 44, 17, 31, 5, 85, 60, 28, 14, 26, 12, 51, 62, 58, 77, 4, 30, 43, 52, 11, 49, 13, 50, 10, 80, 72], 'atlasFileName': '/work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz', 'names': ['Unknown', 'Skull', 'Soft_Nonbrain_Tissue', 'Brain-Stem', 'CSF', 'Left-Cerebellum-Cortex', 'Right-Cerebellum-Cortex', '4th-Ventricle', 'Fluid_Inside_Eyes', 'Left-Cerebral-Cortex', 'Right-Cerebral-Cortex', 'Left-Cerebellum-White-Matter', 'Right-Cerebellum-White-Matter', 'Right-Cerebral-White-Matter', 'Left-Cerebral-White-Matter', 'Right-choroid-plexus', 'Right-Amygdala', 'Left-Amygdala', 'Right-Hippocampus', 'Right-Inf-Lat-Vent', 'Left-Hippocampus', 'Left-choroid-plexus', 'Left-Inf-Lat-Vent', 'Optic-Chiasm', 'Right-VentralDC', 'Left-VentralDC', '3rd-Ventricle', 'Left-Accumbens-area', 'Left-Putamen', 'Right-Putamen', 'Right-vessel', 'Right-Accumbens-area', 'WM-hypointensities', 'Left-Lateral-Ventricle', 'Left-vessel', 'Right-Lateral-Ventricle', 'Right-Pallidum', 'Left-Caudate', 'Right-Thalamus', 'Left-Pallidum', 'Right-Caudate', 'Left-Thalamus', 'non-WM-hypointensities', '5th-Ventricle'], 'colors': [[0, 0, 0, 0], [255, 165, 0, 255], [128, 128, 128, 255], [119, 159, 176, 255], [60, 60, 60, 255], [230, 148, 34, 255], [230, 148, 34, 255], [42, 204, 164, 255], [128, 0, 128, 255], [205, 62, 78, 255], [205, 62, 78, 255], [220, 248, 164, 255], [220, 248, 164, 255], [0, 225, 0, 255], [245, 245, 245, 255], [0, 200, 221, 255], [103, 255, 255, 255], [103, 255, 255, 255], [220, 216, 20, 255], [196, 58, 250, 255], [220, 216, 20, 255], [0, 200, 200, 255], [196, 58, 250, 255], [234, 169, 30, 255], [165, 42, 42, 255], [165, 42, 42, 255], [204, 182, 142, 255], [255, 165, 0, 255], [236, 13, 176, 255], [236, 13, 176, 255], [160, 32, 240, 255], [255, 165, 0, 255], [200, 70, 255, 255], [120, 18, 134, 255], [160, 32, 240, 255], [120, 18, 134, 255], [13, 48, 255, 255], [122, 186, 22 0, 255], [0, 118, 14, 255], [12, 48, 255, 255], [122, 186, 220, 255], [0, 118, 14, 255], [164, 108, 226, 255], [120, 190, 150, 255]], 'sharedGMMParameters': [GMMparameter(mergedName='Unknown', numberOfComponents=1, searchStrings=['Unknown', 'Skull']), GMMparameter(mergedName='GlobalWM', numberOfComponents=1, searchStrings=['White', 'Brain-Stem', 'VentralDC', 'Optic-Chiasm', 'Thalamus', 'Pallidum']), GMMparameter(mergedName='GlobalGM', numberOfComponents=1, searchStrings=['Cortex', 'Caudate', 'Hippocampus', 'Amygdala', 'Accumbens', 'hypointensities', 'Thalamus']), GMMparameter(mergedName='GlobalCSF_messy', numberOfComponents=1, searchStrings=['CSF', 'vessel', 'choroid-plexus', 'Fluid']), GMMparameter(mergedName='GlobalCSF_clean', numberOfComponents=1, searchStrings=['Ventricle', 'Inf-Lat-Vent', 'Fluid']), GMMparameter(mergedName='Putamen', numberOfComponents=1, searchStrings=['Putamen']), GMMparameter(mergedName='Soft', numberOfComponents=3, searchStrings=['Soft'])], 'useDiagonalCovarianceMatrices': True, 'maskingProbabilityThreshold': 0.5, 'maskingDistance': 10.0, 'K': 0.1, 'biasFieldSmoothingKernelSize': 50, 'whiteMatterAndCortexSmoothingSigma': 0} optimizationOptions: {'maximumNumberOfDeformationIterations': 1, 'absoluteCostPerVoxelDecreaseStopCriterion': 0.01, 'verbose': False, 'maximalDeformationStopCriterion': 0.01, 'lineSearchMaximalDeformationIntervalStopCriterion': 0.01, 'maximalDeformationAppliedStopCriterion': 0.0, 'BFGSMaximumMemoryLength': 12, 'multiResolutionSpecification': [{'atlasFileName': '/work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz', 'targetDownsampledVoxelSpacing': 2.0, 'maximumNumberOfIterations': 50, 'estimateBiasField': True}, {'atlasFileName': '/work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz', 'targetDownsampledVoxelSpacing': 1..0, 'maximumNumberOfIterations': 2, 'estimateBiasField': True}]} performing affine atlas registration image: /[...redacted...]/jobs/release/volume.nii.gz template: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii maximalDeformation=1.0000 minLogLikelihood=-0.7440 maximalDeformation=1.0371 minLogLikelihood=-0.7600 maximalDeformation=0.8439 minLogLikelihood=-0.7668 maximalDeformation=8.9885 minLogLikelihood=-0.8230 maximalDeformation=2.1805 minLogLikelihood=-0.8250 maximalDeformation=1.8946 minLogLikelihood=-0.8368 maximalDeformation=3.3974 minLogLikelihood=-0.8455 maximalDeformation=0.0787 minLogLikelihood=-0.8459 maximalDeformation=0.0193 minLogLikelihood=-0.8459 maximalDeformation=0.0000 minLogLikelihood=-0.8459 appliedScaling: 1.0158 maximalDeformation=1.0000 minLogLikelihood=-0.8630 maximalDeformation=0.2734 minLogLikelihood=-0.8636 maximalDeformation=0.2836 minLogLikelihood=-0.8638 maximalDeformation=0.1536 minLogLikelihood=-0.8640 maximalDeformation=0.5760 minLogLikelihood=-0.8641 maximalDeformation=0.3851 minLogLikelihood=-0.8642 maximalDeformation=0.0000 minLogLikelihood=-0.8642 appliedScaling: 1.0047 maximalDeformation=1.0000 minLogLikelihood=-0.8699 maximalDeformation=0.0000 minLogLikelihood=-0.8699 appliedScaling: 1.0017 writing template transform to /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/template.lta writing talairach transform to /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/samseg.talairach.lta atlas registration complete: 0:01:34.254165 [1. 1. 1.] Unknown Unknown (100%) Skull (100%) GlobalWM Brain-Stem (100%) Left-Cerebellum-White-Matter (100%) Right-Cerebellum-White-Matter (100%) Right-Cerebral-White-Matter (100%) Left-Cerebral-White-Matter (100%) Optic-Chiasm (100%) Right-VentralDC (100%) Left-VentralDC (100%) Right-Pallidum (100%) Right-Thalamus (50%) Left-Pallidum (100%) Left-Thalamus (50%) GlobalGM Left-Cerebellum-Cortex (100%) Right-Cerebellum-Cortex (100%) Left-Cerebral-Cortex (100%) Right-Cerebral-Cortex (100%) Right-Amygdala (100%) Left-Amygdala (100%) Right-Hippocampus (100%) Left-Hippocampus (100%) Left-Accumbens-area (100%) Right-Accumbens-area (100%) WM-hypointensities (100%) Left-Caudate (100%) Right-Thalamus (50%) Right-Caudate (100%) Left-Thalamus (50%) non-WM-hypointensities (100%) GlobalCSF_messy CSF (100%) Fluid_Inside_Eyes (50%) Right-choroid-plexus (100%) Left-choroid-plexus (100%) Right-vessel (100%) Left-vessel (100%) GlobalCSF_clean 4th-Ventricle (100%) Fluid_Inside_Eyes (50%) Right-Inf-Lat-Vent (100%) Left-Inf-Lat-Vent (100%) 3rd-Ventricle (100%) Left-Lateral-Ventricle (100%) Right-Lateral-Ventricle (100%) 5th-Ventricle (100%) Putamen Left-Putamen (100%) Right-Putamen (100%) Soft Soft_Nonbrain_Tissue (100%) ==================== Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz Transforming points Transforming points 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 1 0.398942 SLIDING 1 0.398942 SLIDING Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 1 [BRACKETING] Hit a really bad solution -- ready for zooming: 1 [ZOOMING] Zooming with low=0 and high=1 bisected: 0.5 bisected: 0.25 bisected: 0.125 interpolated: 1.2403e-11 Too small for current range [0 0.125]; using something forcibly bigger instead: 0.0125 interpolated: 1.22363e-11 Too small for current range [0 0.0125]; using something forcibly bigger instead: 0.00125 [ZOOMING] Zooming interval size too low; returning best: 0 ----------------------- Optimizer: maximalDeformation is too small; stopping 1 0.398942 SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.01 MaximalDeformationStopCriterion: 0.01 MaximumNumberOfIterations: 1 Verbose: 0 1 0.398942 SLIDING Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Constructing image-to-world transform from header information (/[...redacted...]/jobs/release/volume.nii.gz) Read image: /[...redacted...]/jobs/release/volume.nii.gz Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz niiRead(): detected input as 64 bit double, reading in as 32 bit float Read mesh collection: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz { depth: 1 maximumNumberOfDeformationIterations: 1 absoluteCostPerVoxelDecreaseStopCriterion: 0.01 verbose: False maximalDeformationStopCriterion: 0.01 lineSearchMaximalDeformationIntervalStopCriterion: 0.01 maximalDeformationAppliedStopCriterion: 0.0 BFGSMaximumMemoryLength: 12 multiResolutionSpecification: { depth: 2 atlasFileName: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz targetDownsampledVoxelSpacing: 2.0 maximumNumberOfIterations: 50 estimateBiasField: True }, { depth: 2 atlasFileName: /work2/08266/psadil/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz targetDownsampledVoxelSpacing: 1.0 maximumNumberOfIterations: 2 estimateBiasField: True } } ==================== iterationNumber: 0 EM converged! blockNumber 0 efficiency: 127.8986 % relative size: 19.7796 % setup time: 0.6695 sec blockNumber 1 efficiency: 129.5280 % relative size: 20.8106 % setup time: 0.4791 sec blockNumber 2 efficiency: 124.7648 % relative size: 23.2798 % setup time: 0.4969 sec blockNumber 3 efficiency: 127.9526 % relative size: 20.9638 % setup time: 0.4770 sec blockNumber 4 efficiency: 124.4211 % relative size: 23.4852 % setup time: 0.4918 sec blockNumber 5 efficiency: 127.3941 % relative size: 18.5357 % setup time: 0.4698 sec Total time spent: 0.0033 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.0000 ======================================================= iterationNumber: 1 EM converged! ProbabilisticAtlas reusing warm optimizers!! Total time spent: 0.0034 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.0000 ======================================================= iterationNumber: 2 EM converged! ProbabilisticAtlas reusing warm optimizers!! Total time spent: 0.0034 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.0000 ======================================================= iterationNumber: 0 EM converged! blockNumber 0 efficiency: 118.7363 % relative size: 20.8927 % setup time: 1.6169 sec blockNumber 1 efficiency: 121.0767 % relative size: 20.8433 % setup time: 1.0427 sec blockNumber 2 efficiency: 123.9971 % relative size: 18.9659 % setup time: 1.0240 sec blockNumber 3 efficiency: 118.9662 % relative size: 20.6564 % setup time: 1.0509 sec blockNumber 4 efficiency: 117.7030 % relative size: 19.9348 % setup time: 1.0399 sec blockNumber 5 efficiency: 122.6568 % relative size: 19.1271 % setup time: 1.0273 sec Total time spent: 0.0124 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.0000 ======================================================= iterationNumber: 1 EM converged! ProbabilisticAtlas reusing warm optimizers!! Total time spent: 0.0089 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.0000 ======================================================= using default intracranial structures to compute sbtiv measure Saving the template warp run_samseg complete: 0:04:08.072359 GCAMwrite @#@FSTIME 2023:05:17:17:32:00 run_samseg N 9 e 276.60 S 6.87 U 226.42 P 84% M 5448744 F 4116 R 1612330 W 0 c 42 w 14636 I 267688 O 323136 L 0.01 1.32 2.98 @#@FSLOADPOST 2023:05:17:17:36:36 run_samseg N 9 0.96 1.06 2.44 run_samseg complete Wed May 17 17:36:36 CDT 2023 lta_convert --inlta /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/samseg.talairach.lta --outmni /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/samseg.talairach.xfm 7.3.2 --inlta: /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/samseg.talairach.lta input LTA transform. --outmni: /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/samseg.talairach.xfm output MNI/XFM matrix. LTA read, type : 1 1.02236 0.01245 0.12949 0.58992; -0.00437 1.08080 -0.00870 2.62878; -0.15613 0.06510 1.14175 12.21557; 0.00000 0.00000 0.00000 1.00000; lta_convert successful. mri_segstats --ctab-default --seg /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz --sum /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.stats Using defalt ctab /work2/08266/psadil/freesurfer/FreeSurferColorLUT.txt 7.3.2 cwd cmdline mri_segstats --ctab-default --seg /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz --sum /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.stats sysname Linux hostname c103-211.frontera.tacc.utexas.edu machine x86_64 user psadil whitesurfname white UseRobust 0 Loading /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1436 segmentations Computing statistics for each segmentation Reporting on 44 segmentations Using PrintSegStat mri_segstats done Started at Wed May 17 17:31:59 CDT 2023 Ended at Wed May 17 17:36:40 CDT 2023 Samseg-Run-Time-Min 4.68 Samseg-Run-Time-Hours 0.08 samseg Done @#@FSTIME 2023:05:17:17:31:59 samseg N 9 e 280.79 S 6.97 U 230.29 P 84% M 5448744 F 4122 R 1647009 W 0 c 108 w 15165 I 283968 O 323472 L 0.01 1.32 2.98 @#@FSLOADPOST 2023:05:17:17:36:40 samseg N 9 0.96 1.06 2.43 mri_binarize --i /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz --match 2 3 7 8 16 24 41 42 46 47 165 259 4 5 10 11 12 13 17 18 26 28 30 31 14 15 16 77 85 43 44 49 50 51 52 53 54 58 60 62 63 --o /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg.bin.dil.mgz --dilate 1 7.3.2 cwd /[...redacted...]/jobs/release cmdline mri_binarize --i /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz --match 2 3 7 8 16 24 41 42 46 47 165 259 4 5 10 11 12 13 17 18 26 28 30 31 14 15 16 77 85 43 44 49 50 51 52 53 54 58 60 62 63 --o /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg.bin.dil.mgz --dilate 1 sysname Linux hostname c103-211.frontera.tacc.utexas.edu machine x86_64 user psadil input /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/seg.mgz frame 0 nErode3d 0 nErode2d 0 output /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg.bin.dil.mgz Binarizing based on matching values nMatch 41 0 2 1 3 2 7 3 8 4 16 5 24 6 41 7 42 8 46 9 47 10 165 11 259 12 4 13 5 14 10 15 11 16 12 17 13 18 17 19 18 20 26 21 28 22 30 23 31 24 14 25 15 26 16 27 77 28 85 29 43 30 44 31 49 32 50 33 51 34 52 35 53 36 54 37 58 38 60 39 62 40 63 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 1843081 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 2059752 voxels in final mask Writing output to /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg.bin.dil.mgz Count: 2059752 2059752.000000 8530021 24.147092 mri_binarize done mri_concatenate_lta /work2/08266/psadil/freesurfer/average/mideface-atlas/reg.samseg-default.lta /[...redacted...]/jobs/release/tmpdir.midefacer.205539/samseg/template.lta /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input.lta Read individual LTAs Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2.... Writing combined LTA to file /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input.lta... mri_concatenate_lta successful. lta_convert --subject defacing-atlas --invert --inlta /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input.lta --outlta /[...redacted...]/jobs/release/tmpdir.midefacer.205539/input2atlas.lta 7.3.2 --s: defacing-atlas subject name --invert: will invert transform. --inlta: /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input..lta input LTA transform. --outlta: /[...redacted...]/jobs/release/tmpdir.midefacer.205539/input2atlas.lta output LTA. LTA read, type : 1 0.92032 0.00244 -0.09021 -0.96096; 0.00139 0.90319 0.03621 -3.20219; 0.11587 -0.08143 0.79401 -4.69215; -0.00000 -0.00000 -0.00000 1.00000; setting subject to defacing-atlas Writing LTA to file /[...redacted...]/jobs/release/tmpdir.midefacer.205539/input2atlas.lta... lta_convert successful. mris_apply_reg --lta /work2/08266/psadil/freesurfer/average/mideface-atlas/average.head.dec44.us7.remesh3.ripple.surf /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input.lta /[...redacted...]/jobs/release/tmpdir.midefacer.205539/template.surf Reading in /work2/08266/psadil/freesurfer/average/mideface-atlas/average.head.dec44.us7.remesh3.ripple.surf Reading in /[...redacted...]/jobs/release/tmpdir.midefacer.205539/atlas2input.lta Changing type to REGISTER_DAT MRISltaMultiply(): applying matrix 0.92032 -0.09021 -0.00244 1.39829; 0.11587 0.79401 0.08143 -47.35222; 0.00139 0.03621 -0.90319 7.85163; -0.00000 -0.00000 0.00000 1.00000; ----------------------------------- Determinant of linear transform is negative, so reversing face order Writing surf to /[...redacted...]/jobs/release/tmpdir.midefacer.205539/template.surf mris_apply_reg done mkheadsurf -i /[...redacted...]/jobs/release/volume.nii.gz -o /[...redacted....]/jobs/release/tmpdir.midefacer.205539/head.mgz -surf /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.surf -rescale -no-inflate -fill-holes-islands -mc -no-curv INFO: log file is /[...redacted...]/jobs/release/tmpdir.midefacer.205539/mkheadsurf.log -------------------------------- Wed May 17 17:36:46 CDT 2023 /[...redacted...]/jobs/release mri_seghead --invol /[...redacted...]/jobs/release/volume.nii.gz --outvol /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.mgz --fill 1 --thresh1 20 --thresh2 20 --nhitsmin 2 --rescale --fill-holes-islands -------------------------------- input volume: /[...redacted...]/jobs/release/volume.nii.gz output volume: /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.mgz threshold1: 20 threshold2: 20 nhitsmin: 2 fill value: 1 Loading input volume niiRead(): detected input as 64 bit double, reading in as 32 bit float Changing type, rescale = 1 MRIchangeType: Building histogram -68.7235 1307.2 1000, flo=0, fhi=255, dest_type=0 Filling Columns Filling Rows Filling Slices Merging nhits = 2945860 Removing islands MRIremoveVolumeIslands() thresh=0.5, nKeep=1, nclusters = 687 Removing Volume Holes MRIremoveVolumeHoles() thresh=0.5, nKeep=1 MRIremoveVolumeIslands() thresh=0.5, nKeep=1, nclusters = 1 Filling axial Slice Holes ostr LPS slicedir 6 slicediruse 3 slicedim 193 229 1 MRIremoveSliceHodes() removed 16112 voxels Filling sag Slice Holes ostr LPS slicedir 4 slicediruse 1 slicedim 1 229 193 MRIremoveSliceHodes() removed 2775 voxels Filling cor Slice Holes slicedir 2 slicediruse 2 slicedim 193 1 193 MRIremoveSliceHodes() removed 822 voxels Counting N Head Voxels = 2964151 N Back Voxels = 5565870 Avg. Back Intensity = 13.248070 Max. Back Intensity = 1151.476440 Writing output Done -------------------------------- Wed May 17 17:36:58 CDT 2023 /[...redacted...]/jobs/release mri_mc /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.mgz 1 /[....redacted...]/jobs/release/tmpdir.midefacer.205539/head.surf -------------------------------- preprocessing...done starting generation of surface... slice nb 10... slice nb 20... slice nb 30... slice nb 40... slice nb 50... slice nb 60... slice nb 70... slice nb 80... slice nb 90... slice nb 100... slice nb 110... slice nb 120... slice nb 130... slice nb 140... slice nb 150... slice nb 160... constructing final surface... (surface with 354632 faces and 177302 vertices)...done computing the maximum edge length...1.414214 mm reversing orientation of faces... checking orientation of surface... 0.000 % of the vertices (0 vertices) exhibit an orientation change counting number of connected components... 177302 voxel in cpt #1: X=-14 [v=177302,e=531948,f=354632] located at (2.291599, -29.413504, -3.787194) For the whole surface: X=-14 [v=177302,e=531948,f=354632] One single component has been found nothing to do writing out surface...done -------------------------------- Wed May 17 17:37:01 CDT 2023 /[...redacted...]/jobs/release mris_smooth -n 10 -nw /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.surf /[...redacted...]/jobs/release/tmpdir.midefacer.205539/head.surf -------------------------------- smoothing for 10 iterations smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... Started at: Wed May 17 17:36:46 CDT 2023 Ended at: Wed May 17 17:37:05 CDT 2023 mkheadsurf done @#@FSTIME 2023:05:17:17:36:46 mkheadsurf N 11 e 18.35 S 0.59 U 17.37 P 97% M 434560 F 3 R 278026 W 0 c 49 w 584 I 21736 O 25328 L 0.97 1.06 2.42 @#@FSLOADPOST 2023:05:17:17:37:05 mkheadsurf N 11 0.97 1.05 2.39 mri_defacer --i /[...redacted...]/jobs/release/volume.nii.gz --ts /[...redacted...]/jobs/release/tmpdir.midefacer.205539/template.surf --min /[...redacted...]/jobs/release/tmpdir.midefacer.205539/min.surf --max /[...redacted....]/jobs/release/tmpdir.midefacer.205539/max.surf --m /[...redacted...]/jobs/release/tmpdir.midefacer.205539/face.mask.mgz --o /[...redacted...]/jobs/release/defaced.nii.gz --hm /[...redacted...]/jobs/release/tmpdir.midefacer..205539/head.mgz --distdat /[...redacted...]/jobs/release/tmpdir.midefacer.205539/dist.samples --stats /[...redacted...]/jobs/release/tmpdir.midefacer..205539/stats.dat --w /work2/08266/psadil/freesurfer/average/mideface-atlas/mideface.watermark.dec44.us7.remesh3.label 5 --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.lower.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.upper.no-eyes.no-nose.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.nose.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.eyes.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.left.dec44.us7.remesh3.label 2 3 --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.right.dec44.us7.remesh3.label 2 3 --xmask /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg.bin.dil.mgz 7.3.2 cd /[...redacted...]/jobs/release mri_defacer --i /[...redacted...]/jobs/release/volume.nii.gz --ts /[...redacted...]/jobs/release/tmpdir.midefacer.205539/template.surf --min /[...redacted...]/jobs/release/tmpdir.midefacer.205539/min.surf --max /[...redacted....]/jobs/release/tmpdir.midefacer.205539/max.surf --m /[...redacted...]/jobs/release/tmpdir.midefacer.205539/face.mask.mgz --o /[...redacted...]/jobs/release/defaced.nii.gz --hm /[...redacted...]/jobs/release/tmpdir.midefacer..205539/head.mgz --distdat /[...redacted...]/jobs/release/tmpdir.midefacer.205539/dist.samples --stats /[...redacted...]/jobs/release/tmpdir.midefacer..205539/stats.dat --w /work2/08266/psadil/freesurfer/average/mideface-atlas/mideface.watermark.dec44.us7.remesh3.label 5 --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.lower.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.upper.no-eyes.no-nose.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.nose.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.eyes.dec44.us7.remesh3.label --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.left.dec44.us7.remesh3.label 2 3 --l /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.right.dec44.us7.remesh3.label 2 3 --xmask /[...redacted...]/jobs/release/tmpdir.midefacer.205539/seg.bin.dil.mgz sysname Linux hostname c103-211.frontera.tacc.utexas.edu machine x86_64 user psadil niiRead(): detected input as 64 bit double, reading in as 32 bit float Applying watermark d=5 Applying watermark 2207 DeltaDist = 0.333333, dL = 0.111111 DistInMin 2 DistInMax 100 DistInFrac 0.9 DistOutMin 2 DistOutMax 100 DistOutFrac 1 DeltaDist 0.333333 dL 0.111111 Pad 5 5 5 FillType 1 FillConstIn 0 FillConstOut 0 DoRipple 0 =============================================== Label 0 /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.lower.dec44.us7.remesh3.label 2 20 MiDeface::DistanceBounds() DeltaDist=0.333333 Raw DistIn = 0, DistOut = 0 DistIn=0 < DistInMin=2, resetting DistOut=0 < DistOutMin=2, resetting PostMinCheck DistIn = 2, DistOut = 2 MiDeface::SegFace() =============================================== Label 1 /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.upper.no-eyes.no-nose.dec44.us7.remesh3.label 2 20 MiDeface::DistanceBounds() DeltaDist=0.333333 Raw DistIn = 1, DistOut = 9.33333 DistIn=1 < DistInMin=2, resetting PostMinCheck DistIn = 2, DistOut = 9.33333 MiDeface::SegFace() =============================================== Label 2 /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.nose.dec44.us7.remesh3.label 2 20 MiDeface::DistanceBounds() DeltaDist=0.333333 Raw DistIn = 2.66667, DistOut = 2.66667 PostMinCheck DistIn = 2.66667, DistOut = 2.66667 MiDeface::SegFace() =============================================== Label 3 /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.eyes.dec44.us7.remesh3.label 2 20 MiDeface::DistanceBounds() DeltaDist=0.333333 Raw DistIn = 7, DistOut = 6.66667 PostMinCheck DistIn = 7, DistOut = 6.66667 MiDeface::SegFace() =============================================== Label 4 /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.left.dec44.us7.remesh3.label 2 3 MiDeface::DistanceBounds() DeltaDist=0.333333 Raw DistIn = 3, DistOut = 2 PostMinCheck DistIn = 3, DistOut = 2 MiDeface::SegFace() =============================================== Label 5 /work2/08266/psadil/freesurfer/average/mideface-atlas/average.face.ear.right.dec44.us7.remesh3.label 2 3 MiDeface::DistanceBounds() DeltaDist=0.333333 Raw DistIn = 3, DistOut = 5.33333 PostMinCheck DistIn = 3, DistOut = 5.33333 MiDeface::SegFace() *** Error in `mri_defacer': double free or corruption (!prev): 0x000000000f9e1090 *** ======= Backtrace: ========= /lib64/libc.so.6(+0x81329)[0x2b0d12670329] mri_defacer[0x4aaa0e] mri_defacer[0x423bd5] mri_defacer[0x4163d8] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b0d12611555] mri_defacer[0x419327] ======= Memory map: ======== 00400000-006f7000 r-xp 00000000 3d8:ad14e 144121710017324715 /work2/08266/psadil/freesurfer/bin/mri_defacer 008f6000-008fe000 r--p 002f6000 3d8:ad14e 144121710017324715 /work2/08266/psadil/freesurfer/bin/mri_defacer 008fe000-00928000 rw-p 002fe000 3d8:ad14e 144121710017324715 /work2/08266/psadil/freesurfer/bin/mri_defacer 00928000-011c1000 rw-p 00000000 00:00 0 026c1000-13727000 rw-p 00000000 00:00 0 [heap] 2b0d11411000-2b0d11433000 r-xp 00000000 fd:00 402880897 /usr/lib64/ld-2.17.so 2b0d11433000-2b0d11437000 rw-p 00000000 00:00 0 2b0d11454000-2b0d11456000 rw-p 00000000 00:00 0 2b0d11456000-2b0d1145e000 r--p 00000000 fd:00 278039021 /opt/apps/gcc/8.3.0/lib64/libgomp.so.1.0.0 2b0d1145e000-2b0d1147c000 r-xp 00008000 fd:00 278039021 /opt/apps/gcc/8.3.0/lib64/libgomp.so.1.0.0 2b0d1147c000-2b0d11484000 r--p 00026000 fd:00 278039021 /opt/apps/gcc/8.3.0/lib64/libgomp.so.1.0.0 2b0d11484000-2b0d11485000 r--p 0002d000 fd:00 278039021 /opt/apps/gcc/8.3.0/lib64/libgomp.so.1.0.0 2b0d11485000-2b0d11486000 rw-p 0002e000 fd:00 278039021 /opt/apps/gcc/8.3.0/lib64/libgomp.so.1.0.0 2b0d11486000-2b0d11487000 rw-p 00000000 00:00 0 2b0d11487000-2b0d11518000 r--p 00000000 fd:00 278039063 /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25 2b0d11518000-2b0d115c4000 r-xp 00091000 fd:00 278039063 /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25 2b0d115c4000-2b0d11602000 r--p 0013d000 fd:00 278039063 /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25 2b0d11602000-2b0d11603000 ---p 0017b000 fd:00 278039063 /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25 2b0d11603000-2b0d1160d000 r--p 0017b000 fd:00 278039063 /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25 2b0d1160d000-2b0d1160f000 rw-p 00185000 fd:00 278039063 /opt/apps/gcc/8.3.0/lib64/libstdc++.so.6.0.25 2b0d1160f000-2b0d11613000 rw-p 00000000 00:00 0 2b0d11613000-2b0d11616000 r--p 00000000 fd:00 278039010 /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1 2b0d11616000-2b0d11627000 r-xp 00003000 fd:00 278039010 /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1 2b0d11627000-2b0d1162a000 r--p 00014000 fd:00 278039010 /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1 2b0d1162a000-2b0d1162b000 ---p 00017000 fd:00 278039010 /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1 2b0d1162b000-2b0d1162c000 r--p 00017000 fd:00 278039010 /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1 2b0d1162c000-2b0d1162d000 rw-p 00018000 fd:00 278039010 /opt/apps/gcc/8.3.0/lib64/libgcc_s.so.1 2b0d1162d000-2b0d11632000 rw-p 00000000 00:00 0 2b0d11632000-2b0d11633000 r--p 00021000 fd:00 402880897 /usr/lib64/ld-2.17.so 2b0d11633000-2b0d11634000 rw-p 00022000 fd:00 402880897 /usr/lib64/ld-2.17.so 2b0d11634000-2b0d11635000 rw-p 00000000 00:00 0 2b0d11635000-2b0d11675000 r-xp 00000000 fd:00 269642820 /opt/apps/xalt/2.10.34/lib64/libxalt_init.so 2b0d11675000-2b0d11875000 ---p 00040000 fd:00 269642820 /opt/apps/xalt/2.10.34/lib64/libxalt_init.so 2b0d11875000-2b0d11876000 r--p 00040000 fd:00 269642820 /opt/apps/xalt/2.10.34/lib64/libxalt_init.so 2b0d11876000-2b0d11877000 rw-p 00041000 fd:00 269642820 /opt/apps/xalt/2.10.34/lib64/libxalt_init.so 2b0d11877000-2b0d11878000 rw-p 00000000 00:00 0 2b0d11878000-2b0d1188d000 r-xp 00000000 fd:00 404656596 /usr/lib64/libz.so.1.2.7 2b0d1188d000-2b0d11a8c000 ---p 00015000 fd:00 404656596 /usr/lib64/libz.so.1.2.7 2b0d11a8c000-2b0d11a8d000 r--p 00014000 fd:00 404656596 /usr/lib64/libz.so.1.2.7 2b0d11a8d000-2b0d11a8e000 rw-p 00015000 fd:00 404656596 /usr/lib64/libz.so.1.2.7 2b0d11a8e000-2b0d11aa5000 r-xp 00000000 fd:00 402965799 /usr/lib64/libpthread-2.17.so 2b0d11aa5000-2b0d11ca4000 ---p 00017000 fd:00 402965799 /usr/lib64/libpthread-2.17.so 2b0d11ca4000-2b0d11ca5000 r--p 00016000 fd:00 402965799 /usr/lib64/libpthread-2.17.so 2b0d11ca5000-2b0d11ca6000 rw-p 00017000 fd:00 402965799 /usr/lib64/libpthread-2.17.so 2b0d11ca6000-2b0d11caa000 rw-p 00000000 00:00 0 2b0d11caa000-2b0d11cac000 r-xp 00000000 fd:00 402880903 /usr/lib64/libdl-2.17.so 2b0d11cac000-2b0d11eac000 ---p 00002000 fd:00 402880903 /usr/lib64/libdl-2.17.so 2b0d11eac000-2b0d11ead000 r--p 00002000 fd:00 402880903 /usr/lib64/libdl-2.17.so 2b0d11ead000-2b0d11eae000 rw-p 00003000 fd:00 402880903 /usr/lib64/libdl-2.17.so 2b0d11eae000-2b0d11faf000 r-xp 00000000 fd:00 402880909 /usr/lib64/libm-2.17.so 2b0d11faf000-2b0d121ae000 ---p 00101000 fd:00 402880909 /usr/lib64/libm-2.17.so 2b0d121ae000-2b0d121af000 r--p 00100000 fd:00 402880909 /usr/lib64/libm-2.17.so 2b0d121af000-2b0d121b0000 rw-p 00101000 fd:00 402880909 /usr/lib64/libm-2.17.so 2b0d121b0000-2b0d121b8000 r-xp 00000000 fd:00 402704011 /usr/lib64/libcrypt-2.17.so 2b0d121b8000-2b0d123b7000 ---p 00008000 fd:00 402704011 /usr/lib64/libcrypt-2.17.so 2b0d123b7000-2b0d123b8000 r--p 00007000 fd:00 402704011 /usr/lib64/libcrypt-2.17.so 2b0d123b8000-2b0d123b9000 rw-p 00008000 fd:00 402704011 /usr/lib64/libcrypt-2.17.so 2b0d123b9000-2b0d123e7000 rw-p 00000000 00:00 0 2b0d123e7000-2b0d123ee000 r-xp 00000000 fd:00 403139684 /usr/lib64/librt-2.17.so 2b0d123ee000-2b0d125ed000 ---p 00007000 fd:00 403139684 /usr/lib64/librt-2.17.so 2b0d125ed000-2b0d125ee000 r--p 00006000 fd:00 403139684 /usr/lib64/librt-2.17.so 2b0d125ee000-2b0d125ef000 rw-p 00007000 fd:00 403139684 /usr/lib64/librt-2.17.so 2b0d125ef000-2b0d127b3000 r-xp 00000000 fd:00 402704007 /usr/lib64/libc-2.17.so 2b0d127b3000-2b0d129b2000 ---p 001c4000 fd:00 402704007 /usr/lib64/libc-2.17.so 2b0d129b2000-2b0d129b6000 r--p 001c3000 fd:00 402704007 /usr/lib64/libc-2.17.so=============================================== MiDeface::FaceIntensityStats() Mode2 12 12 4352 @#@FSTIME 2023:05:17:17:37:05 mri_defacer N 39 e 12.40 S 0.44 U 11.68 P 97% M 801792 F 1 R 283367 W 0 c 2 w 129 I 10144 O 1392 L 0.97 1.05 2.39 @#@FSLOADPOST 2023:05:17:17:37:17 mri_defacer N 39 0.98 1.05 2.38 ERROR: Patrick Sadil, PhD (he/him/his) Research Associate psadil.github.io/psadil _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1zAGHDjLv0cEFFcHUwZV0UwFrJRbZndb6D7V-kbbDSW6rz… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1Ik2XgIi9JI6jyIG7mtSp6lJHT-sodGM6CBmxlMEEzOG4e… <https://secure-web.cisco.com/1Ik2XgIi9JI6jyIG7mtSp6lJHT-sodGM6CBmxlMEEzOG4eUhqaf_vcQqr8RiwfPo5hg4-545zbjpmzL3ii1BHuZu66f75-h5URCdmjFLbUueG18kNVbRsnOYKTwQ12r_hvyl0swhI2qaDadned13wZ79YXcHx8Oaeo33crNWxVokahWNyJyur5Q83kCFEZ7NPO3VoWotP9YCr_q5agVy3w5ezyLOgKymeTnG9TxRBvZbuvhKa3sOitLzggi6bvCN2dnp04QmuBzlipm-Ma8qZZpaUXJ3kv2TJy7yYc6Z5VPpUecdzB9jZxaHyauuOu-cocIIbACPr7lmFazKU44rn0SGObNQvneOXYx59N6Nqbog/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1ZHeKepKCm3hit_Sx5u0RQNVsHfnkjDjGMqOLfhF_ioF90… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1k5wPkgJftsakro9goteULefYgZ1UMRrY-MEjUwJH3tuDk… <https://secure-web.cisco.com/1kMnrOmLbKR4ZauwxGRc-GrB2y_R2AyaqynC34qZRITMCZdSdY1Ub9ftocqFfNBclw9oZEQNMOk_hYtKmcZC1LOQ6x7orxVc8QBVs3mDwnGVF32i8CIVjrsH1828LW3t4DGQCkSPXgP4pheiKf6CGE7d5_nlncnUE4uew8wZrvXX304hwmBceqibasBvndv6_h-OPJo9NOu-NBHLBZSi4WKrQIiRslfMomLYE5ptPpDDLEAOs6M9rBURofNrszVmsZ0zLj4vcF5dVju51TIifvHk1FBQP9pSpLtzqBRDg5lYzAU3KuG7DoGTB4brB9FM_4J57pLtY6nE7DajpHwvE3RTCibK-f504ywwXF-tY4tI/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

2 2

Re: [Freesurfer] Issue with running recon-all
by hmarzban＠student.ubc.ca 24 May '23

24 May '23

External Email - Use Caution Hello No, I can not load /arc/project/3T/fsaverage/surf/lh.sphere.reg in freeview. I am encountering the "readFloat: fread failed" error. Also I cant attach the log file because I encounter with this response: Your email Is being held until the list moderator can review it for approval. The reason it is being held: Message body is too big: 22531815 bytes with a limit of 10000 KB Regards Hengameh ________________________________ From: hmarzban(a)student.ubc.ca Sent: Tuesday, May 23, 2023 2:07:10 PM To: Freesurfer support list Subject: Re: Issue with running recon-all Sure. I have attached it. No, I can not load /arc/project/3T/fsaverage/surf/lh.sphere.reg in freeview. I am encountering the "readFloat: fread failed" error. Regards Hengameh ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> Sent: Tuesday, May 23, 2023 1:49:41 PM To: Freesurfer support list Subject: Re: [Freesurfer] Issue with running recon-all [CAUTION: Non-UBC Email] External Email - Use Caution Hmm, can you send us the recon-all.log file? Can you load /arc/project/3T/fsaverage/surf/lh.sphere.reg in freeview? Maybe it was corrupted at some point? From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of hmarzban(a)student.ubc.ca Sent: Tuesday, May 23, 2023 4:48 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Issue with running recon-all External Email - Use Caution Hello Bruce, Thank you for your response. I have verified the available disk space, and it appears that I have sufficient space. I am currently using freesurfer-darwin-macOS-dev.pkg, which was developed in March 2023. It seems that the issue lies in the inability to generate just the BA.stats files, including rh.BA_exvivo.stats, rh.BA_exvivo.thresh.stats, and others. Do you have any additional suggestions or recommendations? Thank you once again for your assistance. Best regards, Hengameh ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: Monday, May 15, 2023 10:21:58 AM To: Freesurfer support list Subject: Re: [Freesurfer] Issue with running recon-all [CAUTION: Non-UBC Email] External Email - Use Caution Hi Hengameh By far the most common reason for this is running out of disk space. Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of hmarzban(a)student.ubc.ca<mailto:hmarzban@student.ubc.ca> Sent: Monday, May 15, 2023 1:02 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Issue with running recon-all External Email - Use Caution Dear developers, I am writing to report an issue I encountered while running recon-all on some subjects. Specifically, I received an error message stating "error: freadFloat: fread failed" for several of the subjects. Starting surface-based mapping Reading source registration /arc/project/3T/fsaverage/surf/lh.sphere.reg error: freadFloat: fread failed error: freadFloat: fread failed ... I am wondering if any of you have experienced this issue before, and if so, I would greatly appreciate any recommendations on how to proceed with resolving it. Thank you for your help. Hengameh

2 1

Re: [Freesurfer] Issue with running recon-all
by hmarzban＠student.ubc.ca 23 May '23

23 May '23

External Email - Use Caution Hello Bruce, Thank you for your response. I have verified the available disk space, and it appears that I have sufficient space. I am currently using freesurfer-darwin-macOS-dev.pkg, which was developed in March 2023. It seems that the issue lies in the inability to generate just the BA.stats files, including rh.BA_exvivo.stats, rh.BA_exvivo.thresh.stats, and others. Do you have any additional suggestions or recommendations? Thank you once again for your assistance. Best regards, Hengameh ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> Sent: Monday, May 15, 2023 10:21:58 AM To: Freesurfer support list Subject: Re: [Freesurfer] Issue with running recon-all [CAUTION: Non-UBC Email] External Email - Use Caution Hi Hengameh By far the most common reason for this is running out of disk space. Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of hmarzban(a)student.ubc.ca Sent: Monday, May 15, 2023 1:02 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Issue with running recon-all External Email - Use Caution Dear developers, I am writing to report an issue I encountered while running recon-all on some subjects. Specifically, I received an error message stating "error: freadFloat: fread failed" for several of the subjects. Starting surface-based mapping Reading source registration /arc/project/3T/fsaverage/surf/lh.sphere.reg error: freadFloat: fread failed error: freadFloat: fread failed ... I am wondering if any of you have experienced this issue before, and if so, I would greatly appreciate any recommendations on how to proceed with resolving it. Thank you for your help. Hengameh

2 1

question about freeview in freesurfer 7.4.0 and qt
by tulu＠ms36.hinet.net 22 May '23

22 May '23

External Email - Use Caution Dear freesurfer experts, recently I update freesurfer to freesurfer 7.4.0 under Ubuntu 20.04. when I try to launch freeview, I get error message as: freeview This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb. Abort (core dumped) could anyone can direct me how to solve this problem ? sincerely Jung Lung Hsu

1 0

Exporting an advanced segmentation mask for the ROI-based analyses
by Yoo, Chi-Hyeon 22 May '23

22 May '23

External Email - Use Caution Hello, I am Chi-Hyeon, a postdoc at the Martinos Center. One of my colleagues wants to try to use advance segmentations: brainstem substructures segmentation (https://secure-web.cisco.com/10i08joHQng6yy87_-Iv618kYQPXRW-hpxjKH9kcjO2KOq…) and limbic segmentation (https://secure-web.cisco.com/1G7Fom1uIgN-gFY6zk_6Hke0zvGSdyKnPlI53oHnUoBSck…) Thanks to the instructions, I was able to generate the segmentations but I cannot find the lookup table for the labels for this versions of segmentation. I will need a look-up table to generate binary masks from these segmentations to eventually export PET values from that binary segmentation masks. Please let me know where I could find the labels for these sets of segmentations. Chi-Hyeon

2 1

make brainstem surface file and make average brainstem surface
by tulu＠ms36.hinet.net 22 May '23

22 May '23

External Email - Use Caution Dear Freesurfer experts, Could I use the brainstem file (brainstemSsLabels.v1x.FSvoxelSpace.mgz) and make it as surface file ? if I have multiple subjects' file, how to make the average surface file for visualization ? Sincerely Jung Lung Hsu

2 1

How can I increase radius of a binary disk?
by Andy Kim 20 May '23

20 May '23

External Email - Use Caution Dear Dr. Douglas N. Greve, Thanks to you, I could have a binary disk approximately 3mm in radius by the codes you told me (https://secure-web.cisco.com/1z0F3-vP1KDJI6B_AsTyKAaKNmMd0vO7tGkwv_YiAe4mgt…) mri_volsynth --dim-surf fsaverage/surf/lh.white --pdf delta --delta-crsf ${vertexno} 0 0 0 --0 delta.mgh mris_fwhm --i delta.mgh --o delta.sm3.mgh --s fsaverage --hemi lh mri_binarize --i delta.sm3.mgh --min 0.5 --o delta.sm3.bin.mgh I have sincerely appreciated your help. Now I'm wondering how to modulate the radius. I guess I can do it by adding --fwhm option to mris_fwhm command, for example: mris_fwhm --i delta.mgh --o delta.sm3.mgh --s fsaverage --hemi lh --fwhm 5 At the end, I will get a binary disk with 5mm in radius. Am I right? And does this mean that --fwhm 3 is default for mris_fwhm? How could you define 3mm? Kind Regards, Andy (Junghyun) Kim

2 2

Volume transformation issue
by Carlos Alcocer 19 May '23

19 May '23

External Email - Use Caution Hi, I am trying to transform a volumetric ROI from MNI152 space to native space. I am doing this in 2 steps. First (1) I am creating a registration file using bb register to create a registration file and then (2) I am using mri_vol2vol to transform volume onto my subject using the registration file I created in step 1. 1. bbregister --s subjid --mov roi_in_MNI152.mgz --t1 --reg register.dat 2. mri_vol2vol --targ subjid/mri/T1.mgz --mov roi_in_MNI152.mgz --reg register.dat --o roi_in_native.mgz However, the transformed volume is not anatomically positioned where it is supposed to be. Is there an error in my method? Thank you, Carlos

2 1

Re: [Freesurfer] FSL not installed in setup
by fsbuild 18 May '23

18 May '23

External Email - Use Caution FSL is not included in the freesurfer distribution and is covered by its own license, i.e. for release 6, FMRIB Software Library, Release 6.0 (c) 2018, The University of Oxford.  It can be downloaded and installed from their wiki page, https://secure-web.cisco.com/16O3UT_MWu0a4Jy2ifmfNIL0rCFkh8zn4r2… If you install it on the same system(s) with the freesurfer installation, e.g., under /usr/local/fsl, then freesurfer should find that path autoamtically and set FSL_DIR to it when you setup the freesurfer environment. You may however already have FSL installed on your servers in which case you can set FSL_DIR in your shell initialization file to point to that.  Subsequently, freesurfer should use that predefined setting for FSL_DIR when you start a new terminal window and display that setting of  FSL_DIR when you setup the freesurfer environment. I think some people here may still use FSL version 5.0.7, but the latest version we have on hand is 6.0.6 - R. On May 18, 2023, at 15:38, Lauren Stephens <laurenss(a)stanford.edu> wrote:        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/7.3.2FSFAST_HOME       /Applications/freesurfer/7.3.2/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.3.2/subjectsMNI_DIR           /Applications/freesurfer/7.3.2/mniSLE-PBS-h4tkn18vq6x3:~ timothydurazzo$ bedpostx_datacheck-bash: bedpostx_datacheck: command not foundSLE-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@stanford.edu P: (650)-725-1716_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Tracula Bedpost error
by Lauren Stephens 18 May '23

18 May '23

External Email - Use Caution Dear Freesurfer experts, We are attempting to run tracula on one of our files in preparation for running an entire data set. We were able to successfully run trac-all -prep and were attempting to run trac-all -bedp and received: ----- Bedpostx Monitor ----- An error ocurred. Please check file /Users/corpuscallosum/Desktop/Freesurfer/BRASS/R001A/R001A/dmri.bedpostX/logs/bedpostx_pre.e11191 Killed We are using Freesurfer 7.3.2 on an iMac Pro running Ventura 13.3.1 in a bash shell. I have attached the dmri.bedpostX, logs with the specific error. I have also attached the trac-all.log. Thank you for any help you are able to provide to clear this error! 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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