Freesurfer May 2023

freesurfer@nmr.mgh.harvard.edu

75 participants
109 discussions

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

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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

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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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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

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