Freesurfer August 2021

freesurfer@nmr.mgh.harvard.edu

73 participants
101 discussions

BrainSegVol above 2 mio mm³
by Petersen, Marvin 23 Aug '21

23 Aug '21

External Email - Use Caution Dear FreeSurfer Team, we use smriprep for structural preprocessing and surface reconstruction on our local HPC. It contains freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a. The image outputs look flawless. However, BrainSeg and BrainSegNotVent reported in aseg.stats are far above expected values (for instance larger than eTIV; example output attached). We have processed 600 subjects and the issue applies to all of them. We are currently trying to reproduce these results with freesurfer on a local machine to make sure it's not flawed data or smriprep that is responsible for the issue. As computing brain volume by hand with aseg.mgz yields sensible results (~1.3 mio mm³) we consider mri_segstats in smriprep to be the problem. Grateful for any input. Cheers, Marvin # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /work/fatx405/local/freesurfer-6.0.0/ASegStatsLUT.txt --subject sub-003db57e # sysname Linux # hostname node001 # machine x86_64 # user fatx405 # anatomy_type volume # # SUBJECTS_DIR /work/fatx405/projects # subjectname sub-003db57e # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 2142619.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 2096581.000000, mm^3 # Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation Volume Without Ventricles from Surf, 1306062.635541, mm^3 # Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 39720.000000, mm^3 # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 243502.815347, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 247635.016739, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 491137.832086, mm^3 # Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 229977.705303, mm^3 # Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 231861.098152, mm^3 # Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 461838.803455, mm^3 # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 97441.000000, mm^3 # Measure TotalGray, TotalGrayVol, Total gray matter volume, 789956.832086, mm^3 # Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 1083680.635541, mm^3 # Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume, 1043960.635541, mm^3 # Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial volume voxel count, 1840953.000000, mm^3 # Measure Mask, MaskVol, Mask Volume, 2714626.000000, mm^3 # Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV, 1.272865, unitless # Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 1.612677, unitless # Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces prior to fixing, 37, unitless # Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces prior to fixing, 25, unitless # Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces prior to fixing, 62, unitless # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1683304.717707, mm^3 # SegVolFile mri/aseg.mgz # SegVolFileTimeStamp 2021/08/19 16:13:35 # ColorTable /work/fatx405/local/freesurfer-6.0.0/ASegStatsLUT.txt # ColorTableTimeStamp 2018/08/13 14:53:06 # InVolFile mri/norm.mgz # InVolFileTimeStamp 2021/08/19 16:13:32 # InVolFrame 0 # PVVolFile mri/norm.mgz # PVVolFileTimeStamp 2021/08/19 16:13:32 # Excluding Cortical Gray and White Matter # ExcludeSegId 0 2 3 41 42 # VoxelVolume_mm3 0.578704 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVoxels # TableCol 3 FieldName Number of Voxels # TableCol 3 Units unitless # TableCol 4 ColHeader Volume_mm3 # TableCol 4 FieldName Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader StructName # TableCol 5 FieldName Structure Name # TableCol 5 Units NA # TableCol 6 ColHeader normMean # TableCol 6 FieldName Intensity normMean # TableCol 6 Units MR # TableCol 7 ColHeader normStdDev # TableCol 7 FieldName Itensity normStdDev # TableCol 7 Units MR # TableCol 8 ColHeader normMin # TableCol 8 FieldName Intensity normMin # TableCol 8 Units MR # TableCol 9 ColHeader normMax # TableCol 9 FieldName Intensity normMax # TableCol 9 Units MR # TableCol 10 ColHeader normRange # TableCol 10 FieldName Intensity normRange # TableCol 10 Units MR # NRows 45 # NTableCols 10 # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 4 20298 11994.6 Left-Lateral-Ventricle 27.8315 11.9737 11.0000 93.0000 82.0000 2 5 500 344.7 Left-Inf-Lat-Vent 45.6800 12.3120 15.0000 78.0000 63.0000 3 7 27409 16402.5 Left-Cerebellum-White-Matter 82.5499 5.4997 37.0000 97.0000 60.0000 4 8 96661 55934.2 Left-Cerebellum-Cortex 62.4935 9.7135 0.0000 133.0000 133.0000 5 10 13493 7617.2 Left-Thalamus-Proper 90.8387 9.8593 30.0000 114.0000 84.0000 6 11 5022 2935.7 Left-Caudate 83.4389 8.1582 38.0000 107.0000 69.0000 7 12 7212 4143.9 Left-Putamen 91.5836 7.3237 47.0000 109.0000 62.0000 8 13 3570 2071.3 Left-Pallidum 103.8275 4.9761 56.0000 119.0000 63.0000 9 14 2192 1353.2 3rd-Ventricle 32.0027 11.5672 15.0000 79.0000 64.0000 10 15 1986 1251.9 4th-Ventricle 35.6591 12.4108 12.0000 76.0000 64.0000 11 16 41250 24051.8 Brain-Stem 81.4896 9.2479 22.0000 111.0000 89.0000 12 17 7369 4120.0 Left-Hippocampus 72.6194 8.3441 33.0000 106.0000 73.0000 13 18 3042 1695.2 Left-Amygdala 71.5999 6.1066 37.0000 99.0000 62.0000 14 24 2140 1185.9 CSF 43.4280 13.4853 16.0000 89.0000 73.0000 15 26 666 384.1 Left-Accumbens-area 78.7327 4.1748 55.0000 92.0000 37.0000 16 28 7719 4298.9 Left-VentralDC 91.9097 10.6368 29.0000 121.0000 92.0000 17 30 181 126.6 Left-vessel 54.9834 12.0437 28.0000 77.0000 49.0000 18 31 1531 819.7 Left-choroid-plexus 49.5532 11.3961 22.0000 81.0000 59.0000 19 43 15549 9136.9 Right-Lateral-Ventricle 29.6998 13.2484 9.0000 94.0000 85.0000 20 44 403 267.4 Right-Inf-Lat-Vent 45.0025 12.8842 16.0000 80.0000 64.0000 21 46 26601 15867.2 Right-Cerebellum-White-Matter 82.2607 5.5614 35.0000 97.0000 62.0000 22 47 99608 57495.8 Right-Cerebellum-Cortex 62.0247 9.5405 17.0000 106.0000 89.0000 23 49 13412 7495.8 Right-Thalamus-Proper 87.9864 9.8004 31.0000 110.0000 79.0000 24 50 5187 3006.0 Right-Caudate 81.9400 8.5023 44.0000 105.0000 61.0000 25 51 7601 4339.7 Right-Putamen 89.1673 7.5487 44.0000 109.0000 65.0000 26 52 3692 2139.9 Right-Pallidum 102.9976 4.7986 61.0000 117.0000 56.0000 27 53 7445 4205.5 Right-Hippocampus 71.2660 7.9302 27.0000 99.0000 72.0000 28 54 3503 1970.0 Right-Amygdala 71.8310 5.9510 43.0000 100.0000 57.0000 29 58 849 475.8 Right-Accumbens-area 79.5324 5.1089 62.0000 99.0000 37.0000 30 60 7709 4301.8 Right-VentralDC 91.0214 11.1633 24.0000 117.0000 93.0000 31 62 76 55.6 Right-vessel 55.0132 13.2991 26.0000 75.0000 49.0000 32 63 1439 795.1 Right-choroid-plexus 48.4830 10.2814 17.0000 78.0000 61.0000 33 72 0 0.0 5th-Ventricle 0.0000 0.0000 0.0000 0.0000 0.0000 34 77 2497 1370.8 WM-hypointensities 73.4529 12.6269 14.0000 113.0000 99.0000 35 78 0 0.0 Left-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 36 79 0 0.0 Right-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 37 80 0 0.0 non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 38 81 0 0.0 Left-non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 39 82 0 0.0 Right-non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 40 85 248 153.8 Optic-Chiasm 78.9476 17.7778 26.0000 115.0000 89.0000 41 251 1428 779.4 CC_Posterior 101.7458 17.1102 32.0000 121.0000 89.0000 42 252 734 379.2 CC_Mid_Posterior 93.2657 16.0395 36.0000 114.0000 78.0000 43 253 759 388.9 CC_Central 93.6245 16.6766 41.0000 113.0000 72.0000 44 254 785 422.7 CC_Mid_Anterior 100.7949 14.9042 47.0000 116.0000 69.0000 45 255 1539 836.8 CC_Anterior 100.6595 16.0710 32.0000 121.0000 89.0000 -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | http://secure-web.cisco.com/17VjZXcH_ZmxP3P2zvHN91bs12aBujGcggjGsam1FAh9Lu6… Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

3 4

LGI - output issue
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 19 Aug '21

19 Aug '21

External Email - Use Caution Good afternoon FreeSurfer experts, Hope that everyone is well and staying safe! I tried opening LGI freeview (or tksurferfv) output, and I have been running into the following issues (see code and error message outputs below). Any ideas how I could fix this? Please let me know if additional details are needed. Bolded code is what I inserted. Outputs are not bolded. *tksurfer HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi* zsh: command not found: tksurfer *tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi* ERROR: cannot find lh.pial_lgi *cd $SUBJECTS_DIR/HAR30303_srs2_2/surf* *tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi* freeview -f /Applications/ace_complete/HAR30303_srs2_2/surf/lh.inflated:curvature=/Applications/ace_complete/HAR30303_srs2_2/surf/lh.curv:overlay=lh.pial_lgi:overlay_threshold=2,2,5 -viewport 3d /Applications/freesurfer/bin/fsvglrun: line 20: conditional binary operator expected /Applications/freesurfer/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN' /Applications/freesurfer/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then' Also within the surf folder, I tried something like: *freesurfer -v lh.pial_lgi* Output in freeview was just a dark screen - tried changing the color map but nothing improved this issue. Thank you so much!

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Hippocampal, thalamus and brainstem subfields: Matlab crash bump on macOS Big Sur
by Francesco Cardinale 19 Aug '21

19 Aug '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute hippocampal, thalamus and brainstem subfields on my laptop (MacBook Pro, MacOS Big Sur, Freesurfer 7.1.1 or 7.2.0) with segmentHA_T1.sh, segmentThalamicNuclei.sh and segmentBS.sh scripts, respectively. All the three pipelines fail because of a Matlab Crash Dump. You can find the error logged in the bash console text reported in the last part of this email. I also attached the file brainstem-substructures-T1.log Please, note that everything works fine with previous versions of MacOS, including Mojave. All the updates of Big Sur didn’t solve the problem. Is it possible to use these tools with an updated Matlab Runtime? Another note, probably helpful to somebody else: sometimes these tools fail also in previous version of MacOS, but I discovered that it happens for a different Matlab Crash Dump due to some screen savers. Avoiding the use of screen savers solved the problem under Mojave (but not under Big Sur). Best regards Cico Cardinale ------------------------------------------------------------------------ Segmentation violation detected at Thu Aug 5 00:29:40 2021 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : US-ASCII MATLAB Architecture: maci64 MATLAB Root : /Applications/freesurfer/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Darwin 20.5.0 Darwin Kernel Version 20.5.0: Sat May 8 05:10:33 PDT 2021; root:xnu-7195.121.3~9/RELEASE_X86_64 x86_64 Processor ID : x86 Family 6 Model 78 Stepping 3, GenuineIntel Software OpenGL : 0 Virtual Machine : Java 1.7.0_55-b13 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode Window System : Quartz Fault Count: 1 Abnormal termination: Segmentation violation Register State (from fault): RAX = 0000000000000000 RBX = 0000000000000000 RCX = 0000000000000000 RDX = 0000000000000000 RSP = 0000000000000000 RBP = 0000000000000000 RSI = 0000000000000000 RDI = 0000000000000000 R8 = 0000000000000000 R9 = 0000000000000000 R10 = 0000000000000000 R11 = 0000000000000000 R12 = 0000700008d9bd00 R13 = 00007fff205294bd R14 = 00007fff87277d38 R15 = 0000700008d9bda0 RIP = 0000000000003002 RFL = 00007f8b5b737b30 CS = 0000000000000000 FS = 0000000000000000 GS = 000000010c5bb560 Stack Trace (from fault): [ 0] 0x000000010c208e64 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x000000010c20ca2a /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x000000010c20c477 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x0000000111b3db7a /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x0000000111b3de58 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x0000000111b3b733 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fff205a9d7d /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029 [ 7] 0x0000000000000000 <unknown-module>+00000000 [ 8] 0x0000000109c546ca /Applications/freesurfer/lib/gcc/lib/libstdc++.6.dylib+00063178 _ZNK10__cxxabiv121__vmi_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE+00000186 If this problem is reproducible, please submit a Service Request via: http://secure-web.cisco.com/1r6MICtmf5EwCmlXokWPh6xbfJIxsDgSIeH9_RH4qZaI_Yb… A technical support engineer might contact you with further information. Thank you for your help.** This crash report has been saved to disk as /Users/cico/matlab_crash_dump.19318-1 ** Caught "std::exception" Exception message is: FatalException ------------------------------------------------------------------------ std::terminate() detected at Thu Aug 5 00:29:40 2021 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : US-ASCII MATLAB Architecture: maci64 MATLAB Root : /Applications/freesurfer/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Darwin 20.5.0 Darwin Kernel Version 20.5.0: Sat May 8 05:10:33 PDT 2021; root:xnu-7195.121.3~9/RELEASE_X86_64 x86_64 Processor ID : x86 Family 6 Model 78 Stepping 3, GenuineIntel Software OpenGL : 0 Virtual Machine : Java 1.7.0_55-b13 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode Window System : Quartz Fault Count: 2 Abnormal termination: Segmentation violation Register State (from fault): RAX = 0000000000000000 RBX = 0000000000000000 RCX = 0000000000000000 RDX = 0000000000000000 RSP = 0000000000000000 RBP = 0000000000000000 RSI = 0000000000000000 RDI = 0000000000000000 R8 = 0000000000000000 R9 = 0000000000000000 R10 = 0000000000000000 R11 = 0000000000000000 R12 = 0000700008d9bd00 R13 = 00007fff205294bd R14 = 00007fff87277d38 R15 = 0000700008d9bda0 RIP = 0000000000003002 RFL = 00007f8b5b737b30 CS = 0000000000000000 FS = 0000000000000000 GS = 000000010c5bb560 Stack Trace (from fault): [ 0] 0x000000010c208e64 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x000000010c20ca2a /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x000000010c20c477 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x0000000111b3db7a /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x0000000111b3de58 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x0000000111b3b733 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fff205a9d7d /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+00000029 [ 7] 0x0000000000000000 <unknown-module>+00000000 [ 8] 0x0000000109c546ca /Applications/freesurfer/lib/gcc/lib/libstdc++.6.dylib+00063178 _ZNK10__cxxabiv121__vmi_class_type_info11__do_upcastEPKNS_17__class_type_infoEPKvRNS1_15__upcast_resultE+00000186 Abnormal termination: std::terminate() Register State (captured): RAX = 0000000000000000 RBX = 0000700008da1578 RCX = 0000000000000000 RDX = 0000000000000000 RSP = 0000700008da0e10 RBP = 0000700008da1130 RSI = 0000000000000000 RDI = 0000000000000000 R8 = 0000000000000000 R9 = 0000000000000000 R10 = 0000000000000000 R11 = 0000000000000000 R12 = 0000700008da1d00 R13 = 0000000000000000 R14 = 00007fff8085dcf0 R15 = 0000000000000000 RIP = 000000010c20de8b RFL = 0000000000000000 CS = 0000000100000001 FS = fffffffffffffff8 GS = 0000000000000000 Stack Trace (captured): [ 0] 0x000000010c208e64 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x000000010c20ca2a /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x000000010c20c477 /Applications/freesurfer/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x0000000111b3db7a /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x0000000111b3de58 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x0000000111b3d3a0 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00385952 _Z32mnRunPathDependentInitializationv+00001136 [ 6] 0x0000000111b3ce54 /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00384596 _Z22mnInstallCrashHandlersv+00000420 [ 7] 0x0000000109c52698 /Applications/freesurfer/lib/gcc/lib/libstdc++.6.dylib+00054936 _ZN10__cxxabiv111__terminateEPFvvE+00000008 [ 8] 0x00000001127d27f1 /Applications/freesurfer/MCRv84/bin/maci64/libmwiqm.dylib+00075761 _ZN3iqm3Iqm15setupIqmFcnPtrsEv+00004945 [ 9] 0x0000000109ff2005 /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205 [ 10] 0x0000000112cb9a65 /Applications/freesurfer/MCRv84/bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501 [ 11] 0x000000010a0c1a45 /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693 [ 12] 0x000000010a0bd152 /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834 [ 13] 0x000000010a0bce5e /Applications/freesurfer/MCRv84/bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078 [ 14] 0x0000000111afc18f /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095 [ 15] 0x0000000111afc49f /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335 [ 16] 0x0000000111ae2d1b /Applications/freesurfer/MCRv84/bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059 [ 17] 0x00007fff205648fc /usr/lib/system/libsystem_pthread.dylib+00026876 _pthread_start+00000224 [ 18] 0x00007fff20560443 /usr/lib/system/libsystem_pthread.dylib+00009283 thread_start+00000015 If this problem is reproducible, please submit a Service Request via: http://secure-web.cisco.com/1r6MICtmf5EwCmlXokWPh6xbfJIxsDgSIeH9_RH4qZaI_Yb… A technical support engineer might contact you with further information. Thank you for your help.** This crash report has been saved to disk as /Users/cico/matlab_crash_dump.19318-2 ** MATLAB is exiting because of fatal error /Applications/freesurfer/bin/run_SegmentSubject.sh: line 33: 84854 Killed: 9 /Applications/freesurfer/bin/segmentSubject.app/Contents/MacOS/segmentSubject ctrl16_paola_01 /Users/cico/Documents/subjects_fs 0.5 /Applications/freesurfer/average/BrainstemSS/atlas/AtlasMesh.gz /Applications/freesurfer/average/BrainstemSS/atlas/AtlasDump.mgz /Applications/freesurfer/average/BrainstemSS/atlas/compressionLookupTable.txt 0.05 L-BFGS v12 '/Applications/freesurfer/bin/fs_run_from_mcr /Applications/freesurfer/bin/' Darwin CicoPro17.local 20.5.0 Darwin Kernel Version 20.5.0: Sat May 8 05:10:33 PDT 2021; root:xnu-7195.121.3~9/RELEASE_X86_64 x86_64 T1 Brainstem Substructures exited with ERRORS at Gio 5 Ago 2021 00:29:40 CEST Francesco Cardinale, MD Neurosurgeon "Claudio Munari" Centre for Epilepsy and Parkinson Surgery ASST GOM Niguarda "Ca' Granda" Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia <x-apple-data-detectors://0/0> phone + 39 02 64442867 fax +39 02 64442868 e-mail francesco.cardinale(a)ospedaleniguarda.it <mailto:francesco.cardinale@ospedaleniguarda.it>

3 2

infant freesurfer
by Jonathan A Winawer 19 Aug '21

19 Aug '21

External Email - Use Caution Dear All, I am running into errors using the infant freesurfer tool. Specifically, the error I am getting now is this: Traceback (most recent call last): File "/Applications/freesurfer/infantFreesurfer/python/scripts/sscnn_skullstrip", line 74, in <module> cor_img_data = predict('cor') File "/Applications/freesurfer/infantFreesurfer/python/scripts/sscnn_skullstrip", line 64, in predict wmp_standardize=False File "/Applications/freesurfer/infantFreesurfer/python/packages/sscnn_skullstripping/deeplearn_utils/DeepImageSynth.py", line 261, in from_file model = load_model(model_filename, custom_objects={'dice_coef_loss2': dice_coef_loss2}) File "/Applications/freesurfer/infantFreesurfer/python/lib/python3.6/site-packages/keras/engine/saving.py", line 259, in load_model model_config = json.loads(model_config.decode('utf-8')) AttributeError: 'str' object has no attribute 'decode' Maybe the skull stripping is failing because of the shoulders in the image? [image: Screen Shot 2021-08-18 at 12.01.46 PM.png] -- Jonathan Winawer Associate Professor of Psychology and Neural Science New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer(a)nyu.edu http://secure-web.cisco.com/1FTYuRoQ-0hleS-C5onGuzk4JNWPfWogv-vlqseY0HzyUjJ…

2 1

Issue with tksurfer-sess
by Lauri Tuominen 18 Aug '21

18 Aug '21

External Email - Use Caution Dear Surfers, I ran into a problem with tksurfer-sess. See below. I have a mac big sur. I wonder if there is a bug. Any help would be appreciated. Thank you Lauri Tuominen tksurfer-sess -s subj1 -d ../subjects -analysis ftap.sm05.rh -c ftap -freeview Surface fsaverage rh Map Surface fsaverage rh FreeSurferEnv.csh 7.1.1 Darwin Lauris-MacBook-Pro.local 20.6.0 Darwin Kernel Version 20.6.0: Wed Jun 23 00:26:31 PDT 2021; root:xnu-7195.141.2~5/RELEASE_X86_64 x86_64 Wed 18 Aug 2021 10:35:41 EDT tksurfer: Command not found. list ftap con/map ftap /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/ftap/sig.nii.gz maplist /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/ftap/sig.nii.gz mri_concat /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/ftap/sig.nii.gz --o /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/tksconcat.nii ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/tksconcat.nii cd /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/mkanalysis setenv SUBJECTS_DIR /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/SUBJECTS_DIR tksurferfv fsaverage rh inflated -overlay /Users/laurituominen/Documents/Learning/Turku_teaching/fMRI_demo/subjects/subj1/bold/ftap.sm05.rh/tksconcat.nii -annot aparc -surf white -surf pial -fminmax 2 4 Contrasts 0 ftap /Applications/7.1.1/freesurfer/bin/fsvglrun: line 20: conditional binary operator expected /Applications/7.1.1/freesurfer/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN' /Applications/7.1.1/freesurfer/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then'

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visualizing regional significant correlation with clinical traits by group
by Zeng, Qi 18 Aug '21

18 Aug '21

External Email - Use Caution Hi Experts, I've finished my run of generating volumetric and Tracula data for subjects. I was wondering if there is a way of displaying significant regions that correlate with clinical traits and also by groups. If there is a page describing this function, please help to share. I only find knowledge about group analysis. Thank you so much and I really appreciate it! Best, Qi

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FreeSurfer questions exchange
by 刘亚飞 18 Aug '21

18 Aug '21

External Email - Use Caution Hello! In the process of learning freeSurefer, I have two questions: The first question is that I want to convert a file in .stl format to a .pial file, but the error "does not apear to be an STL file" appears when using the mris_convert command, and I confirm that my stl file path is Accurate, do you know how to convert stl files to pial files? The second question is how to use freesurfer to perform cortial surface parcellation with only .pial files? Thank you！

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Unsubscribe
by Rollo, Patrick 17 Aug '21

17 Aug '21

External Email - Use Caution I've tried several times to unsubscribe from the mailing list. Please help, I'm inundated with emails that are no longer relevant to me.

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LGI - trouble creating output file for each subject
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 17 Aug '21

17 Aug '21

External Email - Use Caution Hello again FreeSurfer experts, I am having some issues creating the output file with the LGI data for each subject. Could you please help me with this? See below the code (in bold) that I used and the outputs that I got. Please let me know if you need additional information! *mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i $SUBJECTS_DIR/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi --sum rh.DCNL_001_aparc.pial_lgi.stats* 7.1.0 cwd cmdline mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i /Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi --sum rh.DCNL_001_aparc.pial_lgi.stats sysname Darwin hostname CCAPSY-0GYM0XV machine x86_64 user ajobsaid whitesurfname white UseRobust 0 Constructing seg from annotation error: No such file or directory error: MRISread(/Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white): could not open file The lh or rh.pial_lgi file is located in the surf folder in each subject. Should I transfer them to the stats folder and try something like *asegstats2table -s subjectID --statsfile=rh.pial_lgi --meas mean --tablefile SubjectID_rh_lgi_final.txt ? * Thank you so much!!

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Re: [Freesurfer] Setting up Freesurfer
by fsbuild 17 Aug '21

17 Aug '21

External Email - Use Caution Hello Haley, You could try bringing up a new terminal window and then do the following, $ cd $HOME$ bash… output deleted …$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1 The ls command below should show you the two .sh files needed to setup the environment.  If you don’t see those two files listed, then something is likely wrong with the installation and you could try re-installing freesurfer (see download links at the end of this message). $ ls -l $FREESURFER_HOME/*Surfer*.sh-rwxr-xr-x  1 root  wheel  18223 Aug 11  2020 /Applications/freesurfer/7.1.1/FreeSurferEnv.sh* -rwxr-xr-x  1 root  wheel   1350 Aug 11  2020 /Applications/freesurfer/7.1.1/SetUpFreeSurfer.sh* Check you can read both of those files with the head command, $ head -1 $FREESURFER_HOME/FreeSurferEnv.sh#!/bin/bash -p $ head -1 $FREESURFER_HOME/SetUpFreeSurfer.sh#!/bin/bash -p If you don’t see that output from the head command for the first line in each file, then there could be a permission error.  In that case you could try manually setting the permissions with the chmod command,$ sudo chmod 755  $FREESURFER_HOME/FreeSurferEnv.sh$ sudo chmod 755  $FREESURFER_HOME/SetUpFreeSurfer.sh Then try the "head -1" command again to test reading the first line in each file. If the above all worked, then try source’ing the SetUpFreeSurfer.sh file (which in turn runs the FreeSurferEnv.sh file that you reported could not be found),$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.1.1 FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.1.1/subjects MNI_DIR           /Applications/freesurfer/7..1.1/mni If you need to re-install 7.1.1 for MacOS, the link for that is here, https://secure-web.cisco.com/1bISb5L_RaO9qHLk_GCjwJOWorsxrzGoSJ2… If you don’t need to continue to work with the 7.1.1 release, you could try the newer 7.2.0 release.  You can have both 7.1.1 and 7.2.0 installed and set FREESURFER_HOME to point to either one of them.  The link for the 7.2.0 release for MacOS is,https://secure-web.cisco.com/1zRdDSXh-D1BWJw53Mbc6pYU1EIIskfcqIPD-acokQW… You need admin/root privileges to run the .pkg installer files. - R. On Aug 17, 2021, at 17:41, Haley Park <hparkit(a)gmail.com> wrote:        External Email - Use Caution        Hello,I was able to run Freesurfer before but when I try to source it now with the codesource $FREESURFER_HOME/7.1.1/SetUpFreesurfer.shI get the message:/Applications/freesurfer/7..1.1/SetUpFreeSurfer.sh:source:42: no such file or directory: /Applications/freesurfer/FreeSurferEnv.shBut I do see that file in the directory in Finder.Any ideas?Thank you,Haley_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer August 2021