Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] 回复： Recon-all run error
by fsbuild 06 Nov '18

06 Nov '18

External Email - Use Caution Hello Yujunjie, Bruce, This file in the packages archive, ./netcdf_3_6_0_p1/putget.c, has an assertion at line 322 that looks like the failure.  I don't know this code, but something is going wrong trying to fill the buffer, e.g., maybe it works for smaller images but not for larger images ?  It could be that older version of freesurfer used a different version of netcdf.  I've attached a screenshot of the code. You could try setting all the soft limits for the shell to be unlimited, e.g., in bash, $ ulimit -c unlimited 1013364183 November 5, 2018 at 21:22 via Postbox         External Email - Use Caution        Dear Bruce,  I found the error location in the recon-all.log folder. Here is the place where it went wrong，I don't think it's the reason for insufficient memory..  ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' failed.''  This data is ok when we run with versions prior to freesurfer 6.0. But after we run the 6.0 version and set the expert file, this error will occur.Do I need to step through the instructions to see the problem? How should this error be solved? Thanks in advance yours yujunjie

2 1

Longitudinal brainstem structures / thalamic nuclei
by Niels Bergsland 05 Nov '18

05 Nov '18

External Email - Use Caution Hi Eugenio, Just wanted to ask quickly if there is plan to implement longitudinal processing for the brainstem structures and thalamic nuclei modules? Thanks! Niels

2 2

T-value in qdec
by Vikas Bandalli 05 Nov '18

05 Nov '18

External Email - Use Caution Dear freesurfer team, I'm sorry I'm reposting this but I really want a solution tho this . I am running an analysis betweene two groups Normal and Patients. Here is an example of my particular design diagnosis :- Normal vs Bipolar Co-variate :- Age Nuisance factor :- Total_Intra cranial volume I would please like to know a couple of things related to QDEC 1.I am looking for difference in volume between patients and controls and the analysis. For correcting for multiple comparisons I ran Monte carlo - Z simulation at threshold of 1.3 My understanding is the analysis overall runs a two-tailed t-test first and then when we select to run MC-z simulation it iterates for multiple comparisions (by repeating the saem say 1000 times ) and gives out 'clusterwise p-value' Is my understanding correct? 2.I would like to extract T-values for the same . Are we getting cluster wise T-value similar to cluster wise p-value ? in the terminal 3. Where would I find t-values for the analysis ??? 4.Are there any methods to extract T-values in qdec or freesurfer . If so,please specify. I am enclosing screenshots from my analysis for the same . Kindly request you to please have a look please help me out with this ?? Thanking You, Yours sincerely , Dr.Vikas Bandalli

1 0

Re: [Freesurfer] Tutorial Data Set - Won't Download
by fsbuild 05 Nov '18

05 Nov '18

External Email - Use Caution Hello Emma, We're taking a look at those links which seem to not be working right now, so stay tuned. On Nov 5, 2018, at 05:30, Bunting, Emma <e.bunting.18(a)ucl.ac.uk> wrote:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data

1 0

Compiling same-subject data across multiple scanning sessions
by Anna Mynick 05 Nov '18

05 Nov '18

External Email - Use Caution Hi all, I'm wondering whether there's a way to compile same-subject data across multiple sessions into the same analysis. More specifically, I've run all my individual scanning sessions through preproc-sess (same subject, different scanning days) and am now hoping to compile same-subject sessions into a file that can be fed into mkanalysis-sess, mkcontrast-sess and selxavg3-sess. One concern I have is that all of the .para files that list stimulus onsets and durations are separate, so I imagine those would need to be concatenated along with the preprocessed functional data. Thanks very much for any help, Anna

1 0

problems concerning mris_prepoc
by Larissa Bechtle 05 Nov '18

05 Nov '18

1 0

Matlab Segmentation error when running hippocampal segmentation in dev version
by Jaime Gomez 05 Nov '18

05 Nov '18

External Email - Use Caution Hi, I think I have the same or similar error than [Freesurfer] error in hippocampal subfields and nuclei of amygdala segmentation <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg59953.html> I am running segmentHA_T1.sh for one subject and I get this matlab segmentation error bellow: I have 16GB memory in a MacOS, and when the process finished with the error I still have 7 GB of memory free to use. I installed the Matlab R2014b runtime as it is explained here <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…> and I have a Matlab 2016 installed. Thanks! Jaime ------------------------------------------------------------------------ Segmentation violation detected at Tue Oct 30 13:06:09 2018 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : ISO-8859-1 MATLAB Architecture: maci64 MATLAB Root : /Applications/freesurfer/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Darwin 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 Processor ID : x86 Family 6 Model 62 Stepping 4, 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 = 00007fb47210a800 RBX = 00007fb47210a800 RCX = 00007000050c92f0 RDX = 0000000112fb097e RSP = 00007fb47210a800 RBP = 00009b63050c92f0 RSI = 00007fb470d3f910 RDI = 0000000000000000 R8 = 00007fb47691da70 R9 = 00007fb47210a800 R10 = 000000011d44376a R11 = 0000000000000000 R12 = 00007000050c9350 R13 = 0000000112dfe3c7 R14 = 00007000050c93c0 R15 = 000000011d443777 RIP = 0000000117f94f40 RFL = 00007fb47691da70 CS = 00009b6300305bc3 FS = 000000011d44376a GS = 00007fb47210a9e8 Stack Trace (from fault): [ 0] 0x0000000107817e64 /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x000000010781ba2a /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x000000010781b477 /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x000000010e399b7a /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x000000010e399e58 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x000000010e397733 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fff6b0d9b3d /usr/lib/system/libsystem_platform.dylib+00019261 _sigtramp+00000029 [ 7] 0x0000000112dff6f8 /Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568 _ZN23JNI_ArgumentPusherVaArg7iterateEy+00000000 [ 8] 0x0000000112defd67 /Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679 jni_GetMethodID+00000126 [ 9] 0x00000001117b1271 /Applications/freesurfer/MCRv84//bin/maci64/libmwjmi.dylib+00160369 _Z12mljGetMethodP7_jclassPKcS2_+00000049 [ 10] 0x000000011cc9e366 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00598886 _ZN2ui14JavaScreenData20getPrimaryScreenRectEv+00000150 [ 11] 0x000000011cca3ef4 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00622324 _ZN10ScreenImpl13getScreenSizeEv+00000036 [ 12] 0x000000011cca22e2 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00615138 _ZNK2ui24RootScreenAndPointerImpl13getScreenSizeEv+00000018 [ 13] 0x000000011cca6f58 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00634712 _ZN2ui4Root17getScreenSizeImplEPN4mcos11COSPropInfoEPNS1_9COSClientEPNS1_12COSInterfaceE+00000040 [ 14] 0x000000011d0ddd13 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+05053715 _ZN7hgutils6StubPIIN2ui4RootENS_15PropertyStorageIN8graphics8datatype8PositionENS_6NoModeENS_21NoSerializableStorageEEEE8getValueEPN4mcos12COSInterfaceE+00000099 [ 15] 0x000000010f3e9a6e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00371310 _ZN4mcos13COSInterfaceI18igetDirectInternalEPNS_12COSInterfaceE+00000110 [ 16] 0x000000010f3dfc80 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00330880 _ZN4mcos13COSInterfaceI10igetDirectEPKNS_9COSClientEPNS_12COSInterfaceE+00000128 [ 17] 0x000000010f44f12b /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00786731 _ZN4mcos28getValueOfKnownClassPropertyEP11mxArray_tagmPKS0_NS_15COSInterfacePtrEPKNS_9COSClientE+00000411 [ 18] 0x000000010f450070 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00790640 _ZN4mcos16getPropertyValueEPKNS_9COSClientEPNS_8COSClassEPK11mxArray_tagPKcmPS5_+00000416 [ 19] 0x000000010f450483 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00791683 _ZNK4mcos5GetMI6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000355 [ 20] 0x000000010f4381f2 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00692722 _ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466 [ 21] 0x000000010f43af4e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704334 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494 [ 22] 0x000000010f438b3e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00695102 _Z18mcosCallMethodImplN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_bb+00000286 [ 23] 0x000000010f439a82 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00699010 _Z12omCallMethodN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_b+00000114 [ 24] 0x000000011e44c6c2 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00440002 _ZN7hgutils17MCOSMethodInvoker6invokeEPKN4mcos9COSClientERiPNS1_8COSValueEiPKS6_+00000866 [ 25] 0x000000011e44c220 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00438816 _ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDERKNS0_12MemberAccessEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSD_+00000112 [ 26] 0x000000011e44c1a7 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00438695 _ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSA_+00000055 [ 27] 0x000000011e432292 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00332434 _ZThn8_NK7hgutils22HGPropHandlerClassInfo16areChildrenSavedEv+00029170 [ 28] 0x000000010f4381f2 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00692722 _ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466 [ 29] 0x000000010f43af4e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704334 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494 [ 30] 0x000000010f439d41 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00699713 _Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417 [ 31] 0x000000010f4c5930 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01272112 _Z18omCallOpaqueMethodP11mxArray_tagS0_iPS0_iPPKS_+00000112 [ 32] 0x000000011c4ed353 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgbuiltins.dylib+00193363 hgGetWrapper+00000435 [ 33] 0x000000010f270cc6 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00117958 _ZN11Mfh_builtin11dispatch_mfEiPP11mxArray_tagiS2_+00000086 [ 34] 0x000000010f25912d /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333 [ 35] 0x000000010e616d62 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650 [ 36] 0x000000010e5b8dd8 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136 inPcodeWalker+00022552 [ 37] 0x000000010e5b5917 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124631 inPcodeWalker+00009047 [ 38] 0x000000010e5b0fb7 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935 [ 39] 0x000000010e5b21c6 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470 _Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886 [ 40] 0x000000010e6541f1 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337 [ 41] 0x000000010f2b5c28 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400424 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000600 [ 42] 0x000000010f499e8e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01093262 _ZNK4mcos17MScopedMethodInfo6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000606 [ 43] 0x000000010f437597 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00689559 _ZN24OpaqueMethodCallMetaData11callMMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000359 [ 44] 0x000000010f43ae63 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704099 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000259 [ 45] 0x000000010f439d41 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00699713 _Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417 [ 46] 0x000000010f4c5ee8 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01273576 _Z18omCallStaticMethodP11mxArray_tagiPS0_iPPKS_+00000088 [ 47] 0x000000010f54ee64 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01834596 _ZN17Mfh_opaque_static11dispatch_mfEiPP11mxArray_tagiS2_+00000116 [ 48] 0x000000010f25912d /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333 [ 49] 0x000000010f54bacc /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01821388 _ZN10Mfh_opaque11dispatch_fhEiPP11mxArray_tagiS2_+00000028 [ 50] 0x000000010e616d62 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650 [ 51] 0x000000010e56c59e /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+00824734 inCallFcnFromReference+00000110 [ 52] 0x000000010e5b5003 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01122307 inPcodeWalker+00006723 [ 53] 0x000000010e5b0fb7 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935 [ 54] 0x000000010e5b21c6 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470 _Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886 [ 55] 0x000000010e6541f1 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337 [ 56] 0x000000010f2b5c55 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400469 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000645 [ 57] 0x000000010e616d62 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650 [ 58] 0x000000010e5b8dd8 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136 inPcodeWalker+00022552 [ 59] 0x000000010e5b5702 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124098 inPcodeWalker+00008514 [ 60] 0x000000010e5b0fb7 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935 [ 61] 0x000000010e5b0cad /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105069 inInterPcode+00000157 [ 62] 0x000000010e5a7b9f /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01067935 _ZN12InterpBridge33DoMatlabFcnCallInDesiredWorkspaceEiPP11mxArray_tagiPPKS0_P13Mfh_MATLAB_fnP15inWorkSpace_tag+00004015 [ 63] 0x000000010e5a9a79 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01075833 _Z25in_local_call_with_setjmpIN5boost3_bi6bind_tIvPFvPiP12_pcodeheaderS3_PP11mxArray_tag12inDebugCheckENS1_5list5INS1_5valueIS3_EENSD_IS5_EENS0_3argILi1EEENSG_ILi2EEENSD_IS9_EEEEEEEN6mlutil14cmddistributor17inExecutionStatusET_S3_S8_b+00000073 [ 64] 0x000000010e5a528d /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01057421 _Z12inEvalStringP15_memory_contextRKSbItSt11char_traitsItESaItEE8EvalTypeiPP11mxArray_tag12inDebugCheckP12_pcodeheaderPib+00002877 [ 65] 0x000000010e5a57cd /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01058765 _ZN12InterpBridge22EvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEPibb+00000141 [ 66] 0x000000010e5a5c05 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01059845 _ZN12InterpBridge7EvalCmdERKSbItSt11char_traitsItESaItEEb+00000021 [ 67] 0x000000010e503347 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+00394055 inEvalCmd+00000119 [ 68] 0x000000010e3717fa /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00223226 _Z16mnRunLoginScriptv+00000586 [ 69] 0x000000010e398f63 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00384867 _Z32mnRunPathDependentInitializationv+00000051 [ 70] 0x000000010e37f80c /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00280588 _ZN11mcrInstance26init_on_interpreter_threadEP11MfileReaderP13MexFileReader+00000988 [ 71] 0x000000010e38dfb8 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00339896 _ZN5boost6detail8function21function_obj_invoker0INS_3_bi6bind_tIbNS_4_mfi3mf2Ib11mcrInstanceP11MfileReaderP13MexFileReaderEENS3_5list3INS3_5valueIPS7_EENSE_IS9_EENSE_ISB_EEEEEEbE6invokeERNS1_15function_bufferE+00000040 [ 72] 0x000000010e38cdc1 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00335297 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE29doNotRethrowMxArrayExceptionsERKN5boost8functionIFbvEEE+00000033 [ 73] 0x000000010e38dbd9 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00338905 _ZN5boost6detail11task_objectIbNS_3_bi6bind_tIbPFbRKNS_8functionIFbvEEEENS2_5list1INS2_5valueIS6_EEEEEEE6do_runEv+00000025 [ 74] 0x000000010e38d276 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00336502 _ZN5boost6detail9task_baseIbE3runEv+00000166 [ 75] 0x000000010e38d067 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00335975 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE3runEv+00000023 [ 76] 0x000000010e357f90 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00118672 _ZN3mcr7runtime17InterpreterThread4Impl26invocation_request_handlerEl+00000032 [ 77] 0x0000000105632005 /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205 [ 78] 0x000000010facca65 /Applications/freesurfer/MCRv84//bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501 [ 79] 0x0000000105701a45 /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693 [ 80] 0x00000001056fd152 /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834 [ 81] 0x00000001056fce5e /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078 [ 82] 0x000000010e35818f /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095 [ 83] 0x000000010e35849f /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335 [ 84] 0x000000010e33ed1b /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059 [ 85] 0x00007fff6b0e233d /usr/lib/system/libsystem_pthread.dylib+00013117 _pthread_body+00000126 [ 86] 0x00007fff6b0e52a7 /usr/lib/system/libsystem_pthread.dylib+00025255 _pthread_start+00000070 [ 87] 0x00007fff6b0e1425 /usr/lib/system/libsystem_pthread.dylib+00009253 thread_start+00000013 If this problem is reproducible, please submit a Service Request via: http://www.mathworks.com/support/contact_us/ 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/jaime/matlab_crash_dump.9878-1 ** ------------------------------------------------------------------------ Segmentation violation detected at Tue Oct 30 13:06:10 2018 ------------------------------------------------------------------------ Configuration: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : ISO-8859-1 MATLAB Architecture: maci64 MATLAB Root : /Applications/freesurfer/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Darwin 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 Processor ID : x86 Family 6 Model 62 Stepping 4, 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 = 00007fb47210a800 RBX = 00007fb47210a800 RCX = 00007000050c92f0 RDX = 0000000112fb097e RSP = 00007fb47210a800 RBP = 00009b63050c92f0 RSI = 00007fb470d3f910 RDI = 0000000000000000 R8 = 00007fb47691da70 R9 = 00007fb47210a800 R10 = 000000011d44376a R11 = 0000000000000000 R12 = 00007000050c9350 R13 = 0000000112dfe3c7 R14 = 00007000050c93c0 R15 = 000000011d443777 RIP = 0000000117f94f40 RFL = 00007fb47691da70 CS = 00009b6300305bc3 FS = 000000011d44376a GS = 00007fb47210a9e8 Stack Trace (from fault): [ 0] 0x0000000107817e64 /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x000000010781ba2a /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x000000010781b477 /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x000000010e399b7a /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x000000010e399e58 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x000000010e397733 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fff6b0d9b3d /usr/lib/system/libsystem_platform.dylib+00019261 _sigtramp+00000029 [ 7] 0x0000000112dff6f8 /Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568 _ZN23JNI_ArgumentPusherVaArg7iterateEy+00000000 [ 8] 0x0000000112defd67 /Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679 jni_GetMethodID+00000126 [ 9] 0x00000001117b1271 /Applications/freesurfer/MCRv84//bin/maci64/libmwjmi.dylib+00160369 _Z12mljGetMethodP7_jclassPKcS2_+00000049 [ 10] 0x000000011cc9e366 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00598886 _ZN2ui14JavaScreenData20getPrimaryScreenRectEv+00000150 [ 11] 0x000000011cca3ef4 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00622324 _ZN10ScreenImpl13getScreenSizeEv+00000036 [ 12] 0x000000011cca22e2 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00615138 _ZNK2ui24RootScreenAndPointerImpl13getScreenSizeEv+00000018 [ 13] 0x000000011cca6f58 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00634712 _ZN2ui4Root17getScreenSizeImplEPN4mcos11COSPropInfoEPNS1_9COSClientEPNS1_12COSInterfaceE+00000040 [ 14] 0x000000011d0ddd13 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+05053715 _ZN7hgutils6StubPIIN2ui4RootENS_15PropertyStorageIN8graphics8datatype8PositionENS_6NoModeENS_21NoSerializableStorageEEEE8getValueEPN4mcos12COSInterfaceE+00000099 [ 15] 0x000000010f3e9a6e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00371310 _ZN4mcos13COSInterfaceI18igetDirectInternalEPNS_12COSInterfaceE+00000110 [ 16] 0x000000010f3dfc80 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00330880 _ZN4mcos13COSInterfaceI10igetDirectEPKNS_9COSClientEPNS_12COSInterfaceE+00000128 [ 17] 0x000000010f44f12b /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00786731 _ZN4mcos28getValueOfKnownClassPropertyEP11mxArray_tagmPKS0_NS_15COSInterfacePtrEPKNS_9COSClientE+00000411 [ 18] 0x000000010f450070 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00790640 _ZN4mcos16getPropertyValueEPKNS_9COSClientEPNS_8COSClassEPK11mxArray_tagPKcmPS5_+00000416 [ 19] 0x000000010f450483 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00791683 _ZNK4mcos5GetMI6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000355 [ 20] 0x000000010f4381f2 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00692722 _ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466 [ 21] 0x000000010f43af4e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704334 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494 [ 22] 0x000000010f438b3e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00695102 _Z18mcosCallMethodImplN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_bb+00000286 [ 23] 0x000000010f439a82 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00699010 _Z12omCallMethodN4mcos9COSNameIDES0_PKNS_9COSClientEiPP11mxArray_tagiPPKS4_b+00000114 [ 24] 0x000000011e44c6c2 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00440002 _ZN7hgutils17MCOSMethodInvoker6invokeEPKN4mcos9COSClientERiPNS1_8COSValueEiPKS6_+00000866 [ 25] 0x000000011e44c220 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00438816 _ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDERKNS0_12MemberAccessEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSD_+00000112 [ 26] 0x000000011e44c1a7 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00438695 _ZN7hgutils14callMCOSMethodERKN4mcos9COSNameIDEPNS0_8COSClassEPKNS0_9COSClientERiPNS0_8COSValueEiPKSA_+00000055 [ 27] 0x000000011e432292 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgutils.dylib+00332434 _ZThn8_NK7hgutils22HGPropHandlerClassInfo16areChildrenSavedEv+00029170 [ 28] 0x000000010f4381f2 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00692722 _ZN24OpaqueMethodCallMetaData11callCMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000466 [ 29] 0x000000010f43af4e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704334 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000494 [ 30] 0x000000010f439d41 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00699713 _Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417 [ 31] 0x000000010f4c5930 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01272112 _Z18omCallOpaqueMethodP11mxArray_tagS0_iPS0_iPPKS_+00000112 [ 32] 0x000000011c4ed353 /Applications/freesurfer/MCRv84//bin/maci64/libmwhgbuiltins.dylib+00193363 hgGetWrapper+00000435 [ 33] 0x000000010f270cc6 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00117958 _ZN11Mfh_builtin11dispatch_mfEiPP11mxArray_tagiS2_+00000086 [ 34] 0x000000010f25912d /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333 [ 35] 0x000000010e616d62 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650 [ 36] 0x000000010e5b8dd8 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136 inPcodeWalker+00022552 [ 37] 0x000000010e5b5917 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124631 inPcodeWalker+00009047 [ 38] 0x000000010e5b0fb7 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935 [ 39] 0x000000010e5b21c6 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470 _Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886 [ 40] 0x000000010e6541f1 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337 [ 41] 0x000000010f2b5c28 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400424 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000600 [ 42] 0x000000010f499e8e /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01093262 _ZNK4mcos17MScopedMethodInfo6invokeEPKNS_9COSClientERiPNS_8COSValueEiPKS5_+00000606 [ 43] 0x000000010f437597 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00689559 _ZN24OpaqueMethodCallMetaData11callMMethodEPN4mcos13COSMethodInfoEPP11mxArray_tagPKNS0_9COSClientE+00000359 [ 44] 0x000000010f43ae63 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00704099 _ZN24OpaqueMethodCallMetaData23callMethodOrConstructorEP11mxArray_tagbiPS1_iPPKS0_bPKN4mcos9COSClientEPS9_PPNS6_13COSMethodInfoE+00000259 [ 45] 0x000000010f439d41 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+00699713 _Z22omCallMethodWithClientP11mxArray_tagbS0_iPS0_iPPKS_PKN4mcos9COSClientEPS8_PPNS5_13COSMethodInfoE+00000417 [ 46] 0x000000010f4c5ee8 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01273576 _Z18omCallStaticMethodP11mxArray_tagiPS0_iPPKS_+00000088 [ 47] 0x000000010f54ee64 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01834596 _ZN17Mfh_opaque_static11dispatch_mfEiPP11mxArray_tagiS2_+00000116 [ 48] 0x000000010f25912d /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00020781 _ZN13Mfh_MATLAB_fn11dispatch_fhEiPP11mxArray_tagiS2_+00000333 [ 49] 0x000000010f54bacc /Applications/freesurfer/MCRv84//bin/maci64/libmwmcos.dylib+01821388 _ZN10Mfh_opaque11dispatch_fhEiPP11mxArray_tagiS2_+00000028 [ 50] 0x000000010e616d62 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650 [ 51] 0x000000010e56c59e /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+00824734 inCallFcnFromReference+00000110 [ 52] 0x000000010e5b5003 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01122307 inPcodeWalker+00006723 [ 53] 0x000000010e5b0fb7 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935 [ 54] 0x000000010e5b21c6 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01110470 _Z26inExecuteMFunctionOrScriptP6Mfh_mpb+00000886 [ 55] 0x000000010e6541f1 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01774065 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00002337 [ 56] 0x000000010f2b5c55 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_dispatcher.dylib+00400469 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+00000645 [ 57] 0x000000010e616d62 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01523042 _Z19inDispatchFromStackiPKcii+00001650 [ 58] 0x000000010e5b8dd8 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01138136 inPcodeWalker+00022552 [ 59] 0x000000010e5b5702 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01124098 inPcodeWalker+00008514 [ 60] 0x000000010e5b0fb7 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105847 inInterPcode+00000935 [ 61] 0x000000010e5b0cad /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01105069 inInterPcode+00000157 [ 62] 0x000000010e5a7b9f /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01067935 _ZN12InterpBridge33DoMatlabFcnCallInDesiredWorkspaceEiPP11mxArray_tagiPPKS0_P13Mfh_MATLAB_fnP15inWorkSpace_tag+00004015 [ 63] 0x000000010e5a9a79 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01075833 _Z25in_local_call_with_setjmpIN5boost3_bi6bind_tIvPFvPiP12_pcodeheaderS3_PP11mxArray_tag12inDebugCheckENS1_5list5INS1_5valueIS3_EENSD_IS5_EENS0_3argILi1EEENSG_ILi2EEENSD_IS9_EEEEEEEN6mlutil14cmddistributor17inExecutionStatusET_S3_S8_b+00000073 [ 64] 0x000000010e5a528d /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01057421 _Z12inEvalStringP15_memory_contextRKSbItSt11char_traitsItESaItEE8EvalTypeiPP11mxArray_tag12inDebugCheckP12_pcodeheaderPib+00002877 [ 65] 0x000000010e5a57cd /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01058765 _ZN12InterpBridge22EvalCmdWithLocalReturnERKSbItSt11char_traitsItESaItEEPibb+00000141 [ 66] 0x000000010e5a5c05 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+01059845 _ZN12InterpBridge7EvalCmdERKSbItSt11char_traitsItESaItEEb+00000021 [ 67] 0x000000010e503347 /Applications/freesurfer/MCRv84//bin/maci64/libmwm_interpreter.dylib+00394055 inEvalCmd+00000119 [ 68] 0x000000010e3717fa /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00223226 _Z16mnRunLoginScriptv+00000586 [ 69] 0x000000010e398f63 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00384867 _Z32mnRunPathDependentInitializationv+00000051 [ 70] 0x000000010e37f80c /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00280588 _ZN11mcrInstance26init_on_interpreter_threadEP11MfileReaderP13MexFileReader+00000988 [ 71] 0x000000010e38dfb8 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00339896 _ZN5boost6detail8function21function_obj_invoker0INS_3_bi6bind_tIbNS_4_mfi3mf2Ib11mcrInstanceP11MfileReaderP13MexFileReaderEENS3_5list3INS3_5valueIPS7_EENSE_IS9_EENSE_ISB_EEEEEEbE6invokeERNS1_15function_bufferE+00000040 [ 72] 0x000000010e38cdc1 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00335297 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE29doNotRethrowMxArrayExceptionsERKN5boost8functionIFbvEEE+00000033 [ 73] 0x000000010e38dbd9 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00338905 _ZN5boost6detail11task_objectIbNS_3_bi6bind_tIbPFbRKNS_8functionIFbvEEEENS2_5list1INS2_5valueIS6_EEEEEEE6do_runEv+00000025 [ 74] 0x000000010e38d276 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00336502 _ZN5boost6detail9task_baseIbE3runEv+00000166 [ 75] 0x000000010e38d067 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00335975 _ZN3mcr7runtime17InterpreterThread4Impl22TypedInvocationRequestIbE3runEv+00000023 [ 76] 0x000000010e357f90 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00118672 _ZN3mcr7runtime17InterpreterThread4Impl26invocation_request_handlerEl+00000032 [ 77] 0x0000000105632005 /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+00196613 _ZN10eventqueue18UserEventQueueImpl5flushEv+00001205 [ 78] 0x000000010facca65 /Applications/freesurfer/MCRv84//bin/maci64/libmwuix.dylib+00043621 _Z25isHandleUserEventCallbackPFvPvE+00000501 [ 79] 0x0000000105701a45 /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01047109 _Z21svWS_ProcessCallbacksv+00016693 [ 80] 0x00000001056fd152 /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01028434 _Z25svWS_ProcessPendingEventsiib+00000834 [ 81] 0x00000001056fce5e /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01027678 _Z25svWS_ProcessPendingEventsiib+00000078 [ 82] 0x000000010e35818f /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095 [ 83] 0x000000010e35849f /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335 [ 84] 0x000000010e33ed1b /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059 [ 85] 0x00007fff6b0e233d /usr/lib/system/libsystem_pthread.dylib+00013117 _pthread_body+00000126 [ 86] 0x00007fff6b0e52a7 /usr/lib/system/libsystem_pthread.dylib+00025255 _pthread_start+00000070 [ 87] 0x00007fff6b0e1425 /usr/lib/system/libsystem_pthread.dylib+00009253 thread_start+00000013 Abnormal termination: Segmentation violation Register State (from fault): RAX = 00007fb47210a800 RBX = 00007fb47210a800 RCX = 00007000050d1a00 RDX = 0000000112fb097e RSP = 00007fb47210a800 RBP = 00009b63050d1a00 RSI = 00007fb470d3f910 RDI = 0000000000000000 R8 = 00007fb47691da70 R9 = 00007fb47210a800 R10 = 000000011d44376a R11 = 0000000000000000 R12 = 00007000050d1a60 R13 = 0000000112dfe3c7 R14 = 00007000050d1ad0 R15 = 000000011d443777 RIP = 0000000117f94f40 RFL = 00007fb47691da70 CS = 00009b6300305bc3 FS = 000000011d44376a GS = 00007fb47210a9e8 Stack Trace (from fault): [ 0] 0x0000000107817e64 /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052 [ 1] 0x000000010781ba2a /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+00000906 [ 2] 0x000000010781b477 /Applications/freesurfer/MCRv84//bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000119 [ 3] 0x000000010e399b7a /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+00003146 [ 4] 0x000000010e399e58 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+00003880 [ 5] 0x000000010e397733 /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+00000275 [ 6] 0x00007fff6b0d9b3d /usr/lib/system/libsystem_platform.dylib+00019261 _sigtramp+00000029 [ 7] 0x0000000112dff6f8 /Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03192568 _ZN23JNI_ArgumentPusherVaArg7iterateEy+00000000 [ 8] 0x0000000112defd67 /Applications/freesurfer/MCRv84/sys/java/jre/maci64/jre//lib/server/libjvm.dylib+03128679 jni_GetMethodID+00000126 [ 9] 0x00000001117b1271 /Applications/freesurfer/MCRv84//bin/maci64/libmwjmi.dylib+00160369 _Z12mljGetMethodP7_jclassPKcS2_+00000049 [ 10] 0x000000011cc9e366 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00598886 _ZN2ui14JavaScreenData20getPrimaryScreenRectEv+00000150 [ 11] 0x000000011cca323a /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00619066 _ZN10gbtobjects10ScreenData14getScreenWidthEv+00000010 [ 12] 0x000000011ccba1a6 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00713126 _ZN2ui9container9Container16getChildRefFrameEv+00000038 [ 13] 0x000000011ccba55e /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00714078 _ZN2ui9container9Container20fillInUpdateViewInfoERN7hgutils14UpdateViewInfoE+00000046 [ 14] 0x000000011cca74d6 /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00636118 _ZN2ui4Root20fillInUpdateViewInfoERN7hgutils14UpdateViewInfoE+00000022 [ 15] 0x000000011cca279a /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+00616346 _ZN10gbtobjects13UpdateVisitor5applyERN2ui4RootE+00000218 [ 16] 0x000000011cdb7f9a /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+01752986 _ZN10gbtobjects20CommitUpdatesManager13performUpdateEv+00000122 [ 17] 0x000000011cdb807b /Applications/freesurfer/MCRv84//bin/maci64/libmwhg.dylib+01753211 _ZN10gbtobjects20CommitUpdatesManager24commitAllDatabaseUpdatesEbb+00000027 [ 18] 0x00000001057147c8 /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01124296 _Z26svWS_CommitDatabaseUpdates27svCommitDatabaseUpdatesType+00000152 [ 19] 0x00000001056fce2f /Applications/freesurfer/MCRv84//bin/maci64/libmwservices.dylib+01027631 _Z25svWS_ProcessPendingEventsiib+00000031 [ 20] 0x000000010e35818f /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119183 _ZN3mcr7runtime17InterpreterThread4Impl14process_eventsERKN5boost10shared_ptrIS2_EE+00000095 [ 21] 0x000000010e35849f /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00119967 _ZN3mcr7runtime17InterpreterThread4Impl3runERKN5boost10shared_ptrIS2_EEPNS2_12init_contextE+00000335 [ 22] 0x000000010e33ed1b /Applications/freesurfer/MCRv84//bin/maci64/libmwmcr.dylib+00015643 _Z26run_init_and_handle_eventsPv+00000059 [ 23] 0x00007fff6b0e233d /usr/lib/system/libsystem_pthread.dylib+00013117 _pthread_body+00000126 [ 24] 0x00007fff6b0e52a7 /usr/lib/system/libsystem_pthread.dylib+00025255 _pthread_start+00000070 [ 25] 0x00007fff6b0e1425 /usr/lib/system/libsystem_pthread.dylib+00009253 thread_start+00000013 If this problem is reproducible, please submit a Service Request via: http://www.mathworks.com/support/contact_us/ 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/jaime/matlab_crash_dump.9878-2 ** MATLAB is exiting because of fatal error /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37: 9878 Killed: 9 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args Darwin jaimes-Mac-Pro.local 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 T1 hippocampal subfields exited with ERRORS at Tue Oct 30 13:06:10 CET 2018 For more details, see the log file /Users/jaime/vallecas/data/uma/Subject_UMA_0018/UIPA11REV/003_SAG_3D_IR//sujeto_uno/scripts/hippocampal-subfields-T1.log -- Jaime Gomez-Ramirez, PhD Department of NeuroImaging Centre for Research in Neurodegenarative Diseases Fundación Reina Sofia <http://www.fundacionreinasofia.es/EN/Paginas/home.aspx> Valderrebollo, 5 Madrid, Spain

2 2

Tutorial Data Set - Won't Download
by Bunting, Emma 05 Nov '18

05 Nov '18

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to download the tutorial dataset, as described on the FreeSurfer Tutorial Datasets page (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data) It is able to download majority of the buckner_data files, up to: tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/073/surf/lh.pial , but then an error message occurs, and the download stops. The error message reads… gzip: stdin: unexpected end of file tar: Unexpected E0F in archive tar: Unexpected E0F in archive tar: Error is not recoverable: exiting now I have tried downloading it on both windows and linux machines. Does anyone have any thoughts on how to trouble-shoot this one? I have a copy of the recon-all.log upon request if you think it will be of any use, n.b. version of freesurfer: freesurfer-LInux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. Best Wishes, Emma

1 0

Re: [Freesurfer] Third party dependencies directory not found when building from source
by fsbuild 04 Nov '18

04 Nov '18

External Email - Use Caution Hello Kazuhiro, With the old configure/automake tools, I used the following configure command on a CentOS7 machine (release 7.4.17-8) to build with the 5.0.35 Cuda distribution with the CentOS6 packages archive.  (My cuda 5 distribution was installed under /home/osboxes/unzip/centos6-x86_64-packages/CUDA/5.0.35-rh5). $ ./configure —disable-Werror —enable-fermi-gpu —with-cuda=/home/osboxes/unzip/centos6-x86_64-packages/CUDA/5.0.35-rh5 —with-pkgs-dir=/home/osboxes/unzip/centos6-x86_64-packages My understanding is you need to use the —enable-fermi-gpu configure option. I have not yet tried building with cuda in the new cmake build with the new packages archive (see previous thread postings with Christian).   Please be aware that the automake build may no longer be as up to date as the cmake build, and we also do not technically support building with cuda. On Nov 1, 2018, at 09:52, Nakamura Kazuhiro <knam(a)akita-noken.jp> wrote:       External Email - Use Caution        Hi, I'm Kazuhiro.I also met trouble for compilation of freesurfer stable6 repository under my Ubuntu 18.04 LTS machine.Even the binary package of freesurfer6.0(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz) can workunder Ubuntu 18.04, option of '-use-gpu' required cuda runtime library of ver 5.0(libcudart.so.5.0).I have tried to link cuda runtime library of Ubuntu 18.04 (ver9.1) to ver5.0 filename.(ln -s libcudart..so.9.0 libcudart.so.5.0 )It cannot work well.

3 3

Re: [Freesurfer] Third party dependencies directory not found when building from source
by fsbuild 03 Nov '18

03 Nov '18

External Email - Use Caution Hello Christian, When a test fails, it should leave behind a log in the subdir for the command, e.g., if the test for ./mri_aparc2aseg fails, then there should be a /mri_aparc2aseg fails,/test_mri_aparc2aseg.log to look at.  But you will need a python3 with the modules from the scientific stack (scipy, numpy, etc.) installed for some tests to run.  You can use python3 from the anaconda distribution, so you would end up with <base path>/anaconda3/bin in the head of your PATH, and you would also need to add at least <base path>/anaconda3/lib/python3.6/site-packages to PYTHONPATH Please keep in mind that if you are building the latest freesurfer from the git dev branch, then it is not a release and has not been tested like a release.  A more comprehensive test than "make test" is to run a recon-all command on the subject "bert" data.  Please see Example 2 under the section "Testing your Freesurfer Installation" from the web page, https://surfer.nmr..mgh.harvard.edu/fswiki/DownloadAndInstall  (Setup your environment with the shell init files before running recon-all - see the section on the same page for "Setup & Configuration" using wherever you installed Freesurfer from your build). On Nov 2, 2018, at 23:08, Christian Lee Mcdaniel <clm121(a)uga.edu> wrote:        External Email - Use Caution        Thank you to all who are providing input for these issues. After ensuring the correct versions of gcc, g++, and gfortran were installed and being used, I am able to complete the `make` command. However, when I conduct `make test`, I receive the following output: ... output with errors not shown ....

1 0

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