Does anyone have some idea about this? Are there other ways to analyze functional data on surface?
-----原始邮件----- 发件人: "Guochun Yang" yanggc@psych.ac.cn 发送时间: 2017年6月21日 星期三 收件人: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu 抄送: 主题: 答复: [Freesurfer] When running mkcontrast-sess: A fatal error hasbeen detected by the Java Runtime Environment
Yes the matlab runs well. I remember that I have met some error like “ERROR: cannot find matlab. Is it in your path?” Then I recognize that I always open matlab by typing capital MATLAB rather than lowercase. So I copied /usr/local/MATLAB/R2016b/bin/glnxa64/MATLAB as /usr/local/MATLAB/R2016b/bin/glnxa64/matlab. The above error was fixed but I got the errors in my last email.
I don’t know whether the error has something to do with the copyfile. But I cannot delete it, otherwise matlab cannot be found again.
发件人: Douglas Greve 发送时间: 2017年6月20日 11:37 收件人: freesurfer@nmr.mgh.harvard.edu 主题: Re: [Freesurfer] When running mkcontrast-sess: A fatal error hasbeen detected by the Java Runtime Environment
this appears to be some kind of matlab problem. Can you otherwise run matlab ok?
On 6/15/17 5:17 PM, 杨国春 wrote:
Hello FreeSurfer Developers,
I'm attempting to run 1st-level analysis with FS-FAST, following the tutorial here http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLevel. I could run mkanalysis-sess successfully: mkanalysis-sess \ -fsd bold -surface fsaverage lh -fwhm 6 \ -event-related -paradigm onset_cond.par -nconditions 5 \ -spmhrf 0 -TR 2 -refeventdur 2 -nskip 0 -polyfit 2 \ -analysis fmcpr.sm6.fsaverage.lh -per-run -force
But when I run mkmkcontrast-sess with the following parameters: mkmkcontrast-sess -analysis fmcpr.sm6.fsaverage.lh -contrast vSSI-v-vSSC -a 2 -c 1 it failed and reported error:
------------------------------------------Error------------------------------------------------------------------------ INFO: Found 5 Non-Null Conditions INFO: Found 1 Delays Condition Weights: -1.00000000000000000000 1.00000000000000000000 0 0 0 mkcontrast2 -config fmcpr.sm6.fsaverage.lh/vSSI-v-vSSC.config -anadir fmcpr.sm6.fsaverage.lh -wcond -1.00000000000000000000 1.00000000000000000000 0 0 0 -sumconds -o fmcpr.sm6.fsaverage.lh/vSSI-v-vSSC.mat -wdelay 1 -no-octave $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ cmtxfile fmcpr.sm6.fsaverage.lh/vSSI-v-vSSC.mat nconds 5, wcond -1.00000000000000000000 1.00000000000000000000 0 0 0 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau cmtxfile fmcpr.sm6.fsaverage.lh/vSSI-v-vSSC.mat monly 0 NCond 5 WCond -1.00000000000000000000 1.00000000000000000000 0 0 0 NDelay 1 WDelay 1 TER 0.050000 sumconds 1 sumdelays 0 nircorr 0 TPreStim 0 RmPreStim 0 rdelta 0 0 rtau 0 0 ndelays 1 CNorm 1 setwdelay 0 setwcond 0 Matlab file is /tmp/mkcontrast2.4735.m # # A fatal error has been detected by the Java Runtime Environment:
# SIGSEGV (0xb) at pc=0x00007f9d60d795ac, pid
=4928, tid=140313822955264 # # JRE version: Java(TM) SE Runtime Environment (7.0_60-b19) (build 1.7.0_60-b19) # Java VM: Java HotSpot(TM) 64-Bit Server VM (24.60-b09 mixed mode linux-amd64 compressed oops) # Problematic frame: # C [libmwuix.so+0x455ac] uixDisplayInformation::getTopWindow() const+0xc # # Core dump written. Default location: /home/amazinger/Public/share/fMRI/CrossModal/Imges/freesurfer/my-functional/core or core.4928 # # If you would like to submit a bug report, please visit: # http://bugreport.sun.com/bugreport/crash.jsp # The crash happened outside the Java Virtual Machine in native code. # See problematic frame for where to report the bug.
matlab: javainit.cpp:1389: void {anonymous}::mwJavaAbort(): Assertion `Fatal Java Exception. See Java Crash Report for details.' failed.
------------------------------------------------------------------------ Assertion detected at Thu Jun 15 15:57:34 2017 ------------------------------------------------------------------------
Configuration: Crash Decoding : Disabled Crash Mode : continue (default) Current Visual : None Default Encoding : UTF-8 GNU C Library : 2.23 stable Host Name : X1 Java Crash Report : /home/amazinger/hs_error_pid4928.log MATLAB Architecture : glnxa64 MATLAB Root : /usr/local/MATLAB/R2016a MATLAB Version : 9.0.0.341360 (R2016a) Operating System : Linux 4.4.0-79-generic #100-Ubuntu SMP Wed May 17 19:58:14 UTC 2017 x86_64 Processor ID : x86 Family 6 Model 78 Stepping 3, GenuineIntel Virtual Machine : Java 1.7.0_60-b19 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode Window System : No active display
Fault Count: 1
Assertion in void {anonymous}::mwJavaAbort() at javainit.cpp line 1389: Fatal Java Exception. See Java Crash Report for details.
Register State (captured):
RAX = 00007f9d5b92bf60 RBX = 00007f9d751b8878 RCX = 000000000000000a RDX = 00007f9d75198c20 RSP = 00007f9d5b92bd70 RBP = 00007f9d5b92c130 RSI = 00007f9d74f4f3b8 RDI = 00007f9d5b92bd80
R8 = 0000000000000000 R9 = 00007f9d5aa0b8e0 R10 = 00007f9d74dc70b8 R11 = 00007f9d5b92bdf4 R12 = 00007f9d5aa0b1bb R13 = 00007f9d5aa0b8e0 R14 = 00007f9d751a87e8 R15 = 00007f9d5b92c9a0
RIP = 00007f9d74ebc59e EFL = 00007f9d5b92bf88
CS = b94f FS = 7b24 GS = 7f9d
Stack Trace (captured): [ 0] 0x00007f9d74ebc59e /usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01082782 _ZN2fl4diag5linux6x86_6412context_base12capture_dataEv+00000030 [ 1] 0x00007f9d74eb8541 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01066305 [ 2] 0x00007f9d74eb9bd0 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01072080 [ 3] 0x00007f9d74eb9c42 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwfl.so+01072194 [ 4] 0x00007f9d5a9cc75a /usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01099610 [ 5] 0x00007f9d5960f8bb /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+08513723 [ 6] 0x00007f9d5978fbc7 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+10087367 [ 7] 0x00007f9d596147cf /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+08533967 JVM_handle_linux_signal+00000335 [ 8] 0x00007f9d7919b390 /lib/x86_64-linux-gnu/libpthread.so.0+00070544 [ 9] 0x00007f9d60d795ac /usr/local/MATLAB/R2016a/bin/glnxa64/matlab_startup_plugins/../../../bin/glnxa64/libmwuix.so+00284076 _ZNK21uixDisplayInformation12getTopWindowEv+00000012 [ 10] 0x00007f9d60d66425 /usr/local/MATLAB/R2016a/bin/glnxa64/matlab_startup_plugins/../../../bin/glnxa64/libmwuix.so+00205861 [ 11] 0x00007f9d60d667a5 /usr/local/MATLAB/R2016a/bin/glnxa64/matlab_startup_plugins/../../../bin/glnxa64/libmwuix.so+00206757 [ 12] 0x00007f9d6a34cd71 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwiqm.so+00650609 [ 13] 0x00007f9d6a353d7b /usr/local/MATLAB/R2016a/bin/glnxa64/libmwiqm.so+00679291 [ 14] 0x00007f9d6a39c39e /usr/local/MATLAB/R2016a/bin/glnxa64/libmwiqm.so+00975774 [ 15] 0x00007f9d7a4ae656 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwservices.so+02451030 _Z18svWS_PostUserEventil+00000038 [ 16] 0x00007f9d470c54e7 /usr/local/MATLAB/R2016a/bin/glnxa64/libnativejmi.so+01000679 _ZN5boost6detail8function26void_function_obj_invoker3INS_3_bi6bind_tIvPFvP7JNIEnv_P8_jobjectENS3_5list2INS_3argILi1EEENSC_ILi2EEEEEEEvS6_S8_lE6invokeERNS1_15function_bufferES6_S8_l+00000023 [ 17] 0x00007f9d470d13cc /usr/local/MATLAB/R2016a/bin/glnxa64/libnativejmi.so+01049548 _ZNK5boost9function3IvP7JNIEnv_P8_jobjectlEclES2_S4_l+00000028 [ 18] 0x00007f9d470c456e /usr/local/MATLAB/R2016a/bin/glnxa64/libnativejmi.so+00996718 _Z17PostMatlabMessageP7JNIEnv_P8_jobjectS2_l+00000222 [ 19] 0x00007f9d4e3c9d98 <unknown-module>+00000000 [ 20] 0x00007f9d4e3bd058 <unknown-module>+00000000 [ 21] 0x00007f9d4e3bd058 <unknown-module>+00000000 [ 22] 0x00007f9d4e3bd058 <unknown-module>+00000000 [ 23] 0x00007f9d4e3bd058 <unknown-module>+00000000 [ 24] 0x00007f9d4e3bd233 <unknown-module>+00000000 [ 25] 0x00007f9d4e3bd233 <unknown-module>+00000000 [ 26] 0x00007f9d4e3b74e7 <unknown-module>+00000000 [ 27] 0x00007f9d593f08f5 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06289653 [ 28] 0x00007f9d593ef358 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06284120 [ 29] 0x00007f9d593b37ca /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06039498 [ 30] 0x00007f9d593b3a24 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre
/lib/amd64/server/libjvm.so+06040100 [ 31] 0x00007f9d593b3e7a /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06041210 [ 32] 0x00007f9d59535b0e /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+07621390 [ 33] 0x00007f9d59535c76 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+07621750 [ 34] 0x00007f9d593e8d1f /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06257951 [ 35] 0x00007f9d4e3d4e88 <unknown-module>+00000000 [ 36] 0x00007f9d4e3bd058 <unknown-module>+00000000 [ 37] 0x00007f9d4e3b74e7 <unknown-module>+00000000 [ 38] 0x00007f9d593f08f5 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06289653 [ 39] 0x00007f9d593ef358 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06284120 [ 40] 0x00007f9d593b37ca /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06039498 [ 41] 0x00007f9d593b3a24 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06040100 [ 42] 0x00007f9d593b3e7a /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06041210 [ 43] 0x00007f9d59467d26 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06778150 [ 44] 0x00007f9d5947835a /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06845274 JVM_FindClassFromClassLoader+00000490 [ 45] 0x00007f9d515df68c /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/libjava.so+00054924 Java_java_lang_Class_forName0+00000300 [ 46] 0x00007f9d4e3c9d98 <unknown-module>+00000000 [ 47] 0x00007f9d4e3bd233 <unknown-module>+00000000 [ 48] 0x00007f9d4e3bd233 <unknown-module>+00000000 [ 49
] 0x00007f9d4e3bd058 <unknown-module>+00000000 [ 50] 0x00007f9d4e3b74e7 <unknown-module>+00000000 [ 51] 0x00007f9d593f08f5 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06289653 [ 52] 0x00007f9d593ef358 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06284120 [ 53] 0x00007f9d59429099 /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06520985 [ 54] 0x00007f9d59431a1d /usr/local/MATLAB/R2016a/sys/java/jre/glnxa64/jre/lib/amd64/server/libjvm.so+06556189 [ 55] 0x00007f9d5a9d3b91 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01129361 [ 56] 0x00007f9d5a9cd9f4 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01104372 [ 57] 0x00007f9d5a9d3174 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01126772 [ 58] 0x00007f9d5a9d3300 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+01127168 [ 59] 0x00007f9d5a99961b /usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+00890395 [ 60] 0x00007f9d5a996bc5 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwjmi.so+00879557 _ZN3jmi3jmi23JmiMethodsUsedByRuntime4initERKN8services6config14JmiInitOptionsE+00000021 [ 61] 0x00007f9d6a03d5c1 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwmcr.so+00783809 [ 62] 0x00007f9d6a0380ab /usr/local/MATLAB/R2016a/bin/glnxa64/libmwmcr.so+00762027 [ 63] 0x00007f9d6a028196 /usr/local/MATLAB/R2016a/bin/glnxa64/libmwmcr.so+00696726 [ 64] 0x00007f9d6a014cfd /usr/local/MATLAB/R2016a/bin/glnxa64/libmwmcr.so+00617725 [ 65] 0x00007f9d791916ba /lib/x86_64-linux-gnu/libpthread.so.0+00030394 [ 66] 0x00007f9d78ec782d /lib/x86_64-linux-gnu/libc.so.6+01075245 clone+00000109 [ 67] 0x0000000000000000 <unknown-module>+00000000
If this problem is reproducible, please submit a Service Request via: http://www.mathworks.com/support/contact_us/
A technical suppo
rt engineer might contact you with further information.
Thank you for your help.** This crash report has been saved to disk as /home/amazinger/matlab_crash_dump.4928-1 **
MATLAB is exiting because of fatal error Killed -----------------------------------------END-------------------------------------------------------------------------
It also created an error log and a matlab crash file, which I attached to this email.
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all. log in case it's of any use.
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu Kylin 16.04 LTS 3) uname -a: Linux X1 4.4.0-79-generic #100-Ubuntu SMP Wed May 17 19:58:14 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log and error logs: see attached
Best Regards
Guochun Yang
Institute of Psychology, Chinese Academy of Sciences
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
祝好！ Best Regards
杨国春（刘勋组） Guochun Yang
中科院心理所 Institute of Psychology, Chinese Academy of Sciences