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