Installation error

[Takehiro_Uda]

I will participate the work shop in Osaka next week.
Now, I prepare the installation of Brainstorm.
However, when I try to run the brainstorm, error message appeared.

(1)From the Brainstorm Download page, I downloaded the files.
I unziped the two downloaded files on my desktop
I createed a folder “brainstorm_db” on my Desktop folder

(2)I downloaded the MCR R2014a (8.3) for my operating system and installed the MCR

(3)I double-clicked on brainstorm3.command. But error message appeared.

error message is as follows:

To execute the Brainstorm binaries, you need to install the Matlab Compiler Runtime 8.3 on your computer (MCR Matlab R2014a).
The MCR is available from the Mathworks website: > google ‘‘download matlab mcr.’’

Now, select the installation folder of the MCR8.3. Examples:
-Mac OSX: /Applications/MATLAB/MATLAB_Compiler Runtime/v83

I already tried to troubleshoot from a terminal as instructed on the installation page.
But, I cannot resolve the installation problem.

My OS version is Mac OS 10.9.2
I don’t have Matlab.

Please help resolving the problem.

[Francois]

Dear Takehiro,

I haven’t tested this installation procedure on the last update of MacOSX (10.9.2).
I will try to help you solving this issue before the workshop.

We just realized that those scripts were not working well when there are space characters in the file path (either the path to the MCR or the path to brainstorm3).
Can you please try replacing any space in the folders with _ characters? Then run brainstorm again from the terminal.
I will fix the scripts later today in the online distribution.

If it doesn’t solve the problem, we will need some more debugging.
From a terminal, can you please run the following commands one after the other, and for each one copy-paste the output:
(this assumes that you installed Brainstorm on your desktop, if not, change the path where Brainstorm is installed)

ls -l /Applications/MATLAB/MATLAB_Compiler_Runtime/v83
ls -l /Applications/MATLAB/MATLAB_Compiler_Runtime/v83/bin/maci64/libnativedl.dylib
/Applications/MATLAB/MATLAB_Compiler_Runtime/v83/sys/java/jre/maci64/jre/java -version
java -version
cd ~/Desktop/brainstorm3/bin/R2014a
./brainstorm3.command /Applications/MATLAB/MATLAB_Compiler_Runtime/v83

Thanks,
Francois

[Takehiro_Uda]

Dear Francois.
Thank you for your kind instructions for installation.
I successfully installed Brainstorm and run the program.
Sincerely,

Takehiro Uda

[Jeff_Eriksen]

Hi Francois,

I tried to install BSt on a new Mac with 10.9 Mavericks, and got the same error as Takehiro originally noted. There are no spaces in my paths. Any other suggestions?

-Jeff

[Jeff_Eriksen]

Francois,

I followed the instructions you gave to Takehiro:

Jeffs-MacBook-Pro:/ jefferiksen$ ls -l /Applications/MATLAB/MATLAB_Compiler_Runtime/v83
total 200
drwxr-xr-x 4 jefferiksen admin 136 Aug 4 21:36 Contents
-r–r--r-- 1 jefferiksen admin 5192 Nov 11 2013 MCR_license.txt
drwxr-xr-x 9 jefferiksen admin 306 Aug 5 10:35 appdata
drwxr-xr-x 17 jefferiksen admin 578 Aug 4 21:36 bin
drwxr-xr-x 5 jefferiksen admin 170 Aug 4 21:36 etc
drwxr-xr-x 5 jefferiksen admin 170 Aug 4 21:36 extern
drwxr-xr-x 5 jefferiksen admin 170 Aug 4 21:36 help
drwxr-xr-x 5 jefferiksen admin 170 Aug 4 21:36 java
-r–r--r-- 1 jefferiksen admin 80401 Feb 20 22:14 license.txt
drwxr-xr-x 4 jefferiksen admin 136 Aug 5 10:34 mcr
-r–r--r-- 1 jefferiksen admin 6826 Jan 20 2014 patents.txt
drwxr-xr-x 4 jefferiksen admin 136 Aug 4 21:36 polyspace
drwxr-xr-x 100 jefferiksen admin 3400 Aug 5 10:34 resources
drwxr-xr-x 4 jefferiksen admin 136 Aug 4 21:36 rtw
drwxr-xr-x 4 jefferiksen admin 136 Aug 4 21:36 runtime
drwxr-xr-x 4 jefferiksen admin 136 Aug 4 21:36 simulink
drwxr-xr-x 11 jefferiksen admin 374 Aug 5 10:34 sys
drwxr-xr-x 17 jefferiksen admin 578 Aug 5 10:34 toolbox
-r–r--r-- 1 jefferiksen admin 248 Dec 26 2007 trademarks.txt

Jeffs-MacBook-Pro:/ jefferiksen$ ls -l /Applications/MATLAB/MATLAB_Compiler_Runtime/v83/bin/maci64/libnativedl.dylib
-r-xr-xr-x 1 jefferiksen admin 23052 Feb 20 22:36 /Applications/MATLAB/MATLAB_Compiler_Runtime/v83/bin/maci64/libnativedl.dylib

Jeffs-MacBook-Pro:/ jefferiksen$ /Applications/MATLAB/MATLAB_Compiler_Runtime/v83/sys/java/jre/maci64/jre/java -version
-bash: /Applications/MATLAB/MATLAB_Compiler_Runtime/v83/sys/java/jre/maci64/jre/java: No such file or directory

Jeffs-MacBook-Pro:/ jefferiksen$ java -version
java version "1.8.0_11"
Java™ SE Runtime Environment (build 1.8.0_11-b12)
Java HotSpot™ 64-Bit Server VM (build 25.11-b03, mixed mode)

Jeffs-MacBook-Pro:R2014a jefferiksen$ ./brainstorm3.command /Applications/MATLAB/MATLAB_Compiler_Runtime/v83

BST> Starting Brainstorm:
BST> =================================
BST> Version: 3.2.140730 (30-Jul-2014)
BST> Compiling main interface files…
BST> Emptying temporary directory…
BST> Deleting old process reports…
BST> Loading configuration file…
BST> Loading default montages…
BST> Initializing user interface…
BST> Starting OpenGL engine…
BST> Reading plugins folder…
Invalid character was detected.
Invalid character was detected.

(Francois, at this point I think the license agreement came up, then it let me chosse the db directory)

BST> License accepted.
BST> Loading current protocol…
BST> =================================

(here the Brainstorm GUI came up OK, then I closed it)

BST> Brainstorm stopped.

---

      std::terminate() detected at Tue Aug  5 10:45:54 2014

---

Configuration:
Crash Decoding : Disabled
Current Visual : Quartz
Default Encoding : ISO-8859-1
MATLAB Architecture: maci64
MATLAB Root : /Applications/MATLAB/MATLAB_Compiler_Runtime/v83
MATLAB Version : 8.3.0.532 (R2014a)
Operating System : Darwin 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64
Processor ID : x86 Family 6 Model 70 Stepping 1, GenuineIntel
Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot™ 64-Bit Server VM mixed mode
Window System : Quartz

Fault Count: 1

Abnormal termination:
std::terminate()

Register State (captured):
RAX = 00007fff6b4820b0 RBX = 00000001039a3ab8
RCX = 00007fff6b4820b0 RDX = 00007f8132c57520
RSP = 00000001039a3350 RBP = 00000001039a3670
RSI = 00007fff6b45f1a1 RDI = 00000001039a3400

R8 = 00007fff6b4820b0 R9 = 000000000000000f
R10 = 00000001078d96db R11 = 00000001039a34c0
R12 = 00000001039a4200 R13 = 0000000000000000
R14 = 00007fff75b35420 R15 = 0000000000000000

RIP = 000000010774767b RFL = 000000000000000f

CS = 00000001078daf20 FS = 00000001078d96eb GS = 000000010783eb88

Stack Trace (captured):
[ 0] 0x0000000107742874 /Applications/MATLAB/MATLAB_Compiler_Runtime/v83/bin/maci64/libmwfl.dylib+00030836 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+00000052
[ 1] 0x00000001077462aa /Applications/MATLAB/MATLAB_Compiler_Runtime/v83/bin/maci64/libmwfl.dylib+00045738 _ZN2fl4test17terminate_handledEv+00000906
[ 2] 0x0000000107745cf5 /Applications/MATLAB/MATLAB_Compiler_Runtime/v83/bin/maci64/libmwfl.dylib+00044277 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+00000117
[ 3] 0x000000010a2b8d07 /Applications/MATLAB/MATLAB_Compiler_Runtime/v83/bin/maci64/libmwmcr.dylib+00269575 _Z32mnRunPathDependentInitializationv+00003127
[ 4] 0x000000010a2b8ff8 /Applications/MATLAB/MATLAB_Compiler_Runtime/v83/bin/maci64/libmwmcr.dylib+00270328 _Z32mnRunPathDependentInitializationv+00003880
[ 5] 0x000000010a2b8540 /Applications/MATLAB/MATLAB_Compiler_Runtime/v83/bin/maci64/libmwmcr.dylib+00267584 _Z32mnRunPathDependentInitializationv+00001136
[ 6] 0x000000010a2b7ff2 /Applications/MATLAB/MATLAB_Compiler_Runtime/v83/bin/maci64/libmwmcr.dylib+00266226 _Z22mnInstallCrashHandlersv+00000530
[ 7] 0x00007fff919a11d1 /usr/lib/libc++abi.dylib+00147921 _ZSt11__terminatePFvvE+00000008
[ 8] 0x00007fff919a0e7b /usr/lib/libc++abi.dylib+00147067 __cxa_rethrow+00000109
[ 9] 0x0000000109dfdfef /Applications/MATLAB/MATLAB_Compiler_Runtime/v83/bin/maci64/libmwmclmcr.dylib+00085999 ZN17MclMvmMcrInstance5fevalEPKciPP11mxArray_tagiPKPKS2+00001743
[ 10] 0x00000001098f3125 /Applications/MATLAB/MATLAB_Compiler_Runtime/v83/bin/maci64/libnativemcl.dylib+00749861 Java_com_mathworks_toolbox_javabuilder_internal_MWMCR_mclFeval+00001189
[ 11] 0x00000001039bbf90 <unknown-module>+00000000

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/jefferiksen/matlab_crash_dump.366-1 **

MATLAB is exiting because of fatal error
libc++abi.dylib: terminate_handler unexpectedly returned./brainstorm3.command: line 125: 366 Killed: 9 “$JAVA_EXE” -jar "$JAR_FILE"
Jeffs-MacBook-Pro:R2014a jefferiksen$

[Francois]

Hi Jeff,

So if I understand well, Brainstorm works correctly but the process crashes when you close it?

I have no control over how the end of the execution of a compiled Matlab program behaves on any platform. This is a Matlab crash, not a Brainstorm one.
I also noticed that on a few computers it was never ending without a crash and core dump.
As it is indicated at the of the Matlab error report, you can report the bug on the Mathworks website.

Cheers,
Francois

[findjoshgold]

I have just installed brainstorm_221014.zip and MatlabR2022b and have selected brainstorm 3 in the current folder and typed "brainstorm in the command line but only receive the following error, "Unrecognized function or variable 'brainstorm'."

I am running this on Macbook pro 2018 on macOS 12.6.

What am i doing wrong?

Thank you
Josh

[tourette95]

you need not just select the folder but get In the folder, once you are inside, you can type brainstorm