BS3 installation using Matlab Runtime - JAVA NOT FOUND Error

Hello BS team. New user here.

I would like to install BS together with the Matlab Runtime. I have worked through your installation instructions ( up to step “Without Matlab - Step 5.” I tried different installation locations for BS and Matlab runtime. (I am on a network and am network admin.)

I have opened and edited brainstorm3.bat to various file paths for MATLABROOT and TEST_JAVA. No matter what I have tried, I am getting the JAVA NOT FOUND error. Is this possibly because I am on a network?

What do you suggest?

OS: Windows 7 64Bit



The goal of those batch files is only to find a working version of the JVM on your computer.
You should be able to track what the problem is by reading the .bat file and following what is tested in it.

If you defined the MATLABROOT, one of the two following folders must exist on the computer:

  • %MATLABROOT%\sys\java\jre\win64\jre\bin\java.exe
  • %MATLABROOT%\sys\java\jre\win32\jre\bin\java.exe

I’m not sure what you mean with " various file paths for TEST_JAVA": this is a label in the script, not a variable.
If you want to track what is happening in the cmd/powershell command window, remove all the “@” characters from the script.

Note that on most windows computers, if you have a version of Java correctly installed on your computer, you should be able to simply double-click on the .jar file to start Brainstorm.


Thank you very much Francois. I have reinstalled Java just in case that was the issue. When I click on \brainstorm3\bin\R2014b\brainstorm3.bat the command window seems to open and close very quickly. When I click on \brainstorm3\bin\R2014b\brainstorm3.jar Nothing happens. I am not getting the error, but I am still not sure how to start BS. I am very sorry to impose on you. Thank you for your help!

To be able to see the error message:

  • Open a windows terminal (cmd or powershell)
  • Go to the bin folder: cd “path_to_brainstorm_bat”
  • type “brainstorm3.bat”

Can you locate the file “MATLABROOT\sys\java\jre\win64\jre\bin\java.exe” on your computer?
If not, you have to install Matlab or the MCR library.
Once you found it (for example in: C:\Program Files\MATLAB\R2015b\sys\java\jre\win64\jre\bin\java.exe)

  • Restore the original brainstorm3.bat file (download again brainstorm again)
  • Edit the .bat file: @SET MATLABROOT=C:\Program Files\MATLAB\R2015b

If you really don’t understand how to edit this batch file, you can run it from the command line:
“C:\Program Files\MATLAB\R2015b\sys\java\jre\win64\jre\bin\java.exe” -jar brainstorm3.jar

Thank you again Francois! Issue resolved.