Installation

Installation

The following page provides instructions for installing from Brainstorm. First, install brainstorm using the following tutorial: https://neuroimage.usc.edu/brainstorm/Installation

Without Matlab*, is already shipped within Brainstorm With Matlab, NIRSTORM can be downloaded using Brainstorm's plugin system: https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins

Additional tools for NIRSTORM

Monte Carlo eXtreme MCX

Monte Carlo eXtreme MCX is a tool used in NIRSTORM to simulate NIRS light propagation (computation of NIRS forwar) model. Two version can be downloaded using Brainstorm's plugin system : MXClab-cuda using GPU acceleration using a single or multiple GPUs with CUDA; or MXCLAB-opencl using OpenCL. More information here

IBM ILOG CPLEX Optimizer (CPLEX)

CPLEX is the tool used to compute Optimal montage in NIRSTORM. Tutorial on how to download and install CPLEX can be found here: https://www.ibm.com/support/pages/how-do-i-download-cplex-optimization-studio?lc=fr&mhsrc=ibmsearch_a&mhq=cplex

Note: NIRSTORM has been tested with the version 12.8 and 12.3.

Installation [deprecated]

The following provide instructions for installing from a stable release downloaded from the project release page.

To synchronize with the bleeding-edge (and possibly unstable) version using git, see the wiki page Git workflow.

Brainstorm must be installed prior to installing nirstorm.

In the source nirstorm folder (either uncompressed from the release archive or synchronized using git), the script nst_install.m takes care of copying or linking processes and functions into the brainstorm user folder.

Parts of the nirstorm plugin may already be shipped with the lastest brainstorm version and are available in the process selection menu in the "NIRS" submenu (modified bear lambert law and bad channel tagging). The current installation will override them.

Run brainstorm before installing nirstorm. All commands indicated below must be run in the nirstorm folder where the archive was uncrompressed.

Copy installation (windows, linux)

To copy all processes and functions into the brainstorm user folder, run under matlab:

>> nst_install('copy');

When updates are downloaded, this installation command must be run again for changes to take effect.

Linked installation (linux only)

To create symbolic links of all processes and functions into the brainstorm user folder, run under matlab:

>> nst_install('link');

When updates are downloaded, this installation command has to be run again only if there are new files.

Troubleshooting

Clean bad installation

Due to a bug in the installation on windows, there were some errors in the uninstallation scripts that were generated in the brainstorm user folder.

While running nst_install('copy'), if you had some warnings like:

Warning: Escaped character '\U' is not valid. See 'doc sprintf' for supported special characters.
In install_package>execute_file_operations (line 247)
In install_package (line 77)
In nst_install (line 70)

or errors like:

Error: File: uninstall_brainentropy.m Line: 2 Column: 6
Character vector is not terminated properly.

then make sure to clean your brainstom user folder (should something like C:\Users\MyUser\brainstorm), by removing the following files:

uninstall_brainentropy.m
process/uninstall_nirstorm.m

Then you can run nst_install('copy') again. It should warn you about already existing files and show you where they will be backuped in your brainstom home folder. Finally, you can check these files and see if you want to clean them.