Mini course 2024
This page corresponds the mini-course given at the fNIRS conference in 20224. More information here: https://fnirs2024.fnirs.org/educational-course/minicourses/minicourse-edda-cg16/
- Hardware: a basic recent laptop should be fine.
- An internet connection. A dedicated wifi connection will be available on site for the participants of the workshop.
- Operating system: Linux, windows or Mac OS. Everything should work on all systems though we recommend using Linux since more tests have been done with it.
- Disk space: the full installation with dependencies and sample data should take no more than 4Gb. Some space can be freed by cleaning the CPLEX dependency (saves ~3Gb).
- Matlab: version > R2015b is recommended.
- Before attending the workshop: Please complete the following Setup section.
If Brainstorm is already installed, update to the latest version (Menu bar: Update > Update Brainstorm).
For a new installation, Brainstorm requires a user to be registered in order to download it. This allows their development team to track their usage. Consult Brainstorm tutorial for instruction on how to download Brainstorm
For the first time it runs, brainstorm asks to specify a database folder. This will be the place where all the data imported by brainstorm will go. Create a folder named brainstorm_db in your Documents folder and specify it as your main brainstorm database. Then, the main brainstorm interface will be displayed.
No prior knowledge of brainstorm is mandatory for the current workshop session which should cover the basics. However, if one wishes to get familiar with brainstorm features, we refer to the brainstorm tutorials page.
Important for mac users: If the right-click doesn't work anywhere in the Brainstorm interface and you cannot get to see the popup menus in the database explorer, try to change the configuration of your trackpad in the system preferences and enable left-click. Alternatively, connect a standard external mouse with two buttons. Some Apple pointing devices do not interact very well with Java/Matlab.
CPLEX is a set of tools to perform functional optimization edited by IBM. It is used here to solve the integer programming problem during the optimal montage computation (last tutorial of this workshop).
For license concerns, we cannot bundle the CPLEX library within NIRSTORM. One can purchase a free copy of CPLEX if they are students or academics.
For this tutorial, download CPLEX 12.10.
To download CPLEX :
- Visit http://ibm.biz/CPLEXonAI and create an account using your institutional email
- Once you are connected; go down the page and click on software and then ILOG CPLEX Optimization Studio and click on download. A new page will open
- In the search options, select text, and write: "IBM ILOG CPLEX Optimization Studio V12.10 Multiplatform Multilingual eAssembly"
- Download "IBM ILOG CPLEX Optimization Studio V12.10 for X Multiplatform Multilingual" where X is your operating system (eg. Windows, Linux, MacOs)
- For MacOs, install CPlex.
- For Linux, and Windows, unzip the file in your Documents
Finally, add the path to the CPLEX Matlab bindings to the Matlab path: go to the "Home" tab, click "Set path" (yellow folder icon) then click on "Add with subfolders" and select the folder of the CPLEX Matlab bindings.
In Mac, this file is in your application folder.
If you cannot get a working version of CPLEX, let us know during the workshop and we'll try to help you.
Using Brainstorm plug-in system, download the following plugins :
- NIRS > NIRSTORM
- NIRS > MCXLAB-cl
- SPM12
- Inverse > Brainentropy
The total disk space required after data download and installation is ~1.3Go. The size is quite large because of the optical data that are required for the computation of the forward model. The dataset can be downloaded from: https://osf.io/md54y/?view_only=0d8ad17d1e1449b5ad36864eeb3424ed .
For the optimal montage, download Colin27 template, to do so, execute the following command in Matlab : nst_bst_set_template_anatomy('Colin27_4NIRS_Jan19', 0, 1)
** Licence ** This tutorial dataset (NIRS and MRI data) remains proprietary of the MultiFunkIm Laboratory of Dr Grova, at PERFORM centre, Concordia University, Montreal. Its use and transfer outside the Brainstorm tutorial, e.g. for research purposes, is prohibited without written consent from our group. For questions please contact Christophe Grova: christophe.grova@concordia.ca
Presentation slides linked to this tutorial can be found at: https://docs.google.com/presentation/d/1coEdtI50Xpc_v4R9Vn5UiK0tkW4mUZuw/edit?usp=share_link&ouid=114007975416410855082&rtpof=true&sd=true
A detailed version of the tutorial described in the slides will be available soon.
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