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Workshop fNIRS 2022

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Edouard Delaire edited this page Oct 8, 2022 · 22 revisions

NIRSTORM

This page corresponds the mini-course given at the fNIRS conference in 20222. More information here: https://fnirs2022.fnirs.org/educational/mini-courses/minicourse-20/

Authors

  • Edouard Delaire, Physics Department and PERFORM Center, Concordia University, Montreal, Canada
  • Thomas Vincent, EPIC center, Montreal Heart Institute, Montreal, Canada
  • Zhengchen Cai, Physics Department and PERFORM Center, Concordia University, Montreal, Canada
  • Christophe Grova, Physics Department and PERFORM Center, Concordia University, Montreal, Canada

Outline:

Requirements

  • 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.
    The Matlab Curve Fitting Toolbox is required to perform motion correction. If you don't have it, you may skip this step in the first tutorial. The provided data do not contain too much movement.
  • Before attending the workshop: Please complete the following Setup section.

Setup

Brainstorm

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

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.

Plug-In

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Using Brainstorm plug-in system, dowload the following plugins :

  • NIRS > NIRSTORM
  • NIRS > MCXLAB-cl
  • SPM12
  • Inverse > Brainentropy

Tutorials

The tutorial is separated in three modules

  • Module 1: Channel-space analysis: extraction of the motor response
  • Module 2: Source-space analysis: Reconstruction of the motor response on the cortical surface
  • Module 3: Optimal montage computation

Presentation of the experiment

  • One subject, one run of 19 minutes acquired with a sampling rate of 10Hz
  • Finger tapping task: 20 blocks of 10 seconds each, with rest period of 30 to 60 seconds
  • 3 sources, 15 detectors and 1 proximity detector
  • 2 wavelengths: 685nm and 830nm
  • 3T MRI anatomy processed by FreeSurfer 5.3.0 and SPM12

Download data sets and check installation

The total disk space required after data download and installation is ~1.3Go. The size is quite large because of optical data which are required for the computation of the forward model. The dataset can be downloaded from : https://drive.google.com/file/d/1b8AYRc7_4vIxdFCpMs5QCri_kTcCK-G7/view?usp=sharing

** 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: [email protected]

References

Boas D, Culver J, Stott J, Dunn A. Three dimensional Monte Carlo code for photon migration through complex heterogeneous media including the adult human head. Opt Express. 2002 Feb 11;10(3):159-70 pubmed

Boas D.A., Dale A.M., Franceschini M.A. Diffuse optical imaging of brain activation: approaches to optimizing image sensitivity, resolution, and accuracy. NeuroImage. 2004. Academic Press. pp. S275-S288 pubmed

Hansen C. and O’Leary DP., The Use of the L-Curve in the Regularization of Discrete Ill-Posed Problems. SIAM J. Sci. Comput., 14(6), 1487–1503 SIAM

Arridge SR, Methods in diffuse optical imaging. Philos Trans A Math Phys Eng Sci. 2011 Nov 28;369(1955):4558-76 pubmed

Amblard C,, Lapalme E. and Jean-Marc Lina JM, Biomagnetic source detection by maximum entropy and graphical models. IEEE Trans Biomed Eng. 2004 Mar;51(3):427-42 pubmed

Grova, C. and Makni, S. and Flandin, G. and Ciuciu, P. and Gotman, J. and Poline, JB. Anatomically informed interpolation of fMRI data on the cortical surface Neuroimage. 2006 Jul 15;31(4):1475-86. Epub 2006 May 2. pubmed

Chowdhury RA, Lina JM, Kobayashi E, Grova C., MEG source localization of spatially extended generators of epileptic activity: comparing entropic and hierarchical bayesian approaches. PLoS One. 2013;8(2):e55969. doi: 10.1371/journal.pone.0055969. Epub 2013 Feb 13. pubmed

Machado A, Marcotte O, Lina JM, Kobayashi E, Grova C., Optimal optode montage on electroencephalography/functional near-infrared spectroscopy caps dedicated to study epileptic discharges. J Biomed Opt. 2014 Feb;19(2):026010 pubmed

Pellegrino G, Machado A, von Ellenrieder N, Watanabe S, Hall JA, Lina JM, Kobayashi E, Grova C., Hemodynamic Response to Interictal Epileptiform Discharges Addressed by Personalized EEG-fNIRS Recordings Front Neurosci. 2016 Mar 22;10:102. pubmed

Fang Q. and Boas DA., Monte Carlo simulation of photon migration in 3D turbid media accelerated by graphics processing units, Opt. Express 17, 20178-20190 (2009) pubmed

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