Tutorial: Import and visualize functional NIRS data

Authors: Thomas Vincent, Zhengchen Cai

The current tutorial assumes that the tutorials 1 to 5 have been performed. Even if they focus on MEG data, they introduce Brainstorm features that are used in this tutorial.

List of prerequisites:

• Create a new protocol

• Import the subject anatomy

• Display the anatomy

• Channel file / MEG-MRI coregistration

• Review continuous recordings

Download

The dataset used in this tutorial is available online .

• Go to the Download link page of this website, and download the file: nirs_sample.zip

• Unzip it in a folder that is not in any of the Brainstorm folders

Presentation of the experiment

• One subject, one acquisition run of XXX minutes

• Finger tapping task: 10 stimulation blocks of 30 seconds each, inter-stimulus interval of XXX seconds

• 4 sources and 12 detectors (+ 4 proximity channels) placed above the right motor region
• Two wavelengths: 690nm and 830nm

• MRI anatomy 3T from scanner type

Create the data structure

Create a protocol called "TutorialNIRSTORM":

• Got to File -> New Protocol

• Use the following setting :

  • Default anatomy: Use individual anatomy.

  • Default channel file: Use one channel file per subject (EEG).

In term of sensor configuration, NIRS is very similar to EEG and the placement of optodes may change from subject to the other. Should we add (EEG or NIRS) in the interface?

Create a subject called "Subject01" (Go to File -> New subject), with the default options

Import anatomy

Import MRI

Make sure you are in the anatomy view of the protocol. Right-click on "Subject01 -> Import MRI". Select T1_MRI.nii from the NIRS_sample data folder. This will open the MRI review panel where you have to set the fudicial points (See Import the subject anatomy).

Import Meshes

The head and white segmentations provided in the NIRS sample data were computed with Brainvisa.

Right-click on "Subject01 -> Import surfaces". From the NIRS sample data folder, select files: head_10000V.mesh, hemi_8003V.mesh and white_8003V.mesh.

You can check the regristration between the MRI and the loaded meshes by right-clicking on each meash element and going to "MRI registration -> Check MRI/Surface registration".

Import NIRS functional data

The functional data used in this tutorial was exported from the Brainsight acquisition software and is available in the NIRS sample folder in S01_Block_FO_LH_Run01.bs. This folder contains the following files:

• fiducials.txt: the coordinates of the fudicials (nasion, left ear, right ear).
  These positions should have been digitized at the same location as the fiducials previously marked on the anatomical MRI. These points will be used by Brainstorm for the registration, hence the consistency between the digitized and marked fiducials is essential for good

• optodes.txt: the coordinates of the optodes (sources and detectors), in the same referential as for the fiducials. Note: the actual referential is not relevant here, as the registration will be performed by Brainstorm afterwards.

• S01_Block_FO_LH_Run01.nirs: the NIRS data in a HOMer-based format document format.
  Note: The fields SrcPos and DetPos will be overwritten to match the given coordinates in "optodes.txt"

To import this data set in Brainstorm:

• Go to the "functional data" view of the protocol.

• Right-click on "Subject01 -> Import MEG/EEG/NIRS"

  • Select file type "NIRS: BS (.bs)"
  • Load the folder "S01_Block_FO_LH_Run01.bs" in the NIRS sample folder.

• Refine registration now? YES
  This operation is detailed in the next section

Registration

As in the tutorial The resitration between the MRI and the NIRS is done in two steps

Review Channel information

The resulting data organization should be:

This indicates that the data comes from the Brainsight system (BS) and comprises 97 channels.

To review the content of channels, right-click on "BS channels -> Edit channel file".

• The channel named "TAPPING" encodes the stimulation paradigm
• The channel named "WLs" defines the set of wavelengths
• Other channels contain the NIRS time-series measurements. For a given NIRS channel, its name is composed of the pair Source / Detector and the wavelength index. Column Loc(1) contains the coordinates of the source, Loc(2) the coordinates of the associated detector and Loc(3) the coordinates of the middle point between the source and the detector.
• The group "NIRS_PROX" indicates that the channel is a close-source measurement.

NIRS-MRI coregistration

Use automatic registration

Keep only step 1

Display Optodes (adapted from “Display Sensors”)

- no helmet here -> should be able to show optode positions over head meshSKip manual registration

Edit the channel file

Introduce new nomenclature

S1D1WL1 NIRS_WL1 …S1D1WL2 NIRS_WL2 …

Visualize NIRS signals

Depends on tut #5

Introduce default channel groups: ALL, WL1, WL2

Just adapt sections “Montage selection” and “Channel selection”