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).

Add screenshot

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

In the same way as in the tutorial "Channel file / MEG-MRI coregistration", the registration between the MRI and the NIRS is first based on three reference points. It can then be refined with the either the full head shape of the subject or with manual adjustmen.

Step 1: Fiducials

* The initial registration is based on the three fiducial point that define the Subject Coordinate System (SCS): nasion, left ear, right ear. You have marked these three points in the MRI viewer in the previous part. * These same three points have also been marked before the acquisition of the NIRS recordings. The person who recorded this subject digitized their positions with a tracking device (such as a Polhemus FastTrak or Patriot). The position of these points are saved in the NIRS datasets (see NIRS_sample/fiducials.txt). * When we bring the NIRS recordings into the Brainstorm database, we align them on the MRI using these fiducial points: we match the NAS/LPA/RPA points digitized with Brainsight with the ones we placed in the MRI Viewer. * This registration method gives approximate results. It can be good enough in some cases, but not always because of the imprecision of the measures. The tracking system is not always very precise, the points are not always easy to identify on the MRI slides, and the very definition of these points does not offer a millimeter precision. All this combined, it is easy to end with an registration error of 1cm or more. * The quality of the source analysis we will perform later is highly dependent on the quality of the registration between the sensors and the anatomy. If we start with a 1cm error, this error will be propagated everywhere in the analysis.

Step 2: Head shape

We don't have digitized head points for this data set. We should skip this

Step 3: manual adjustment

If the registration you get with automatic alignment techniques described previously, or if there was an issue when you digitized the position of the fiducials or the head shape, you may have to realign manually the optodes on the head. Right-click on the channel file > MRI Registration:

• Check: Show all the possible information that may help to verify the registration.

• Edit: Opens a window where you can move manually the MEG helmet relative to the head.
  Read the tooltips of the buttons in the toolbar to see what is available, select an operation and then right-click+move up/down to apply it. From a scientific point of view this is not exactly a rigorous operation, but sometimes it is much better than using wrong default positions.
  IMPORTANT: this refinement can only be used to better align the headshape with the digitized points - it cannot be used to correct for a subject who is poorly positioned in the helmet (i.e. you cannot move the helmet closer to the subjects head if they were not seated that way to begin with!)

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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”