Tutorial: Import and visualize functional NIRS data

<!> This tutorial is under construction <!>

Authors: Thomas Vincent, Zhengchen Cai

The current tutorial assumes that the tutorials 1 to 6 have been performed. Even if they focus on MEG data, they introduce Brainstorm features that are required for this tutorial.

List of prerequisites:

Download

The dataset used in this tutorial is available online.

Presentation of the experiment

Create the data structure

Create a protocol called "TutorialNIRSTORM":

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).

NIRSTORM_tut1_MRI_edit.gif

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 registration between the MRI and the loaded meshes by right-clicking on each mesh element and going to "MRI registration -> Check MRI/Surface registration".

NIRSTORM_tut1_new_MRI_meshes.gif

Import NIRS functional data

The functional data used in this tutorial was produced by 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:

To import this data set in Brainstorm:

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 Nasion, Left and Right ears. It can then be refined with the either the full head shape of the subject or with manual adjustment.

Step 1: Fiducials

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:

/!\ Add screenshots

As reference, the following figures show the position of the fiducials and the optodes as they were digitized by Brainsight:

NIRSTORM_tut1_brainsight_head_mesh_fiducials_1.gif NIRSTORM_tut1_brainsight_head_mesh_fiducials_2.gif NIRSTORM_tut1_brainsight_head_mesh_fiducials_3.gif

Review Channel information

The resulting data organization should be:

func_data_loading_result.gif

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".

Name

Type

Group

Comment

Loc(1)

Loc(2)

Loc(3)

...

1

TAPPING

Stim

N/A

N/A

N/A

2

WLs

NIRS_WL_DEF

N/A

N/A

N/A

3

S1D1WL1

NIRS

NIRS_WL1

coords S1

coords D1

coords middle [S1-D1]

4

S1D1WL2

NIRS

NIRS_WL2

coords S1

coords D1

coords middle [S1-D1]

5

S1D2WL1

NIRS

NIRS_WL1

coords S1

coords D2

coords middle [S1-D2]

6

S1D2WL2

NIRS

NIRS_WL2

coords S1

coords D2

coords middle [S1-D2]

7

S1P1WL1

NIRS

NIRS_WL1

(PROXY)

coords S1

coords D2

coords middle [S1-D2]

8

S1P1WL2

NIRS

NIRS_WL2

(PROXY)

coords S1

coords D2

coords middle [S1-D2]

Visualize NIRS signals

Right-clicking on the raw file shows the list of channel types:

Select -> NIRS -> Display time series

It will open a new figure with superimposed channels

/!\ add screenshot

Which can also be viewed in butterfly mode

/!\ add screenshot

We refer to the tutorial for navigating in these views "Review continuous recordings"

Montage selection

Within the NIRS channel type, the following channel groups are available:

/!\ Add screenshot

Tutorials/NIRSDataImport (last edited 2015-10-29 14:19:05 by ?ThomasVincent)