Differences between revisions 2 and 10 (spanning 8 versions)

This tutorial is under construction

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:

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, two acquisition runs of $/!\$ XXX minutes
Finger tapping task: $/!\$ XXX stimulation blocks of 30 seconds each, inter-stimulus interval of $/!\$ XXX seconds
$/!\$ XXX sources and $/!\$ XXX detectors (+ 4 proximity channels) placed above the right motor region
Two wavelengths: 690nm and 830nm
MRI anatomy 3T from $/!\$ scanner type

Create 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

Go to the "functional data" view of the protocol. Right-click on "Subject01 -> Import MEG/EEG/NIRS", select file type "NIRS: BS (.bs)" and load the folder "S01_Block_FO_LH_Run01.bs" in the NIRS sample folder. Exported from the Brainsight acquisition software, 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.
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 HOMer format.
The fields SrcPos and DetPos will be overwritten to match the given coordinates in "optodes.txt"

The resulting data organization should be:

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_WL1			coords S1	coords D1	coords middle [S1-D1]
4	S1D1WL2	NIRS_WL2			coords S1	coords D1	coords middle [S1-D1]
5	S1D2WL1	NIRS_WL1			coords S1	coords D2	coords middle [S1-D2]
6	S1D2WL2	NIRS_WL2			coords S1	coords D2	coords middle [S1-D2]

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.

dataset files:

* 2 nirs files with proper SrcPos and DetPos fields

-> generate these from brainsight output merged with montage coords

-> check if there is a way to directly have this from brainsight without having to forge it

1 file of digitized coords of fiducials (NAS, LE, RE) as a txt file. Coords should be in the same referential as SrcPos and DetPos

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”

-  ⇤ ← Revision 2 as of 2015-10-26 21:35:59 → 
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  Editor: ?ThomasVincent
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+   ← Revision 10 as of 2015-10-28 02:41:18 → ⇥
  Size: 6079
  Editor: ?ThomasVincent
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-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.
+||<40%> || <!> ~+'''This tutorial is under construction'''+~ <!> ||


''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.
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-    * [[http://neuroimage.usc.edu/brainstorm/Tutorials/CreateProtocol|Create a new protocol]]
    * [[http://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy|Import the subject anatomy]]
    * [[http://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy|Display the anatomy]]
    * [[http://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile|Channel file / MEG-MRI coregistration]]
    * [[http://neuroimage.usc.edu/brainstorm/Tutorials/ReviewRaw|Review continuous recordings]]
+ * [[http://neuroimage.usc.edu/brainstorm/Tutorials/CreateProtocol|Create a new protocol]]
 * [[http://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy|Import the subject anatomy]]
 * [[http://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy|Display the anatomy]]
 * [[http://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile|Channel file / MEG-MRI coregistration]]
 * [[http://neuroimage.usc.edu/brainstorm/Tutorials/ReviewRaw|Review continuous recordings]]
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+Line 17:
+The dataset used in this tutorial is available online .
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+Line 19:
-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
+ * 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, two acquisition runs of /!\ ''' XXX ''' minutes
 * Finger tapping task: /!\ ''' XXX ''' stimulation blocks of 30 seconds each,  inter-stimulus interval of /!\ ''' XXX ''' seconds
 * /!\ ''' XXX ''' sources and /!\ ''' XXX ''' detectors (+ 4 proximity channels) placed above the right motor region
 * Two wavelengths: 690nm and 830nm
 * MRI anatomy 3T from /!\ ''' scanner type '''

= Create 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 [[http://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy|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".

{{attachment:NIRSTORM_tut1_new_MRI_meshes.gif||height="335",width="355"}}

= Import NIRS functional data =
Go to the "functional data" view of the protocol. Right-click on "Subject01 -> Import MEG/EEG/NIRS", select file type "NIRS: BS (.bs)" and load the folder "S01_Block_FO_LH_Run01.bs" in the NIRS sample folder. Exported from the Brainsight acquisition software, this folder contains the following files:

 * fiducials.txt: the coordinates of the fudicials (nasion, left ear, right ear).<<BR>>These positions should have been digitized at the same location as the fiducials previously marked on the anatomical MRI.
 * 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 HOMer format.<<BR>>The fields SrcPos and DetPos will be overwritten to match the given coordinates in "optodes.txt"

The resulting data organization should be:

{{attachment:func_data_loading_result.gif}}

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_WL1 || || ||coords S1 ||coords D1 ||coords middle [S1-D1] || ||
||4 ||S1D1WL2 ||NIRS_WL2 || || ||coords S1 ||coords D1 ||coords middle [S1-D1] || ||
||5 ||S1D2WL1 ||NIRS_WL1 || || ||coords S1 ||coords D2 ||coords middle [S1-D2] || ||
||6 ||S1D2WL2 ||NIRS_WL2 || || ||coords S1 ||coords D2 ||coords middle [S1-D2] || ||
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-= Presentation of the experiment =
 
 * One subject, two acquisition runs of /!\ ''' XXX ''' minutes
 * Finger tapping task: /!\ ''' XXX ''' stimulation blocks of 30 seconds each,  inter-stimulus interval of /!\ ''' XXX ''' seconds
 * /!\ ''' XXX ''' sources and /!\ ''' XXX ''' detectors arranged in a /!\ ''' XXX ''' montage, with /!\ ''' XXX ''' proximity channels
 * Two wavelengths: 690nm and 860nm
 * MRI anatomy 3T from /!\ ''' scanner type '''
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-= Create a subject =
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-= Import anatomy =

import Brainvisa head mesh and MRI file + provide datasets

mark fudicials

= Import NIRS functional data =

NIRS Acquisition + description
+ * 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.
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+Line 94:
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