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| ||<40%> || <!> ~+'''This tutorial is under construction'''+~ <!> || {{attachment:NIRSTORM_tut1_new_MRI_meshes.gif||height="335",width="355"}} ''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: * [[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]] = 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 arranged in a /!\ ''' XXX ''' montage, with /!\ ''' XXX ''' proximity channels * Two wavelengths: 690nm and 860nm * 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". /!\ '''Add screenshot''' [[Tutorial/NIRSTORM_tut1_new_MRI_meshes|MRI meshes]] import Brainvisa head mesh and MRI file + provide datasets mark fudicials = Import NIRS functional data = Go to the "functional data" view of the protocol. NIRS Acquisition + description 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” |
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