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| ||<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. 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''' 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” |
Differences between revisions 5 and 40 (spanning 35 versions)