University:
Boston University
Course:
CAS CS 501 | Computer Science Practicum
Academic year:

2024
Views:

464

Pages:

12
Author:

daven8b2x

fNIRS Data Analysis with Homer3 Outline ◊ Homer file formats ◊ Basic processing : ◊ Intensity to hemoglobin concentrations ◊ Filtering ◊ Block-averaging ◊ More advanced processing : ◊ ◊ ◊ ◊ Other useful Homer functions Exporting results Plot probe Group analysis File formats Probe source-detector geometry : .sd files fNIRS experimental data : .nirs files fNIRS experimental data* : .snirf files (new) Data processing stream : .cfg files Processed data files : groupResults.mat .SD file format Describes the 2D source/detector geometry Matlab .sd file containing the structured variable SD with the following fields: Field Definition Size Example Lambda Wavelengths used for data acquisition 1 × nWavelengths [690 830] nSrcs Number of sources 1×1 1 nDets Number of detectors 1×1 2 SrcPos Array of source coordinates nSrcs × 3 [ 0 0 0] DetPos Array of detector coordinates nDets × 3 [30 0 0; 0 30 0] MeasList List of measurement channels nChannels × 4 [1 1 1 1; 1 2 1 1; 1 1 1 2; 1 2 1 2] column 1 source idx column 2 detector idx column 3 column 4 unused wavelength idx Note: The SD structure is also incorporated in the .nirs file format we will see in a few slides .SD file format: the SDgui Enables you to create your own .sd files Sub-GUI of AtlasViewer .SD file format: the SDgui Start AtlasViewer Go to Tools > Make Probe → it starts the SDgui 6 SDgui 7 How to start 1. Begin by naming the new probe using the text box at the bottom-center of the GUI 2. Enter the wavelengths of light that will be used in the experiment (690 830) Hint: easier if you have your 2D design on a piece of paper with the distances eg: 30 mm 0, 30, 0 30, 0, 0 0, 0, 0 30 mm 8 Adding sources, detectors and channels 3. Place a source at (0, 0, 0) 4. Add detectors at (30, 0, 0) and (0, 30, 0) 5. Connect measurement channels by clicking on optodes – to remove a channel do the same – you cannot connect two detectors or two sources 9 2D PROBE LAYOUT 3 5 4 1 2 10 .NIRS file format Contains an fNIRS dataset Matlab .nirs file containing the following variables: Field Definition Size SD Probe geometry, same as .sd files Structured variable t Array of data time points NTime_points × 1 d Array of raw intensity time course NTime_points × NChannels s Array of stimulus onsets. Different conditions are a way to separate stimuli into different groups NTime_points × NConditions aux Array of auxiliary signals NTime_points × NAux channels Note 1: In addition to the above parameters, additional parameters can appear in the .nirs file as a result of processing the data set in HOMER3. Note 2: Conversion scripts are available for some other data formats (Hitachi, NIRx, Shimadzu, …), .SNIRF file format • many different fNIRS data file format • difficult to use specific data analysis software and share data with collaborators • Common format: Shared Near InfraRed File Format http://github.com/fNIRS/snirf • SNIRF provides numeric fNIRS data with time stamps and a so-called ‘measurement list’ for detailed measurement information (in HDF5 format)