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

2020
Views:

8

Pages:

19
Author:

lokalnimhb9j

Basic fNIRS Data Analysis with Homer Outline ◊ Homer file formats ◊ Basic processing : ◊ Intensity to hemoglobin concentrations ◊ Filtering ◊ Block-averaging ◊ More advanced processing File formats Probe source-detector geometry : .sd files fNIRS experimental data : .nirs files 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 .SD file format: the SDgui We will go over this in detail on Day 3. 7 .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 Homer2. Note 2: Conversion scripts are available for some other data formats (Hitachi, NIRx, Shimadzu, …), see http://homer-fnirs.org/faq/ .CFG file format A .cfg file describes the steps of data analysis, a sequence of Homer2 functions Simplest processing stream: Intensity Intensity to ΔOD ΔOD ΔOD to Concentration Multiple more advanced functions we can incorporate in the stream: Prune data Regress short SD Ignore segments Identify MAs Band-pass filter Remove / Correct MAs Concentration Block- average Hemodynamic response function (HRF) GLM Note: in options, you can hover over each function to get help on the function and the parameters Let’s create a processing stream. • Launch HOMER2 • • Option 1: Executable version: Run HOMER2.exe Option 2: MATLAB version: Run MATLAB, run “setpaths” function and then call EasyNIRS (or Homer_UI) from command window. • Hit cancel when it asks you to load process options file • Go to File • Change Directory to following folder: \fNIRS_COURSE_2018\EXERCISES\Ex1_Basic_data_analysis\1-basic-steps .CFG file format: the Process Stream GUI The Process Stream GUI enables you to create your own .cfg files Go to Tools > Process Stream GUI → it starts procStreamGUI .CFG file format Add, remove, and move functions in the stream The list of functions to choose from Outputs The help nformation for the selected function Function Name Inputs The processing stream you’re creating Outputs Function Name Inputs .CFG file format Intensity Intensity to ΔOD ΔOD 1 2 .CFG file format Intensity Intensity to ΔOD ΔOD Band-pass filter ΔOD, filtered ΔOD to Concentration Concentration Blockaverage Hemodynamic response function (HRF) Add: • hmrIntensity2OD • hmrBandpassFilt • hmrOD2Conc • hmrBlockAvg .CFG file format 1 2 .CFG file format Give a name to your new processing stream and save .CFG file format You can change your current processing stream in Homer2 File > Load Process Options (*.cfg) .CFG file format 1 2 .CFG file format This will open the ProcessOpt window, where you can modify the parameters of each function Click on ‘Options’