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

2021
Views:

83

Pages:

15
Author:

Phillip Barker

.CFG file format A .cfg file describes the steps of data analysis, a sequence of HOMER3 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 .CFG file format: the Process Stream GUI The Process Stream GUI enables you to create your own .cfg files Start Homer3 Go to Tools > Edit Process Stream → it starts procStreamGUI .CFG file format User functions registry: The list of functions to choose from Help information for the selected function or usage option Function names Add, remove, and move function usages in processing stream Possible usages for function The processing stream you’re creating Function usages .CFG file format Intensity 2 Intensity to ΔOD ΔOD 1 .CFG file format Processing stream loaded from default config file. Start fresh with an empty processing stream by clearing all entries. .CFG file format Your GUI should look like this now, with no entries in Current Processing Stream window .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 config file and save .CFG file format To load and change the processing stream file, open ProcStreamEditGUI: Tools => Edit Processing Stream .CFG file format .CFG file format 1 2 .CFG file format 2 – This will open the ProcStreamEditGUI, where you can modify parameters of each function usage 1 - Click on ‘Options’ Let’s analyze some fNIRS data: HOMER3_UI When opening Homer3, you need to select: • The dataset(s): a folder containing at least one .snirf (or .nirs) file. If all you have are .nirs files, Homer3 will convert the files to the .snirf format. • The data processing stream: a .cfg file. If you click ‘Cancel’, a default process stream will load. • Start Homer3 • When prompted to select a .nirs folder, navigate to and select folder /Exercises/Ex1_Basic_data_analysis/ • When prompted to select a .cfg file, select my_simple_processing.cfg file we just created. Note: If you’re already in Homer3 and need to change the data directory or the .cfg file: • Go to File > Change Directory, and select your nirs folder • Go to Tools > Edit Processing Stream and click the Load button to select .cfg file Homer3 MainGUI Source / detector geometry window Data plot window Select current processing element: run, subject or group. Current element’s data will be calculated and displayed in the data plot window Modify proc stream options and run proc stream What data type to display Motion artifacts/correction options and controls Select which part of the data plot window to view