1. Exclude data in the light graph
1.1 Bad channels
1.2 Bad or undesired periods: e.g., exclude practice tasks so you avoid dealing with those later.
1.3 Exclude trials that the participant failed. For example, if the participant failed to reach the minimum inspiratory pressure in the second trial, exclude the second trial from the analysis for that person. (Click here and scroll to page 20)
2. Select filter options for light graph data
Noisy data: linear phase, low-pass filter (default): after this step, select ‘refined data’ for all further steps
3. Sliding-Window Motion Artifact Rejection (SMAR)
Click here and scroll to page 27
Original publication of the SMAR technique here
H. Ayaz, M. Izzetoglu, P. A. Shewokis and B. Onaral, "Sliding-window motion artifact rejection for Functional Near-Infrared Spectroscopy," 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology, 2010, pp. 6567-6570, doi: 10.1109/IEMBS.2010.5627113.
4. Compute oxygenation signal
This technique uses the Modified Beer Lambert Law (MBLL) by clicking the “Oxy” button in the light file.
5. Exclude data in the oxy graph
5.1 Bad channels
5.2 Bad or undesired periods: e.g., exclude practice tasks so you avoid dealing with those later.
5.3 Exclude trials that the participant failed. For example, if the participant failed to reach the minimum inspiratory pressure in the second trial, exclude the second trial from the analysis for that person.
6. Select filter options for oxy data
Noisy data: linear phase, low-pass filter (default): after this step, select ‘refined data’ for all further steps
Click here and scroll to page 40
7. Apply detrending to refined oxy data
For signal drifts. Click here and scroll to page 43
8. Create blocks in light graph file
Click here and scroll to page 46
9. Work with blocks:
9.1. Save blocks in light graph and export to data space
9.2. Export blocks to Matlab
9.3. Export blocks to text file
Automation
Add new and name:
Automation
Preset
Block
10. Dataspace
10.1. View variables:
10.1.1. Plot Oxy & Deoxy time courses for each channel in the same graph view window (can add more tabs with different views in the graph view window)
10.1.2. Modify as needed: axis range, font, titles; standard error or standard deviation; colors; background; graph type
10.2. AGGREGATE (under ‘draw type’ button): average time series with standard error (which ever type you choose)
11. Multivariable aggregate & grouped temporal graph
CLICK HERE AND SCROLL TO PAGE 84
You can show different signals (e.g. hbo and hbr) in the same graph. You can also use different conditions, e.g. all 3 trials of the valsalva as separate signal lines. Select variables of interest in the data space window. Use the “group” button and add a new group and then assign different groups to your variables.
12. Processing tool
Process tab in data space
This is to create and visualize your outcome signal, such as the average signal across 3 valsalva trials.
Click here and scroll to page 88
Ayaz thesis page 89:
“Temporal processing operation is performed across rows. So, for Temporal Mean, the result variable has the same number of columns with the input and only one row that is the mean values.”
“Spatial processing is performed across columns, so for Spatial Mean, the resultant variable has same number of rows with input variable but one column that contains mean values.”
Columns: Optodes
Rows: Signal per time interval
Cell-by-Cell: I guess this is retaining the time course for each optode
13. Statistical analysis
Compare tab in data space
Click here and scroll to page 91
Test statistics (e.g. F-value) and p-values will be created as separate variables and added to the data space. For example, each optode will get its own F and p-value.
14. Using MBLL to calculate oxygenation from variables
MBLL tab: Creates oxy files (oxy, hbo, hbr, hbt) from light file.
“Programmatic oxygenation calculation from variables can be performed at the “MBLL” tab of “fnirSoft Processing Tool” window as shown below. This tool provides more flexibility and additional features for oxygenation calculation.”
“All input variables should be light intensity content type. Any number of input variables can be used. If no baseline variable is provided, first 20 rows of each input variable will be used for that variable as a baseline. Otherwise, same number of baseline variables needs to be selected so, through one to one matching, first baseline variable will be used for first input variable, etc. If only one baseline variable is selected or at the MBLL settings dialog, ‘use single baseline’ is enabled, all input baseline variables will be averaged and the same baseline will be used for each input variable.”
15. Export data tool
Click here and scroll to page 96
Available formats are:
Matlab (comma-separated)
Excel
Biopac Acqknowledge
fNIRSoft
Text file (tab-separated)
Can choose:
All variables in one file
Each variable in separate file
Summary file can be exported containing summary measures of all optodes and variables.
16. Organizer tool
I believe this is to select different subjects' light graphs to load at once.
17. Topograph tool
Left side of topographic image is participant’s left!
Threshold?
Save activations as image or video.