Baseline
Before you start, you should consider what you want to use as a baseline. This can always be changed later in the process but you need to define it. The following options are possible:
The first 100 samples of the session that are automatically determined as the baseline by the software. Note that these samples won’t show up in the data because the entire signal is already scaled to it by default.
The 5-minute rest task.
The period at the beginning of each task before the first trial starts (e.g. in the sigh task, the one-ish minute before the first sigh signal).
Getting started
Each recorded session has at least 3 files:
Light file
Oxygenation file
Marker file
Open → open the Light File
You will be asked if you also want to load the marker file. Click Load.
When you open the light file, you will see the whole length of the recording session. This includes the MOCA, all performed practice tasks and all performed tasks. The first 100 samples are missing because they are considered the baseline relative to which the rest of the signal is scaled. Therefore, the file starts at 20.4 seconds instead of at zero.
On top, all the orange tags with numbers are the markers that indicate when a task or trial started. Your task is to tell the software which exact periods you want to analyze.
Right-click → optode layout view:
This opens the 2x8 layout view:
There are no saturations in these data, the signal looks fine.
Filtering
Next, we apply a filter.
Now go to the bottom tool bar and click the tab “Refine”
In Step 1, we select raw data because our data have not undergone any processing yet.
Step 2, we select the default filter this time, then apply. You can also click on “Filter Designer Tool” and custominze your own filtering options (see below).
ADD SCREENSHOT
Here you have the option to customize existing filters and save them as new filters that will then appear in the dropdown menu of the screen above. You can see in the graph how these options affect your data.
The application of the default filtering options should lead to a smoothed signal, i.e. the high-frequency noise. In the case below, the default option was not sufficient to make a noticeable difference, therefore, the 10Hz option from the dropdown menu was used. Compare how this signal differs from before:
Exclude bad data
In order to successfully analyze and interpret your data (i.e. bad data won’t lead to good results), you have to judge whether a signal looks adequate or not. Please see below:
Top left: bad optode contact; there is hair trapped under the optode. You can try to resolve this by placing a headband over the optode to keep it closer to the skin or make the strap tighter. Optode 1 and also a little bit 5 and 3 in this example shows the effect of hair. The sharp change towards the end of the x-axis shows an adjustment where the hair was moved out of the way.
Makeup needs to be removed because it reflects a lot of light and will distort the signal.
Top right: Saturated signals mean the signal is larger than the machine can handle and this signal cannot be recovered. We want a maximum of 3,500 mV. Therefore, we need to make sure we prevent this issue. This can be done prior to the experiment by reducing the gain or the light intensity. If this issue remains undetected until after the experiment, the optode where there is saturation will need to be eliminated from the analysis.
Lower left: spike from motion artifact. Can either eliminate (preferred) or correct for it. Try to prevent by tightening the strap without tension but less possibility to move.
Lower right: good signal.
To exclude a whole optode:
Double-click on optode 8, then right-click → evaluate → reject
Now the signal of the optode is no longer shown.
This does not delete the data, it only excludes the data from the analysis.
If you want to undo this step, you go right-click → evaluate → accept.
Define blocks
We start by zooming in on the task we like to investigate.
On the bottom pane, click “Display settings” (alternatively, right-click into the graph and click “Display settings” there).
Go to Time tab and type in the specific time window you would like to see on the screen.
ADD DETAILS AND SCREENSHOTS
Next, click “Define blocks” on the bottom pane. On the left half of the window, you define where you want your block to start, on the right, you define when it ends. Check the box for “Apply the following label” and name your blocks. Then click “Run - Step 1”, followed by “Run - Step 2”. If you have different blocks, you can apply them one at a time.
Here’s the sigh task as an example:
189 = Sigh (protocol start)
188 = Sigh (protocol end)
187 = Sigh (task start)
186 = Sigh (task end)
There are 4 sigh trials. The order is:
189 (start of task)
Sighs 1-3: 187 (Sign signal start) → 186 (Signal signal end)
188 (task end)
What we want is:
Baseline (189 → 187)
Tracking oxygenation AFTER sighs (sigh end until next sigh onset)
187 → 186 (recovery periods after sighs 1-3)
186 → 188 (recovery period after last sigh until end of task)
Automation
Calculate oxygenation
Data viewing options
On the bottom pane, you can toggle between “Graph type”, “Group type” and “Data type”.
Brain view
