How to deal with TMS artifact in BESA Research
| Module information | |
| Modules | BESA Research Standard or higher |
| Version | 6.1 or higher |
Contents
Before you start
This article is created assuming sufficient knowledge about BESA Research, ERP analysis, and source analysis. If you have any doubts it is strongly advised to follow BESA Tutorial chapters indicated in this article or consult with BESA support team.
Make sure that your EEG recording system is suitable for recording during TMS stimulation. That means the maximum input range is high enough for the amplifier not to get saturated (the incoming signal induced by TMS artifact will not be higher than the input range). Most of the modern TMS-EEG systems have the automatic TMS pulse artifact suppression system that prevents EEG amplifier from recording the signal during the stimulation. BESA strongly advises using such option since it makes the analysis much easier and assures that the amplifier is not saturated (contact Brainbox for details). Please note that neither the BESA or any other software cannot "fix" data if the amplifier gets saturated.
During TMS stimulation at least three types of artifacts can be differentiated:
TMS pulse artifact
This artifact is induced directly in EEG electrodes and wires by the induced magnetic field due to Maxwell’s second law. It is a high amplitude, short-latency artifact. Because the best way to handle this artifact is to suppress it during the recording we will not focus on it here.
TMS decay artifact (muscle)
Immediately after the TMS stimulation head muscle response is invoked (also due to Maxwell's second law). It has a large amplitude and it can last long enough to overlay with a cortical response. It has a characteristic shape resembling free induction decay curve. This artifact is of major importance and it will be shown below how to reduce its influence.
Similar to any other strong sensory stimulation, the eye blinks can occur as the derivate response. This type of artifact can be easily solved in BESA Research using traditional artifact reduction approaches. Please check BESA Tutorial chapter 2A for basic or 10 for advanced approach.
Example
The presented data was obtained by Brainbox. It was 30 channel EEG recording of a male adult. During the experiment, TMS stimulation was performed with 120% rMT over the left motor cortex.
Pipeline
In the scheme below the TMS-EEG data handling pipeline is shown. Every part of the analysis is color-coded. The yellow part indicated the preprocessing part that is common for any ERP experiment and is described in more detail in section Preprocessing and averaging. The blue part describes how to prepare the TMS decay artifact topographies and how to send them to the source analysis. The last step indicated by a purple color - Source Analysis - focus on the utility of different artifact topographies (blink, and TMS decay) and performing source localization of underlying ERP activity.
Preprocessing and averaging
After opening the file in BESA Research you should proceed with the data as you used to. For example start with bad channel selection and review data for any parts that you would like to remove from further analysis due to i.e. strong movement. Then perform the blink artifact correction either using an automatic or manual approach, as described in BESA Tutorial (chapter 2A for basic or 10 for advanced approach). When data is ready for the averaging please press ERP button in the ribbon. A new dialog box will open on which you should define the paradigm (assign codes and create conditions) as in the classical ERP experiment (check BESA Tutorial 2B for details). Then switch to the tab Epoch. Now set the Averaging Epoch, Baseline Definition and Artifact Rejection interval to match your experiment. As usual please make sure that you have enough signal in baseline and events are not overlapping. Then in Stimulus Artifact section set the interval to the values which will ensure that the TMS artifact will be not the reason for rejection. In the given example the Stimulus Artifact is starting at -10ms and ending 50ms after event trigger. Please make sure you pressed Assignto All or Assign to Selected to make use of the mentioned seetings.
Now switch to the Artifact tab and press Start Scan button. This tool is described in more details in Besa Tutorial chappter 2C. Please adjust the acceptance threshold to remove all not-TMS related artifacts adn make sure that there is enough epochs accepted for further analysis. In the given example there is 83 events, which should be more than enough. Now in the Average tab press the Average button.
Before the averaging the following warning is presented:
The warning means that the artifact correction (for eyeblink) is currently turned on. Please press Yes button to disable artifact correction for averaging process. The blink artifact correction can be performed later for the averaged file or during the source analysis. Here we will apply blink correction during source analysis to investigate its influence on source waveforms and source localization. Note that if we perform averaging with artifact correction on this will not possible since the data will be already treated on a single trial level.
TMS decay artifact reduction
When average data is prepared we need to start the source analysis window. Please highlight the signal of interest and press the right mouse button on the yellow tinted area. Now select Source Analysis . In the new window, you can trim up the window and set up the filters. Check BESA Tutorial chapter 4C for details. For now, we leave this window open in the background. Please back to the main window of BESA Research (and do not close the Source Analysis window!). Make sure that all filters are off (in the status bar there should be text Filters off). If not please press EdF button and disable all filters. Now press ICA button, and select Current Screen to start ICA decomposition. After the computation is finished you should see data transformed into independent components. while keeping CTRL button pressed select all components that might be related to TMS decay artifact. Note that it is not a problem if more components than needed are selected. In the presented example three components were selected: ICA3, ICA4, and ICA8. While ICA3 and ICA4 are clearly related to the TMS decay artifact, the component ICA8 is questionable. For example, it might be either TMS refractory artifact, some noise or neural response. We can verify that later in Source Analysis.
Note that selected components are just example, in your case, they will look different and will have different labels. Also, the number of components to select might be different
While selected components are highlighted we can send them to the source analysis window. To do so click right mouse button on one of the highlighted labels and select Send Topography To Source Analysis. The source analysis window will be automatically populated with these independent components and bring to front.
Source Analysis
Now the Source analysis with TMS-decay related Independent Components (IC) along the EEG waveforms should be loaded to the Source Analysis module.
Let first add the previously created blink artifact related topography. To do so go to File menu and select Open Solution... (or Append solution... if you already added any source and would like to keep it). Then in a new dialog window please select Artifact Topographies (*.atf,*.art,*.coe) in the Files of type section and select the file that has exactly the same name as the data file but *.atf extension. Press Open to Add this topography to Source Analysis. Now press right mouse button anywwhere in the TMS-decay related ICs area and select Add All ICA Component(s) to Solution. By doing so, BESA autmoaticaly computes the sources of the TMS-decay related IC and adds them to the solution. Press the Residual button to show EEG signal that is not explained by the model (is not removed by artifact corection). You can toggle Data button on and off to compare Residuals with orginal data. It is better however to use residuals for brain source fitting procedure.
By investigating source waveform it can be clearly stated that in the given example the fourth, pink waveform (third selected IC - the questionable TMS refractory artifact -ICA8 mentioned earlier) do not underlay almost any activity in the ERP. In such situation it is good idea to disable it by pressing switching On button to Off nearby the fourth source waveform.
Now have a closer look again on the remaining three source waveforms. The first one - the eyeblink is rather of minor importance here, but since we know that the blinking may occur (and occurred) in the given example we would like to keep this source. The next two source waveforms came from IC indicated as TMS-decay related artifacts. Let's have a look at their sources: both - blue and green sources - are really close to each other and have the same orientation. Importantly they are located around left hemisphere, nearby central sulcus - see Example. Moreover, we can see that the blue source waveform starts much later (c.a. 50ms after stimulus) while the green one starts just after the stimulus. because of this and the fact that the sources are really nearby, it is advisable that the blue source should be disabled. Now we have two artifact related sources - the red one responsible by blink, the green one by TMS-decay artifact. Check out the residuals of EEG - they are resembling classical ERP now!
Now we can fit sources that will explain brain activity. First, the fitting interval should be selected. It is possible to switch the display from imported ICA to PCA decomposition of the residuals by pressing the ICA button (it will be switched to PCA). For the given example I will select the rising part of residual ERP (note that PCA automatically adjusts to selection). Good fitting interval is selected when most of the signal can be explained by one PCA component
Finally, the sources have to be added and fitted. To add the source double left click anywhere in right window area (where heads are drawn). Because it was strong activation (120% rMT) it is possible that there might be cross-talk to the second hemisphere. Therefore the second source should be added. In addition, the symmetry constraint between the first and second source should be set. To do so, while the second source is selected,select in Loc: symetric to from drop-down list. Automatically the second source will be symmetric to the first one after fitting. Now press the All fit button to indicate all cortical source to be fitted together at the same time. Note that for the artifact related source fitting is not possible, therefore this button only switch for fittin two sources that we just added. Press the Start fit button to perform fitting.
The final solution consists of two sources, both located in the precentral cortex, bilaterally. The left source is stronger and starts slightly prior (50ms vs 53ms) to the right source which is plausible concerning the given example.
