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## a commented walkthrough...

In this section, a set of raw data files, that is included in the 'emegsTestData'-folder, will be analysed step by step from rawdata to three dimensional plotting. It is meant to illustrate how the different processing steps are implemented in EMEGS, which programs they require, and how these programs can be used.

To follow along on your own computer, extract the file 'sample.zip' in the folder \emegs\ emegs2dTestData\ EEG\ BinData\ RawData to a location of you choice. It will extract to a 129 channel EGI datafile (*.RAW) and its corresponding impedance- (*.IMP) , zero- (*.ZERO),gain- (*.GAIN) and history-file (*.HIST). This is a dataset collected with a fast picture presentation paradigm (Rapid Serial Visual Presentation), with alternating emotional (pleasant) and neutral pictures. Each picture is presented for 333ms without interstimulus itervall. It is a continuous stream of pictures. The baseline correction in this special is calculated over the entire extracted intervall. With other more standard designs, you will simple have an interstimulus intervall before the trigger, that you can use as baseline.

File types
EGI Format: EGI data files have to be exported using the netstation software, so you end up with a set of 5 files per run (*.RAW,*.HIST,*.ZERO,*.GAIN,*.IMP). The RAW-file is then transformed (pointwise sorting is tranformed to channelwise sorting) into a TAW-file that contains the same data. This file in turn is used for filtering, resulting in a modified TAW-file, for instance *.fl40.TAW for a 40Hz lowpass filtering. During segmentation in 'TransNetGeoHist' the trials are saved in an *.E1 file, containing all trials including artifacts and broken channels. A *.CON file is generated containing the trigger information for each trial. Statistical parameters used for artifact correction and calculated in 'CalcAutoEditMat' are saved in an *.AEM and an *.AEM.AR-file (AEM signifies Auto-Edit-Matrix, AR stands for average reference), flat or corrupted sensors are listed in a *.Xest-file (with X replaced by your number of channels). Editing the data using 'EditAEM' creates two new files: a *.WE-file and a *.TVM-file, both containing good and bad trials and channels. During averaging using 'EmegsAVG', bad sensors in the trials from the *.E1-files are interpolated and trials are averaged based an the *.WE-files, your sensor configuration file (*.ecfg), and the *.CON file, resulting in a set of 3 files for each condition: an *.APPx-file, containing only good and approximated trials of the condition x, a corresponding *.ix file, listing the indices of the good trials for this condition, and an *.atx file, containing the averaged waveform.
Neuroscan Format: Neuroscan *.cnt data files have to be filtered using 'FiltNeuroscanFiles', resulting in a modified cnt-file, for instance *.f.cnt. During segmentation in 'Neuroscan2Egis' the trials are saved in an *.ses file, containing all trials including artifacts and broken channels. A *.CON file is generated containing the trigger information for each trial. Statistical parameters used for artifact correction and calculated in 'CalcAutoEditMat' are saved in an *.AEM and an *.AEM.AR-file (AEM signifies Auto-Edit-Matrix, AR stands for average reference), flat or corrupted sensors are listed in a *.Xest-file (with X replaced by your number of channels). Editing the data using 'EditAEM' creates two new files: a *.WE-file and a *.TVM-file, both containing good and bad trials and channels. During averaging using 'EmegsAVG', bad sensors in the trials from the *.ses-files are interpolated and trials are averaged based an the *.WE-files, your sensor configuration file (*.ecfg), and the *.CON file, resulting in a set of 3 files for each condition: an *.APPx-file, containing only good and approximated trials of the condition x, a corresponding *.ix file, listing the indices of the good trials for this condition, and an *.atx file, containing the averaged waveform.
BTI Format: BTI data files, at the present stage, have to be noisecorrected, cardiaccorrected and filtered externally. EMEGS scripts for this are not yet available.
During segmentation in 'TransMsiContSess', the trials are saved in a *.ses file. A *.CON file is generated containing the trigger information for each trial. Statistical parameters used for artifact correction and calculated in 'CalcAutoEditMEGMat' are saved in an *.AEM -file (AEM signifies Auto-Edit-Matrix). Editing the data using 'EditAEM' creates the *.WE-file, containing good and bad trials and channels. During averaging using 'EmegsAVG', bad sensors in the trials from the *.ses-files are interpolated and trials are averaged based an the *.WE-files, your sensor configuration file (*.ecfg), and the *.CON file, resulting in a set of 3 files for each condition: an *.APPx-file, containing only good and approximated trials of the condition x, a corresponding *.ix file, listing the indices of the good trials for this condition, and an *.atx file, containing the averaged waveform.

Segmentation and filtering

Start Matlab, make sure to include all emegs-folders in your Matlab path, type 'emegs' and hit return. The emegs-launchpad will open, from which you start the preprocessing module. A yellow window appears, titled 'preprocessing menu'. Push the 'open file(s)'-button and select the extracted file 'sample.RAW'. Then choose cancel to stop the input (EMEGS is waiting for you to choose more RAW files to process in batch mode). EMEGS read the file header and displays the number of channels in the RAW-file, the sampling rate, the file format and the number of chosen files at the top of the PrePro-window. Activate a low-pass-filter by clicking the radiobutton above the lowpass box. You are prompted with a filter-configuration window. The default filter is fine for this example, so just click 'apply' to accept the filter settings. The window will close and the settings are stored. Next, choose the time window for the trials that you wish to extract from the continuous data. Enter '83' in the 'PreTrig'-editbox and '84' in the 'PostTrig'-editbox, meaning that with the current sampling rate of 250 Hz (4ms per point), you will extract 332ms (83 X 4ms) before and 336ms (84 X 4ms) after each trigger. Leaving all the other options as they are, you will use the entire extracted intervall for artifact correction (the values '83' pretrigger and '84' posttrigger are automatically copied to the artifact detection section), you will extract trials for all found trigger values and calculate statistical parameters for artifact detection with and without applying an average reference. Hit the 'Run'-button, and follow the output in the command window. If everything works fine, you will end up with a filtered and non-filtered transformed raw-data file (sample.TAW, sample.fl40.TAW), a condition file (sample.fl40.E1.CON), five editing files (sample.fl40.E1.AEM, sample.fl40.E1.AEM.AR ,sample.fl40.E1.AEM.AWE, sample.fl40.E1.128est, sample.fl40.E1.129est) and a segmented data file (sample.fl40.E1).

Data editing
Click the 'Close / EditAEM'-button or start the editing console using the emegs-launchpad. Enter a '2' in the 'NTrials Factor' (because there are 2 conditions/trigger values in the data file) and select the 'Fast Auto I'-button, to launch the automatized editing procedure. Choose the 'sample.fl40.AEM.AR' file and press cancel to stop the input process. For each channel, the MaximumStd for all the trials are displayed as histogram-plots as well as a display of the sum of diff. of the MaximumStd thresholds. After that, the same is repeated for the absolute values. Finally, based on the identified good and bad sensors for each trial, a index is calculated for each trial, describing the quality which missing sensors can be approximated with by remaining ones (using spherical spline interpolation). This index is plotted as a histogram, and you are asked to select a minimal quality of approximation that you will accept as good. To do this, just click in the displayed histogram at the desired position. Using this threshold, the five worst trials are displayed as a green(good) and red(bad) sensor plot. If you feel, that this corresponds the quality of your data, hit return, and the threshold will be saved to disk (creating the files: 'sample.fl40.E1.AR.WE', 'sample.fl40.E1.TVM'). Choose 'Close & EmegsAVG' from the menu on the upper right to close EditAEM and start the averaging console.

Averaging

On the average console, set the 'Max std. baseline [Points]'-edit to '167' (corresponding your baseline intervall set in 'PrePro') and hit return. 'Min std. baseline [Points]' will automatically be set to '1' (alternativly, in this special case, you could click the 'whole intevall' button to select all points for baseline correction) Choose 'Open Files' and select the file 'sample.fl40.E1' of the sample data. Click 'cancel' to stop the input process. EmegsAVG will list the path of your selected file in the message window, then look for and list the path of its corresponding condition file, it's editing file and the current sensor condiguration file. If all files are found, and the listing is done, click 'Run Average' on the EmegsAVG-Menu. The averaging of the trials will start and displayed in the upper left window. Using all the other default options, EmegsAVG will average every condition in the condition file, interpolate missing sensors, and create for each condition three files: an averaged waveform (*.at), an index file (*.i) listing the indices of the trials of the condition that were used for the averaging (the 'good' trials), and a file containing those (interpolated) trials (*.app). In the sample data, the trigger values are '1' and '3', so the following files will be created: 'sample.fl40.E1.at1.ar', 'sample.fl40.E1.at3.ar' , 'sample.fl40.E1.app1' , 'sample.fl40.E1.app3' , 'sample.fl40.E1.i1' and 'sample.fl40.E1.i5'.

2d visualization

Choose 'Close All & Emegs2d' from the bottom right of the EmegsAVG-console to close EmegsAVG and start Emegs2d to display the average waveforms. Click 'Open Dataset' on the Emegs2d-console and select the file 'sample.fl40.E1.at5.ar'. This averaged waveform will be displayed in red in the channel window. It's sampling rate, number of points and number of channels are displayed in the Emegs2d-console. The name of the file is listed on bottom left of the channel window. Enter '84' in the trigger point box and click 'total intervall' in the Emegs2d-baseline-section, to automatically enter '-332' and '336' ms in the 'Min. baseline' and 'Max. baseline' boxes and check the 'calc baseline'-radio. With a standard design using an interstimulus pretrigger 100ms baseline intervall, you would first enter your trigger point ('26') in the trigger point box, then enter '-100' in the 'Min. baseline' -box and finally check the 'calc baseline'-radiobutton. Click 'adust' in the amplitude section of the console to adjust the vertical scaling.

To compare the waveforms with the other condition in the file, select Dataset Slot 2 from 'Actual Dataset'-dropdown-menu and click 'Open Dataset' to load the other condition in slot 2 (a maximum of 6 waveforms can be displayed at a time). Select the file 'sample.fl40.E1.at1.ar', and this waveform will be displayed in blue, using the current baseline and trigger point settings. Note that the polarity of this dataset is inverted due to the measuring setup that was used. Therefore, negative is up and positive down. You can push the 'Polarity'-button on the Emegs2d-console to switch to negative up mode or alternatively mulitply the dataset by -1, using the menuitem \Calculate\Factor.

To get a general impression of the data, click the GP/RMS-button on the bottom right of the Emegs2d-console to display the global power. To zoom in on a special sensor, click the 'mouse'-button below the 'Zoom Sensor'-dropdown-menu on the console and then click slightly below the waveforms of a channel of your choice in the channel window.
Lets calculate the difference between the two conditions (emotional and neutral pictures), selecting the 'Calculate'-menu on the top of the Emegs2d-console and choosing the 'Difference' menu item.
A window will open to let you choose which difference you wish to calculate and into which dataslot you wish to put the result. Click the topmost button on the left column, the second topmost button in the middle column, and the third topmost button on the right column, to calculate dataset 1 - dataset 2 = dataset 3.

3d visualization

Click the 'Emegs3d' button on the Emegs2d-console to open the 3d console. Make sure the difference we just calculated is selected in the 'Actual dataset'-dropdown-menu on the bottom right of the 3d console. Then choose 'Back' from the 'Head View'-dropdown on the upper middle of the 3d console, and select 'Scalp' from the 'Scalp, Lap, Cort'-dropdown on the top left ot the 3d console. This will create a 3d plot of the difference wave over the time window from 0 to 336ms, seen from the back, with blue hues signifying negative amplitudes and red hues for positive differences.