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| <<HTML(<style>.backtick {font-size: 16px;}</style>)>><<HTML(<style>abbr {font-weight: bold;}</style>)>> <<HTML(<style>em strong {font-weight: normal; font-style: normal; padding: 2px; border-radius: 5px; background-color: #EEE; color: #111;}</style>)>> = MEG corticomuscular coherence = ''Authors: Raymundo Cassani '' This is a little text that serves as an introduction of the reason of being for this tutorial. Hopefully it will have 2 or 3 relevant links to information outside or to other tutorials. |
<<HTML(<style>tt {font-size: 16px;}</style>)>><<HTML(<style>abbr {font-weight: bold;}</style>)>> <<HTML(<style>em strong {font-weight: normal; font-style: normal; padding: 2px; border-radius: 5px; background-color: #EEE; color: #111;}</style>)>> = Corticomuscular coherence (CTF MEG) = '''[TUTORIAL UNDER DEVELOPMENT: NOT READY FOR PUBLIC USE] ''' ''Authors: Raymundo Cassani, Francois Tadel & [[https://www.neurospeed-bailletlab.org/sylvain-baillet|Sylvain Baillet]].'' [[https://en.wikipedia.org/wiki/Corticomuscular_coherence|Corticomuscular coherence]] measures the degree of similarity between electrophysiological signals (MEG, EEG, ECoG sensor traces or source time series, especially over the contralateral motor cortex) and the EMG signals recorded from muscle activity during voluntary movements. Cortical-muscular signals similarities are conceived as due mainly to the descending communication along corticospinal pathways between primary motor cortex (M1) and the muscles attached to the moving limb(s). For consistency purposes, the present tutorial replicates, with Brainstorm tools, the processing pipeline "[[https://www.fieldtriptoolbox.org/tutorial/coherence/|Analysis of corticomuscular coherence]]" of the FieldTrip toolbox. |
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| == Dataset description == The dataset is identical to that of the FieldTrip tutorial: [[https://www.fieldtriptoolbox.org/tutorial/coherence/|Analysis of corticomuscular coherence]]: * One participant, * MEG recordings: 151-channel CTF MEG system, * Bipolar EMG recordings: from left and right extensor carpi radialis longus muscles, * EOG recordings: used for detection and attenuation of ocular artifacts, * MRI: 1.5T Siemens system, * Task: The participant lifted their hand and exerted a constant force against a lever for about 10 seconds. The force was monitored by strain gauges on the lever. The participant performed two blocks of 25 trials using either their left or right hand. * Here we describe relevant Brainstorm tools via the analysis of the left-wrist trials. We encourage the reader to practice further by replicating the same pipeline using right-wrist trials! Corticomuscular coherence: * [[Tutorials/Connectivity#Coherence|Coherence]] measures the linear relationship between two signals in the frequency domain. * Previous studies ([[https://dx.doi.org/10.1113/jphysiol.1995.sp021104|Conway et al., 1995]], [[https://doi.org/10.1523/JNEUROSCI.20-23-08838.2000|Kilner et al., 2000]]) have reported corticomuscular coherence effects in the 15–30 Hz range during maintained voluntary contractions. * TODO: IMAGE OF EXPERIMENT, SIGNALS and COHERENCE |
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| Example of performing citations in text, and <<latex(\LaTeX)>>. The '''imaginary coherence''' ([[https://doi.org/10.1016/j.clinph.2004.04.029|Nolte et al., 2004]]), commonly found as: <<latex($IC_{xy}(f)$)>>. === A title in size 3 === ==== A title in size 4 ==== |
'''Pre-requisites''' * Please make sure you have completed the [[Tutorials|get-started tutorials]], prior to going through the present tutorial. * Have a working copy of Brainstorm installed on your computer. * [[Tutorials/SegCAT12#Install_CAT12|Install the CAT12]] Brainstorm plugin, to perform MRI segmentation from the Brainstorm dashboard. '''Download the dataset''' * Download `SubjectCMC.zip` from the FieldTrip FTP server:<<BR>> ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/SubjectCMC.zip * Unzip the downloaded archive file in a folder outside the Brainstorm database or app folders (for instance, directly on your desktop). '''Brainstorm''' * Launch Brainstorm (via the Matlab command line or the Matlab-free stand-alone version of Brainstorm). * Select from the menu '''File > Create new protocol'''. Name the new protocol `TutorialCMC` and select the options:<<BR>> No, use individual anatomy, <<BR>> No, use one channel file per acquisition run. == Importing anatomy == * Right-click on the newly created TutorialCMC node > '''New subject > Subject01'''.<<BR>>Keep the default options defined for the study (aka "protocol" in Brainstorm's vernacular). * Switch to the Anatomy view of the protocol (<<Icon(iconSubjectDB.gif)>>). * Right-click on the Subject01 > '''Import MRI''': * Select the file format: '''All MRI files (subject space)''' * Select the file: `SubjectCMC/SubjectCMC.mri` * This step will launch Brainstorm's MRI viewer, where coronal, sagittal and axial cross-sections of the MRI volume are displayed. note that [[CoordinateSystems|three anatomical fiducials]] (left and right pre-auricular points (LPA and RPA), and nasion (NAS)) are automatically identified. These fiducials are located near the left/right ears and just above the nose, respectively. Click on '''Save'''. <<BR>><<BR>> {{attachment:mri_viewer.gif||height="295",width="344"}} * In all typical Brainstorm workflows from this tutorial handbook, we recommend processing the MRI volume at this stage, before importing the functional (MEG/EEG) data. However, we will proceed differently, for consistency with the original FieldTrip pipeline, and readily obtain sensor-level coherence results. We will proceed with MRI segmentation below, before performing source-level analyses. * We still need to verify the proper geometric registration (alignment) of MRI with MEG. We will therefore now extract the scalp surface from the MRI volume. * Right-click on the MRI (<<Icon(iconMri.gif)>>) > MRI segmentation > '''Generate head surface'''. <<BR>><<BR>> {{attachment:head_process.gif}} * Double-click on the newly created surface to display the scalp in 3-D.<<BR>><<BR>> {{attachment:head_display.gif}} == MEG and EMG recordings == === Link the recordings === * Switch now to the '''Functional data '''view of your database contents (<<Icon(iconStudyDBSubj.gif)>>). * Right-click on Subject01 > '''Review raw file''': * Select the appropriate MEG file format: '''MEG/EEG: CTF(*.ds; *.meg4; *.res4)''' * Select the data file: `SubjectCMC.ds` * A new folder '''SubjectCMC '''is created in the Brainstorm database explorer. Note the "RAW" tag over the icon of the folder (<<Icon(iconRawFolderClose.gif)>>), indicating that the MEG files contain unprocessed, continuous data. This folder includes: * '''CTF channels (191)''' is a file with all channel information, including channel types (MEG, EMG, etc.), names, 3-D locations, etc. The total number of channels available (MEG, EMG, EOG etc.) is indicated between parentheses. * '''Link to raw file '''is a link to the original data file. Brainstorm reads all the relevant metadata from the original dataset and saves them into this symbolic node of the data tree (e.g., sampling rate, number of time samples, event markers). As seen elsewhere in the tutorial handbook, Brainstorm does not create copies by default of (potentially large) unprocessed data files ([[Tutorials/ChannelFile#Review_vs_Import|more information]]). . {{attachment:review_raw.png}} <<BR>> === MEG-MRI coregistration === * This registration step is to align the MEG coordinate system with the participant's anatomy from MRI ([[https://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile#Automatic_registration|more info]]). Here we will use only the three anatomical landmarks stored in the MRI volume and specific at the moment of MEG data collection. From the [[https://www.fieldtriptoolbox.org/tutorial/coherence/|FieldTrip tutorial]]:<<BR>>''"To measure the head position with respect to the sensors, three coils were placed at anatomical landmarks of the head (nasion, left and right ear canal). [...] During the MRI scan, ear molds containing small containers filled with vitamin E marked the same landmarks. This allows us, together with the anatomical landmarks, to align source estimates of the MEG with the MRI." '' * To visually appreciate the correctness of the registration, right-click on the '''CTF channels''' node > '''MRI registration > Check'''. This opens a 3-D figure showing the inner surface of the MEG helmet (in yellow), the head surface, the fiducial points and the axes of the [[CoordinateSystems#Subject_Coordinate_System_.28SCS_.2F_CTF.29|subject coordinate system (SCS)]].<<BR>><<BR>> {{attachment:fig_registration.gif||height="204",width="209"}} === Reviewing === * Right-click on the Link to raw file > '''Switch epoched/continuous''' to convert how the data i stored in the file to a continuous reviewing format, a technical detail proper to CTF file formatting. * Right-click on the Link to raw file > '''MEG > Display time series''' (or double-click on its icon). This will display data time series and enable the Time panel and the Record tab in the main Brainstorm window (see specific features in "[[Tutorials/ReviewRaw|explore data time series]]"). * Right-click on the Link to raw file > '''EMG > Display time series'''. . [[https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence?action=AttachFile&do=get&target=timeseries_meg_emg.png|{{attachment:timeseries_meg_emg.png|https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence?action=AttachFile&do=get&target=timeseries_meg_emg.png}}]] === Event markers === The colored dots at the top of the figure, above the data time series, indicate [[Tutorials/EventMarkers|event markers]] (or triggers) saved along with MEG data. The actual onsets of the left- and right-wrist trials are not displayed yet: they are saved in an auxiliary channel of the raw data named ''Stim''. To add these markers to the display, follow this procedure: * With the time series figure still open, go to the Record tab and select '''File > Read events from channel'''. Event channels = `Stim`, select Value, Reject events shorter than 12 samples. Click '''Run'''. . . {{attachment:read_evnt_ch.gif}} * The rejection of short events is nececessary in this dataset, because transitions between values in the Stim channel may span over several time samples. Otherwise, and for example, an event U1 would be created at 121.76s because the transition from the event U1025 back to zero features two unwanted values at the end of the event. The rejection criteria is set to 12 time samples (10ms), because the duration of all the relevant triggers is longer than 15ms. This value is proper to each dataset, so make sure you verify trigger detections from your own dataset.<<BR>><<BR>> {{attachment:triggers_min_duration.gif}} * New event markers are created and now shown in the Events section of the tab, along with previous event categories. In this tutorial, we will only use events '''U1''' through '''U25''', which correspond to the beginning of each of the 25 left-wrist trials of 10 seconds. Following FieldTrip's tutorial, let's reject trial #7, event '''U7'''. * Delete all unused events: Select all the events '''except''' '''U1-U6''' and '''U8-25''' (Ctrl+click / Shift+click), then menu '''Events > Delete group''' (or press the Delete key). * Merge events: Select all the event groups, then select from the menu '''Events > ''' Merge group > '''"Left"'''. A new event category called "Left" now indicate the onsets of 24 trials of left-wrist movements.<<BR>><<BR>> {{attachment:left_24.gif}} == Pre-processing == {{{#!wiki note In this tutorial, we will analyze only the '''Left''' trials (left-wrist extensions). In the following sections, we will process only the first '''330 s''' of the original recordings, where the left-wrist trials were performed. }}} === Power line artifacts === * In the Process1 box: Drag and drop the '''Link to raw file'''. * Run process '''Frequency > Power spectrum density (Welch)''':<<BR>> * '''Time window''': `0-330 s` * '''Window length''':''' '''`10 s` * '''Overlap''': `50%` * '''Sensor types''': `MEG, EMG` . {{attachment:pro_psd.png||width="60%"}} * Double-click on the new PSD file to visualize the power spectrum density of the data.<<BR>> . {{attachment:psd_before_notch.png||width="70%"}} * The PSD plot shows two groups of sensors: EMG (highlighted in red above) and the MEG spectra below (black lines). Peaks at 50Hz and harmonics (100, 150, 200Hz and above) indicate the European power line frequency and are clearly visible. We will now use notch filters to attenuate power line contaminants at 50, 100 and 150 Hz. * In the Process1 box: Drag and drop the '''Raw | clean''' node. * Run the process '''Pre-processing > Notch filter''' with: <<BR>> * Check '''Process the entire file at once''' * '''Sensor types''': `MEG, EMG` * '''Frequencies to remove (Hz)''': `50, 100, 150` . {{attachment:pro_notch.png||width="60%"}} * In case you get a memory error message:<<BR>>These MEG recordings have been saved before applying the CTF 3rd-order gradient compensation, for noise reduction. The compensation weights are therefore applied on the fly when Brainstorm reads data from the file. However, this requires reading all the channels at once. By default, the frequency filter are optimized to process channel data sequentially, which is incompatible with applying the CTF compensation on the fly. This setting can be overridden with the option '''Process the entire file at once''', which requires loading the entire file in memory at once, which may crash teh process depending on your computing resources (typically if your computer's RAM < 8GB). If this happens: run the process '''Artifacts > Apply SSP & CTF compensation''' on the file first, then rune the notch filter process without the option "Process the entire file at once" ([[https://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag#Existing_SSP_and_pre-processing|more information]]). * A new folder named '''SubjectCMC_clean_notch''' is created. Obtain the PSD of these data to appreciate the effect of the notch filters. As above, please remember to indicate a '''Time window''' restricted from 0 to 330 s in the options of the PSD process.<<BR>><<BR>> . {{attachment:psd_after_notch.png||width="70%"}} === EMG: Filter and rectify === Two typical pre-processing steps for EMG consist in high-pass filtering and rectifying. * In the Process1 box: drag and drop the '''Raw | notch(50Hz 100Hz 150Hz)''' node. * Add the process '''Pre-process > Band-pass filter''' * '''Sensor types''' = `EMG` * '''Lower cutoff frequency''' = `10 Hz` * '''Upper cutoff frequency''' = `0 Hz` * Add the process '''Pre-process > Absolute values''' * '''Sensor types''' = `EMG` * Run the pipeline . {{attachment:emg_processing.png||width="100%"}} * Delete intermediate files that won't be needed anymore: Select folders '''SubjectCMC_notch''' and '''SubjectCMC_notch_high''',''' '''then press the Delete key (or right-click > File > Delete).<<BR>><<BR>> {{attachment:db_filters.gif}} === MEG: Blink SSP and bad segments === Stereotypical artifacts such eye blinks and heartbeats can be identified from their respective characteristic spatial distributions. Their contamination of MEG signals can then be attenuated specifically using Signal-Space Projections (SSPs). For more details, consult the specific tutorial sections about the [[Tutorials/ArtifactsDetect|detection]] and [[Tutorials/ArtifactsSsp|removal of artifacts with SSP]]. The present tutorial dataset features an EOG channel but no ECG. We will therefore only remove artifacts caused by eye blinks. ==== Blink correction with SSP ==== * Right-click on the pre-processed file > '''MEG > Display time series''' and '''EOG > Display time series'''. * In the Record tab: '''Artifacts > Detect eye blinks''', and use the parameters: * '''Channel name'''= `EOG` * '''Time window''' = `0 - 330 s` * '''Event name''' = `blink` . {{attachment:detect_blink_process.png||width="60%"}} * Three categories of blink events are created. Review the traces of the EOG channels around a few of these events to ascertain they are related to eye blinks. In the present case, we note that the '''blink''' group contains genuine eye blinks, and that groups blink2 and blink3 capture saccades. . {{attachment:blinks.png||width="70%"}} * To [[Tutorials/ArtifactsSsp|remove blink artifacts with SSP]], go to '''Artifacts > SSP: Eye blinks''': * '''Event name'''=`blink` * '''Sensors'''=`MEG` . {{attachment:ssp_blink_process.png||width="60%"}} * Display the time series and topographies of the first two SSP components identified. In the present case, only the first SSP component can be clearly related to blinks: the percentage of variance explained is substantially higher than the other compoments', the spatial topography of the component is also typical of eye blinks, and the corresponding time series is similar to the EOG signal around blinks. Select only '''component #1''' for removal. . {{attachment:ssp_blink.png||width="100%"}} * Close all visualization figures by clicking on the large '''×''' at the top-right of the main Brainstorm window. ==== Detection of "bad" data segments ==== Here we will use the [[Tutorials/BadSegments#Automatic_detection|automatic detection of artifacts]] to identify data segments contaminated by e.g., large eye and head movements, or muscle contractions. * Display the MEG and EOG time series. In the '''Record''' tab, select '''Artifacts > Detect other artifacts''' and enter the following parameters: * '''Time window''' = `0 - 330 s` * '''Sensor types'''=`MEG` * '''Sensitivity'''=`3` * Check both frequency bands '''1-7 Hz''' and '''40-240 Hz''' . {{attachment:detect_other.png||width="60%"}} * You are encouraged to review all the segments marked using this procedure. With the present data, all marked segments do contain clear artifacts. * Select the '''1-7Hz''' and '''40-240Hz''' event groups and select '''Events > Mark group as bad'''. Alternatively, you can add the prefix '''bad_''' to the event names. Brainstorm will automatically discard these data segments from further processing. . {{attachment:bad_other.png||width="50%"}} * Close all visualization windows and reply "Yes" to the save the modifications query. == Epoching == We are now finished with the pre-processing of EMG and MEG recordings. We will now extract and import specific data segments of interest into the Brainstorm database for further derivations. As mentioned previously, we will focus on the '''Left''' category of events (left-wrist movements). For consistency with the [[https://www.fieldtriptoolbox.org/tutorial/coherence/|FieldTrip tutorial]], we will analyze 8s of recordings following each movement (from the original 10s around each trial), and split them in 1-s epochs. We will also remove the DC offset from each MEG channel. * In the Process1 box: Drag-and-drop the pre-processed file. * Select the process '''Import > Import recordings > Import MEG/EEG: Events''': * '''Subject name''' = `Subject01` * '''Folder name''' = empty * '''Event names''' = `Left` * '''Time window''' = `0 - 330 s` * '''Epoch time''' = `0 - 8000 ms` * '''Split recordings in time blocks''' = `1 s` * Uncheck '''Create a separate folder for each event type''' * Check '''Ignore shorter epochs''' * Check '''Use CTF compensation''' * Check '''Use SSP/ICA projectors''' * Add the process '''Pre-process > Remove DC offset''': * '''Baseline''' = `All file` * '''Sensor types''' = `MEG` * Run the pipeline || {{attachment:pro_import.png}} || || {{attachment:pro_remove_dc.png}} || * A new folder '''SubjectCMC_notch_high_abs''' without the 'raw' indication is now created, which includes '''192 individual epochs''' (24 trials x 8 1-s epochs each). The epochs that overlap with a "bad" event are also marked as bad, as shown with an exclamation mark in a red circle (<<Icon(iconModifBad.gif)>>). These bad epochs will be automatically ignored by the '''Process1''' and '''Process2''' tabs, and from all further processing. . {{attachment:trials.png||width="40%"}} ==== Comparison with FieldTrip ==== The figures below show the EMG and MRC21 channels (a MEG sensor over the left motor-cortex) from the epoch #1.1, in Brainstorm (left), and from the [[https://www.fieldtriptoolbox.org/tutorial/coherence/|FieldTrip tutorial]] (right). {{attachment:bst_ft_trial1.png||width="100%"}} == Coherence: EMG x MEG == Let's compute the '''magnitude-squared coherence (MSC)''' between the '''left EMG''' and the '''MEG''' channels. * In the Process1 box, drag and drop the '''Left (192 files)''' trial group. . {{attachment:dragdrop_trialgroup.png||width="40%"}} * Select the process '''Connectivity > Coherence 1xN [2021]''': * '''Time window''' = '''All file'''<<BR>>The imported epochs are defined with distinct time stamps (e.g. Left#1.1: 0-1s, Left#1.2: 1-2s, Left#1.8: 7-8s), but the process tab only shows those from the first file. Select "All file" to ensure that the entire trial length is processed, regardless of its actual time stamp. * '''Source channel''' = `EMGlft` * Do not check '''Include bad channels''' nor '''Remove evoke response''' * '''Magnitude squared coherence''' * '''Window length for PSD estimation''' = `0.5 s` * '''Overlap for PSD estimation''' = `50%` * '''Highest frequency of interest''' = `80 Hz` * '''Average cross-spectra of input files (one output file)''' * More details on the '''Coherence''' process can be found in the [[Tutorials/Connectivity#Coherence|Connectivity Tutorial]]. * Add the process '''File > Add tag''' with the following parameters: * '''Tag to add''' = `MEG sensors` * Select '''Add to file name''' * Run the pipeline: || {{attachment:coh_meg_emgleft.png}} || || {{attachment:coh_meg_emgleft2.png}} || * Double-click on the resulting data node '''mscohere(0.6Hz,555win): EMGlft | MEG sensors''' to display the MSC spectra. Click on the maximum peak in the 15 to 20 Hz range, and press `Enter` to display the spectrum from the selected sensor in a new window. This spectrum is that of channel '''MRC21''', and shows a prominent peak at 17.58 Hz. Use the frequency slider (under the Time panel) to explore the MSC output across frequencies. * Right-click on the spectrum and select '''2D Sensor cap''' for a topographical representation of the magnitude of the coherence results across the sensor array. You may also use the shortcut `Ctrl-T`. The sensor locations can be displayed with a right-click and by selecting '''Channels > Display sensors''' from the contextual menu (shortcut `Ctrl-E)`. . {{attachment:res_coh_meg_emgleft.png||width="80%"}} * We can now average the magnitude of the MSC across the beta band (15-20 Hz). <<BR>>In the Process1 box, select the new '''mscohere''' file. * Run process '''Frequency > Group in time or frequency bands''': * Select '''Group by frequency bands''' * Type `cmc_band / 15, 20 / mean` in the text box. . {{attachment:pro_group_freq.png||width="60%"}} * The resulting '''mscohere...|tfbands''' node contains one MSC value for each sensor (the MSC average in the 15-20 Hz band). Right-click on the file to display the 2D or 3D topography of the MSC beta-band measure. <<BR>><<BR>> {{attachment:res_coh_tfgroup.gif}} * Higher MSC values the EMG signal and MEG sensor signals map over the contralateral set of central sensors in the beta band. [[Tutorials/Connectivity#Sensor-level|Sensor-level connectivity]] can be ambiguous to interpret anaotmically though. We will now map the magnitude of EMG-coherence across the brain (MEG sources). == Source estimation == === MRI segmentation === We first need to extract the cortical surface from the T1 MRI volume we imported at the beginning of this tutorial. [[https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12|CAT12]] is a Brainstorm pluing that will perform this task in 30-60min. * Switch back to the Anatomy view of the protocol (<<Icon(iconSubjectDB.gif)>>). * Right-click on the MRI (<<Icon(iconMri.gif)>>) > '''MRI segmentation > CAT12''': * '''Number of vertices'''{{{: }}}`15000` * '''Anatomical parcellations''': `Yes` * '''Cortical maps''': {{{No}}} . {{attachment:cat12.png||width="100%"}} * Keep the low-resolution central surface selected as the default cortex ('''central_15002V'''). This surface is the primary output of CAT12, and is shown half-way between the pial envelope and the grey-white interface ([[https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12|more information]]). The head surface was recomputed during the process and duplicates the previous surface obtained above: you can either delete one of the head surfaces or ignore this point for now. * For quality control, double-click on the head and central_15002V surfaces to visualize them in 3D.<<BR>><<BR>> {{attachment:cat12_files.gif}} === Head models === We will perform source modeling using a [[Tutorials/HeadModel#Dipole_fitting_vs_distributed_models|distributed model]] approach for two different source spaces: the '''cortex surface''' and the entire '''MRI volume'''. Forward models are called ''head models'' in Brainstorm. They account for how neural electrical currents produce magnetic fields captured by sensors outside the head, considering head tissues electromagnetic properties and geometry, independently of actual empirical measurements ([[http://neuroimage.usc.edu/brainstorm/Tutorials/HeadModel|more information]]). A distinct head model is required for the cortex surface and head volume source spaces. ==== Cortical surface ==== * Go back to the '''Functional data''' view of the database. * Right-click on the channel file of the imported epoch folder > '''Compute head model'''. * '''Comment''' = `Overlapping spheres (surface)` * '''Source space''' = `Cortex surface` * '''Forward model''' = `MEG Overlapping spheres`. . {{attachment:pro_head_model_srf.gif}} ==== Whole-head volume ==== * Right-click on the channel file again > '''Compute head model'''. * '''Comment''' = `Overlapping spheres (volume)` * '''Source space''' = `MRI volume` * '''Forward model''' = `Overlapping spheres`. * Select '''Regular grid''' and '''Brain''' * '''Grid resolution''' = `5 mm` . {{attachment:pro_head_model_vol.gif}} * The '''Overlapping spheres (volume)''' head model is now added to the database explorer. The green color of the name indicates this is the default head model for the current folder: you can decide to use another head model available by double clicking on its name. . {{attachment:tre_head_models.gif}} === Noise covariance === The [[Tutorials/NoiseCovariance#The_case_of_MEG|recommendation for MEG]] is to extract basic noise statistics from empty-room recordings. When not available, as here, resting-state data can be used as proxies for MEG noise covariance. We will use a segment of the MEG recordings, away from the task and major artifacts: '''18s-29s'''. * Right-click on the clean continuous file > '''Noise covariance > Compute from recordings'''.<<BR>><<BR>> {{attachment:pro_noise_cov.gif}} * Right-click on the Noise covariance (<<Icon(iconNoiseCov.gif)>>) > '''Copy to other folders'''.<<BR>><<BR>> {{attachment:tre_covmat.gif}} === Inverse models === We will now compute three inverse models, with different source spaces: cortex surface with '''constrained''' dipole orientations (normal to the cortex), cortex surface with '''unconstrained''' orientation, and MRI '''volume''' ([[Tutorials/SourceEstimation|more information]]). ==== Cortical surface ==== * Right-click on '''Overlapping spheres (surface)''' > '''Compute sources''': * '''Minimum norm imaging''' * '''Current density map''' * '''Constrained: Normal to the cortex''' * '''Comment''' = `MN: MEG (surface)` * Repeat the previous step, but this time select '''Unconstrained''' in the Dipole orientations field. || {{attachment:pro_sources_srfc.png}} || || {{attachment:pro_sources_srfu.png}} || ==== Volume ==== * Right-click on the '''Overlapping spheres (volume)''' > '''Compute sources:''' * '''Current density map''' * '''Unconstrained''' * '''Comment''' = `MN: MEG (volume)` . {{attachment:pro_sources_vol.png||width="40%"}} * Three imaging kernels (<<Icon(iconResultKernel.gif)>>) are now available in the database explorer. Note that each trial is associated with three source links (<<Icon(iconResultLink.gif)>>). . {{attachment:tre_sources.gif}} == Coherence: EMG x Sources == We can now compute the coherence between the EMG signal and the brain source time series, for each of the source models. Let's start with the '''surface/constrained''' model. * To select the source maps we want to include in the coherence estimation, click on the [[Tutorials/PipelineEditor#Search_Database|Search Database]] button (<<Icon(iconZoom.gif)>>), and select '''New search'''. Set the parameters as shown below, and click on '''Search'''. . {{attachment:gui_search_srf.png||width="70%"}} * It creates a new tab in the database explorer, showing only the files that match the criteria. . {{attachment:tre_search_srf.gif}} * Click the '''Process2''' tab at the bottom of the main Brainstorm window. * '''Files A''': Drag-and-drop the '''Left (192 files)''' group, select '''Process recordings''' (<<Icon(iconEegList.gif)>>). * '''Files B''': Drag-and-drop the '''Left (192 files)''' group, select '''Process sources''' (<<Icon(iconResultList.gif)>>). * Objective: Extract from the same files the EMG recordings (Files A) and the sources time series (Files B), then compute coherence between these two sets. Note that the blue labels over the file lists indicate that there are 185 "good" files (7 bad epochs). . {{attachment:process2.png||width="80%"}} * Select the process '''Connectivity > Coherence AxB [2021]''': * '''Time window''' = '''All file''' * '''Source channel (A)''' = `EMGlft` * Uncheck '''Use scouts (B)''' * Do not '''Remove evoked responses from each trial''' * '''Magnitude squared coherence''' * Window length''' = `0.5 s, `Overlap''' = `50%` * '''Highest frequency''' = `80 Hz` * '''Average cross-spectra'''. * Add the process '''File > Add tag''': * '''Tag to add''' = `(surface)(Constr)` * Select '''Add to file name''' * Run the pipeline || {{attachment:pro_coh_srf.png}} || || {{attachment:pro_coh_srf2.png}} || * Repeat the steps above to compute the EMG-sources coherence for the other source models: '''surface/unconstrained''' and '''volume''': * Edit the search criteria: Right-click on the search tab > '''Edit search'''. * It updates automatically the file selection in the Process2 tab. * Select the processes: Do not forget to select again '''All file''' and update the '''file tag'''. * Close the search tab. If you don't see the 3 new connectivity files <<Icon(iconConnect1.gif)>>) in the database explorer: refresh it, by pressing '''[F5]''' or clicking again on the selected button "Functional data". <<BR>><<BR>> {{attachment:tre_coh_src_files.gif}} === Surface === Double-click the 1xN connectivity files for the two '''(surface)''' source space to show the results on the cortex. If you are not familiar with the options in the cortex figures, check [[Tutorials/SourceEstimation#Display:_Cortex_surface|Display: Cortex surface]]. Find the location and frequency with the highest coherence value. * In the '''Surface''' tab: Smooth=30%, Amplitude=0%. * To compare visually different cortex maps, set manually the [[Tutorials/Colormaps|colormap]] range (e.g.`[0 - 0.07])` * Explore with coherence spectra with the '''frequency slider''' * The highest coherence value is located at '''14.65 Hz''', in the '''right primary motor cortex''' (precentral gyrus). To observe the coherence spectrum at a given location: right-click on the cortex > '''Source: Power spectrum'''. <<BR>><<BR>> {{attachment:res_coh_surf.gif}} * The analysis using constrained (top) and unconstrained (bottom) orientations agree in the location and frequency of the peak coherence. The main difference between these results is that unconstrained sources appear smoother, due to maximum aggregation performed across directions, explained later. These results agree with our hypothesis, previous results in the literature, and the results presented in the [[https://www.fieldtriptoolbox.org/tutorial/coherence/|FieldTrip tutorial]]. * To get the 3D coordinates of the peak: right-click on the figure > '''Get coordinates'''. Then click on the right motor cortex with the crosshair cursor that appears. These coordinates can be useful to compare with the volume results. <<BR>><<BR>> {{attachment:res_get_coordinates.gif}} === Volume === * Double-click the 1xN connectivity file for the '''(volume)''' source space. * Go to 14.65 Hz, set the data transparency to 20% (Surface tab). * Find the peak by navigating in the volume, or using the coordinates from the surface results. * Right-click on the figure > Anatomical atlas > None. This will show the coherence value under the cursor at the top-right corner, instead of an anatomical label. <<BR>><<BR>> {{attachment:res_coh_vol.gif}} === Method === For '''constrained''' sources, each vertex in the source grid is associated with '''ONE''' time series, as such, when coherence is computed with the EMG signal (also one time series), the result is '''ONE''' coherence spectrum per vertex. In other words, for each frequency bin, there is a coherence brain map. [[https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence?action=AttachFile&do=get&target=diagram_1xn_coh_constr.png|{{attachment:diagram_1xn_coh_constr.png|https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence?action=AttachFile&do=get&target=diagram_1xn_coh_constr.png|width="100%"}}]] In the case of '''unconstrained''' or '''volume''' sources, each vertex in the grid is associated with '''THREE''' time series, each one corresponding to the X, Y and Z directions. Thus, when coherence is computed with the EMG signal (one time series), there are '''THREE''' coherence spectra. To be represented on the cortex, these three values need to be '''flattened''' into one, resulting in one coherence spectrum per vertex. For performing this dimension reduction, we decided to take the '''maximum '''across three directions, for each frequency bin for each vertex. [[https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence?action=AttachFile&do=get&target=diagram_1xn_coh_unconstr.png|{{attachment:diagram_1xn_coh_unconstr.png|https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence?action=AttachFile&do=get&target=diagram_1xn_coh_unconstr.png|width="100%"}}]] {{{#!wiki caution An alternative approach in the literature, to address the 3-dimensional nature of the unconstrained sources, consists in flattening the vertex X, Y and Z time series before the coherence computation; resulting in a similar case as the constrained sources. Common methods for this flattening include: '''PCA''' (only first component is kept), and [[https://en.wikipedia.org/wiki/Norm_(mathematics)|(Euclidean) norm]]. This flattening of the time series can be performed in Brainstorm with the process: Sources > '''Unconstrained to flat map'''. [[https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence?action=AttachFile&do=get&target=diagram_1xn_coh_flattened.png|{{attachment:diagram_1xn_coh_flattened.png||width="100%"}}]] * Flattened sources are saved as full rather than recordings+kernel. * We have tested this flattening approach with simulations and found detrimental effects on the expected results. }}} == Coherence: EMG x Scouts == So far, we have computed coherence at the source level, thus, a coherence spectrum is computed for each of the 15002 source points. This large dimension hinders later analysis of the results. Therefore, the strategy is to reduce the dimensionality of the source space by using a [[Tutorials/Scouts#Scout_toolbar_and_menus|surface-]] or [[Tutorials/DefaultAnatomy#MNI_parcellations|volume-]]parcellation scheme, in Brainstorm jargon this is an '''atlas''' that is made of '''scouts'''. See the [[Tutorials/Scouts|scout tutorial]] for detail information on atlases and scouts in Brainstorm. Under this approach, instead of providing one result (coherence spectrum) per source vertex, one result is computed for each scout. When computing coherence (or other connectivity metrics) at the scout level, it is necessary to provide two parameters that define how the data is aggregated per scout: The '''scout function''' (mean is often used), and when the within-scout aggregation takes place ('''before''' or '''after''' the coherence computation). * '''Before''': The scout function is applied for each direction on the vertices' source time series that make up a scout; resulting in one time series per direction per scout. Then, the scout time series are used to compute coherence with the reference signal (EMG in this tutorial), and the coherence spectra for each scout are aggregated across dimensions, [[#Coherence_with_constrained_and_unconstrained_sources|as shown previously]], to obtain one coherence spectrum per scout. [[https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence?action=AttachFile&do=get&target=diagram_1xn_coh_sct_bef.png|{{attachment:diagram_1xn_coh_sct_bef.png|https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence?action=AttachFile&do=get&target=diagram_1xn_coh_sct_bef.png|width="100%"}}]] * '''After''': Coherence is computed between the reference signal and each direction of the vertices' source time series, [[#Coherence_1xN_.28source_level.29|as in the previous section]]. Then, the scout function is applied on the coherence spectra for each direction of the vertices within a scout, finally these spectra are aggregated across dimensions to obtain a coherence spectrum per scout. This option computes the coherence between the EMG and 45000 source signals, instead of a handful of times with the "before" option. The computation is therefore much longer and demanding in terms of RAM memory. [[https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence?action=AttachFile&do=get&target=diagram_1xn_coh_sct_aft.png|{{attachment:diagram_1xn_coh_sct_aft.png|https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence?action=AttachFile&do=get&target=diagram_1xn_coh_sct_aft.png|width="100%"}}]] Let's here compute the coherence using scouts, using '''mean''' as scout function alongside with the '''Before''' option. We will use the [[https://www.biorxiv.org/content/biorxiv/early/2017/07/16/135632.full.pdf|Schaefer 100 parcellation]] atlas on the results from constrained sources. * Use Search Database (<<Icon(iconZoom.gif)>>) to select the '''Left''' trials with their respective '''(surface)(Constr)''' source maps, as shown in the [[#Coherence_1xN_.28source_level.29|previous section]]. * In the Process2: '''Left '''trial group into both the '''Files A''' and '''Files B''' boxes. Select '''Process recordings''' (<<Icon(iconEegList.gif)>>) for Files A, and '''Process sources''' (<<Icon(iconResultList.gif)>>) for Files B. . {{attachment:process2.png||width="80%"}} Open the '''Pipeline editor''': * Add the process '''Connectivity > Coherence AxB [2021]''' with the following parameters: * '''Time window''' = `0 - 1000 ms` or check '''All file''' * '''Source channel (A)''' = `EMGlft` * Check '''Use scouts (B)''' * From the menu at the right, select '''Schaefer_100_17net''' * Select all the scouts * '''Scout function''': `Mean` * '''When to apply the scout function''': `Before` * Do not '''Remove evoked responses from each trial''' * '''Magnitude squared coherence''', '''Window length''' = `0.5 s` * '''Overlap''' = `50%` * '''Highest frequency''' = `80 Hz` * '''Average cross-spectra'''. * Add the process '''File > Add tag''' with the following parameters: * '''Tag to add''' = `(surface)(Constr)` * Select '''Add to file name''' * Run the pipeline || {{attachment:pro_coh_srfc_bef_sct.png}} || || {{attachment:pro_coh_srfc_bef_sct2.png}} || Open the output file by double-clicking on it. This time the coherence spectra are not displayed on the cortex, but they are plotted for each scout. Moreover, 1xN connectivity file can be shown as image. || {{attachment:res_coh_srfc_bef_sct.png}} || || {{attachment:res_coh_srfc_bef_sct2.png}} || Note that for 14.65 Hz, the highest two peaks correspond to the '''SomMotA_4 R''' and '''SomMotA_2 R''' scouts, both located over the right primary motor cortex. {{{#!wiki caution The choice of the optimal parcellation scheme for the source space is not easy, this is still an active field of research. The only recommendation we can give at the moment is to use regions of interest that are small and homogenous in size. }}} <<TAG(Advanced)>> |
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| * '''Minimum norm''': Baillet S, Mosher JC, Leahy RM<<BR>>[[http://neuroimage.usc.edu/paperspdf/BailletMosherLeahy_IEEESPMAG_Nov2001.pdf|Electromagnetic brain mapping]], IEEE SP MAG 2001. | * Conway BA, Halliday DM, Farmer SF, Shahani U, Maas P, Weir AI, et al. <<BR>> [[https://dx.doi.org/10.1113/jphysiol.1995.sp021104|Synchronization between motor cortex and spinal motoneuronal pool during the performance of a maintained motor task in man]]. <<BR>> The Journal of Physiology. 1995 Dec 15;489(3):917–24. * Kilner JM, Baker SN, Salenius S, Hari R, Lemon RN. <<BR>> [[https://doi.org/10.1523/JNEUROSCI.20-23-08838.2000|Human Cortical Muscle Coherence Is Directly Related to Specific Motor Parameters]]. <<BR>> J Neurosci. 2000 Dec 1;20(23):8838–45. * Liu J, Sheng Y, Liu H. <<BR>> [[https://doi.org/10.3389/fnhum.2019.00100|Corticomuscular Coherence and Its Applications: A Review]]. <<BR>> Front Hum Neurosci. 2019 Mar 20;13:100. * Sadaghiani S, Brookes MJ, Baillet S. <<BR>> [[https://doi.org/10.1016/j.neuroimage.2021.118788|Connectomics of human electrophysiology]]. <<BR>> NeuroImage. 2022 Feb;247:118788. |
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| * Tutorial: [[Tutorials/Connectivity|Functional connectivity]] * Tutorial: [[Tutorials/SourceEstimation|Source estimation]] |
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==== Forum discussions ==== * Forum: Minimum norm units (pA.m): [[http://neuroimage.usc.edu/forums/showthread.php?1246-Doubt-about-current-density-units-pA.m-or-pA-m2|http://neuroimage.usc.edu/forums/showthread.php?1246]] <<HTML(<!-- END-PAGE -->)>> |
* Tutorial: [[Tutorials/Scouts|Scouts]] * Tutorial: [[Tutorials/ConnectivityGraph|Connectivity graphs]] == Scripting == The following script from the Brainstorm distribution reproduces the analysis presented in this tutorial page: [[https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/script/tutorial_coherence.m|brainstorm3/toolbox/script/tutorial_coherence.m]] <<HTML(<div style="border:1px solid black; background-color:#EEEEFF; width:720px; height:500px; overflow:scroll; padding:10px; font-family: Consolas,Menlo,Monaco,Lucida Console,Liberation Mono,DejaVu Sans Mono,Bitstream Vera Sans Mono,Courier New,monospace,sans-serif; font-size: 13px; white-space: pre;">)>><<EmbedContent("https://neuroimage.usc.edu/bst/viewcode.php?f=tutorial_coherence.m")>><<HTML(</div >)>> |
Corticomuscular coherence (CTF MEG)
[TUTORIAL UNDER DEVELOPMENT: NOT READY FOR PUBLIC USE]
Authors: Raymundo Cassani, Francois Tadel & Sylvain Baillet.
Corticomuscular coherence measures the degree of similarity between electrophysiological signals (MEG, EEG, ECoG sensor traces or source time series, especially over the contralateral motor cortex) and the EMG signals recorded from muscle activity during voluntary movements. Cortical-muscular signals similarities are conceived as due mainly to the descending communication along corticospinal pathways between primary motor cortex (M1) and the muscles attached to the moving limb(s). For consistency purposes, the present tutorial replicates, with Brainstorm tools, the processing pipeline "Analysis of corticomuscular coherence" of the FieldTrip toolbox.
Contents
Dataset description
The dataset is identical to that of the FieldTrip tutorial: Analysis of corticomuscular coherence:
- One participant,
- MEG recordings: 151-channel CTF MEG system,
- Bipolar EMG recordings: from left and right extensor carpi radialis longus muscles,
- EOG recordings: used for detection and attenuation of ocular artifacts,
- MRI: 1.5T Siemens system,
- Task: The participant lifted their hand and exerted a constant force against a lever for about 10 seconds. The force was monitored by strain gauges on the lever. The participant performed two blocks of 25 trials using either their left or right hand.
- Here we describe relevant Brainstorm tools via the analysis of the left-wrist trials. We encourage the reader to practice further by replicating the same pipeline using right-wrist trials!
Corticomuscular coherence:
Coherence measures the linear relationship between two signals in the frequency domain.
Previous studies (Conway et al., 1995, Kilner et al., 2000) have reported corticomuscular coherence effects in the 15–30 Hz range during maintained voluntary contractions.
- TODO: IMAGE OF EXPERIMENT, SIGNALS and COHERENCE
Download and installation
Pre-requisites
Please make sure you have completed the get-started tutorials, prior to going through the present tutorial.
- Have a working copy of Brainstorm installed on your computer.
Install the CAT12 Brainstorm plugin, to perform MRI segmentation from the Brainstorm dashboard.
Download the dataset
Download SubjectCMC.zip from the FieldTrip FTP server:
ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/SubjectCMC.zip- Unzip the downloaded archive file in a folder outside the Brainstorm database or app folders (for instance, directly on your desktop).
Brainstorm
- Launch Brainstorm (via the Matlab command line or the Matlab-free stand-alone version of Brainstorm).
Select from the menu File > Create new protocol. Name the new protocol TutorialCMC and select the options:
No, use individual anatomy,
No, use one channel file per acquisition run.
Importing anatomy
Right-click on the newly created TutorialCMC node > New subject > Subject01.
Keep the default options defined for the study (aka "protocol" in Brainstorm's vernacular).Switch to the Anatomy view of the protocol (
). Right-click on the Subject01 > Import MRI:
Select the file format: All MRI files (subject space)
Select the file: SubjectCMC/SubjectCMC.mri
This step will launch Brainstorm's MRI viewer, where coronal, sagittal and axial cross-sections of the MRI volume are displayed. note that three anatomical fiducials (left and right pre-auricular points (LPA and RPA), and nasion (NAS)) are automatically identified. These fiducials are located near the left/right ears and just above the nose, respectively. Click on Save.
In all typical Brainstorm workflows from this tutorial handbook, we recommend processing the MRI volume at this stage, before importing the functional (MEG/EEG) data. However, we will proceed differently, for consistency with the original FieldTrip pipeline, and readily obtain sensor-level coherence results. We will proceed with MRI segmentation below, before performing source-level analyses.
- We still need to verify the proper geometric registration (alignment) of MRI with MEG. We will therefore now extract the scalp surface from the MRI volume.
Right-click on the MRI (
) > MRI segmentation > Generate head surface.
Double-click on the newly created surface to display the scalp in 3-D.
MEG and EMG recordings
Link the recordings
Switch now to the Functional data view of your database contents (
). Right-click on Subject01 > Review raw file:
Select the appropriate MEG file format: MEG/EEG: CTF(*.ds; *.meg4; *.res4)
Select the data file: SubjectCMC.ds
A new folder SubjectCMC is created in the Brainstorm database explorer. Note the "RAW" tag over the icon of the folder (
), indicating that the MEG files contain unprocessed, continuous data. This folder includes: CTF channels (191) is a file with all channel information, including channel types (MEG, EMG, etc.), names, 3-D locations, etc. The total number of channels available (MEG, EMG, EOG etc.) is indicated between parentheses.
Link to raw file is a link to the original data file. Brainstorm reads all the relevant metadata from the original dataset and saves them into this symbolic node of the data tree (e.g., sampling rate, number of time samples, event markers). As seen elsewhere in the tutorial handbook, Brainstorm does not create copies by default of (potentially large) unprocessed data files (more information).
MEG-MRI coregistration
This registration step is to align the MEG coordinate system with the participant's anatomy from MRI (more info). Here we will use only the three anatomical landmarks stored in the MRI volume and specific at the moment of MEG data collection. From the FieldTrip tutorial:
"To measure the head position with respect to the sensors, three coils were placed at anatomical landmarks of the head (nasion, left and right ear canal). [...] During the MRI scan, ear molds containing small containers filled with vitamin E marked the same landmarks. This allows us, together with the anatomical landmarks, to align source estimates of the MEG with the MRI."To visually appreciate the correctness of the registration, right-click on the CTF channels node > MRI registration > Check. This opens a 3-D figure showing the inner surface of the MEG helmet (in yellow), the head surface, the fiducial points and the axes of the subject coordinate system (SCS).
Reviewing
Right-click on the Link to raw file > Switch epoched/continuous to convert how the data i stored in the file to a continuous reviewing format, a technical detail proper to CTF file formatting.
Right-click on the Link to raw file > MEG > Display time series (or double-click on its icon). This will display data time series and enable the Time panel and the Record tab in the main Brainstorm window (see specific features in "explore data time series").
Right-click on the Link to raw file > EMG > Display time series.
Event markers
The colored dots at the top of the figure, above the data time series, indicate event markers (or triggers) saved along with MEG data. The actual onsets of the left- and right-wrist trials are not displayed yet: they are saved in an auxiliary channel of the raw data named Stim. To add these markers to the display, follow this procedure:
With the time series figure still open, go to the Record tab and select File > Read events from channel. Event channels = Stim, select Value, Reject events shorter than 12 samples. Click Run.
The rejection of short events is nececessary in this dataset, because transitions between values in the Stim channel may span over several time samples. Otherwise, and for example, an event U1 would be created at 121.76s because the transition from the event U1025 back to zero features two unwanted values at the end of the event. The rejection criteria is set to 12 time samples (10ms), because the duration of all the relevant triggers is longer than 15ms. This value is proper to each dataset, so make sure you verify trigger detections from your own dataset.
New event markers are created and now shown in the Events section of the tab, along with previous event categories. In this tutorial, we will only use events U1 through U25, which correspond to the beginning of each of the 25 left-wrist trials of 10 seconds. Following FieldTrip's tutorial, let's reject trial #7, event U7.
Delete all unused events: Select all the events except U1-U6 and U8-25 (Ctrl+click / Shift+click), then menu Events > Delete group (or press the Delete key).
Merge events: Select all the event groups, then select from the menu Events > Merge group > "Left". A new event category called "Left" now indicate the onsets of 24 trials of left-wrist movements.
Pre-processing
In this tutorial, we will analyze only the Left trials (left-wrist extensions). In the following sections, we will process only the first 330 s of the original recordings, where the left-wrist trials were performed.
Power line artifacts
In the Process1 box: Drag and drop the Link to raw file.
Run process Frequency > Power spectrum density (Welch):
Time window: 0-330 s
Window length: 10 s
Overlap: 50%
Sensor types: MEG, EMG
Double-click on the new PSD file to visualize the power spectrum density of the data.
- The PSD plot shows two groups of sensors: EMG (highlighted in red above) and the MEG spectra below (black lines). Peaks at 50Hz and harmonics (100, 150, 200Hz and above) indicate the European power line frequency and are clearly visible. We will now use notch filters to attenuate power line contaminants at 50, 100 and 150 Hz.
In the Process1 box: Drag and drop the Raw | clean node.
Run the process Pre-processing > Notch filter with:
Check Process the entire file at once
Sensor types: MEG, EMG
Frequencies to remove (Hz): 50, 100, 150
In case you get a memory error message:
These MEG recordings have been saved before applying the CTF 3rd-order gradient compensation, for noise reduction. The compensation weights are therefore applied on the fly when Brainstorm reads data from the file. However, this requires reading all the channels at once. By default, the frequency filter are optimized to process channel data sequentially, which is incompatible with applying the CTF compensation on the fly. This setting can be overridden with the option Process the entire file at once, which requires loading the entire file in memory at once, which may crash teh process depending on your computing resources (typically if your computer's RAM < 8GB). If this happens: run the process Artifacts > Apply SSP & CTF compensation on the file first, then rune the notch filter process without the option "Process the entire file at once" (more information).A new folder named SubjectCMC_clean_notch is created. Obtain the PSD of these data to appreciate the effect of the notch filters. As above, please remember to indicate a Time window restricted from 0 to 330 s in the options of the PSD process.
EMG: Filter and rectify
Two typical pre-processing steps for EMG consist in high-pass filtering and rectifying.
In the Process1 box: drag and drop the Raw | notch(50Hz 100Hz 150Hz) node.
Add the process Pre-process > Band-pass filter
Sensor types = EMG
Lower cutoff frequency = 10 Hz
Upper cutoff frequency = 0 Hz
Add the process Pre-process > Absolute values
Sensor types = EMG
- Run the pipeline
Delete intermediate files that won't be needed anymore: Select folders SubjectCMC_notch and SubjectCMC_notch_high, then press the Delete key (or right-click > File > Delete).
MEG: Blink SSP and bad segments
Stereotypical artifacts such eye blinks and heartbeats can be identified from their respective characteristic spatial distributions. Their contamination of MEG signals can then be attenuated specifically using Signal-Space Projections (SSPs). For more details, consult the specific tutorial sections about the detection and removal of artifacts with SSP. The present tutorial dataset features an EOG channel but no ECG. We will therefore only remove artifacts caused by eye blinks.
Blink correction with SSP
Right-click on the pre-processed file > MEG > Display time series and EOG > Display time series.
In the Record tab: Artifacts > Detect eye blinks, and use the parameters:
Channel name= EOG
Time window = 0 - 330 s
Event name = blink
Three categories of blink events are created. Review the traces of the EOG channels around a few of these events to ascertain they are related to eye blinks. In the present case, we note that the blink group contains genuine eye blinks, and that groups blink2 and blink3 capture saccades.
To remove blink artifacts with SSP, go to Artifacts > SSP: Eye blinks:
Event name=blink
Sensors=MEG
Display the time series and topographies of the first two SSP components identified. In the present case, only the first SSP component can be clearly related to blinks: the percentage of variance explained is substantially higher than the other compoments', the spatial topography of the component is also typical of eye blinks, and the corresponding time series is similar to the EOG signal around blinks. Select only component #1 for removal.
Close all visualization figures by clicking on the large × at the top-right of the main Brainstorm window.
Detection of "bad" data segments
Here we will use the automatic detection of artifacts to identify data segments contaminated by e.g., large eye and head movements, or muscle contractions.
Display the MEG and EOG time series. In the Record tab, select Artifacts > Detect other artifacts and enter the following parameters:
Time window = 0 - 330 s
Sensor types=MEG
Sensitivity=3
Check both frequency bands 1-7 Hz and 40-240 Hz
- You are encouraged to review all the segments marked using this procedure. With the present data, all marked segments do contain clear artifacts.
Select the 1-7Hz and 40-240Hz event groups and select Events > Mark group as bad. Alternatively, you can add the prefix bad_ to the event names. Brainstorm will automatically discard these data segments from further processing.
- Close all visualization windows and reply "Yes" to the save the modifications query.
Epoching
We are now finished with the pre-processing of EMG and MEG recordings. We will now extract and import specific data segments of interest into the Brainstorm database for further derivations. As mentioned previously, we will focus on the Left category of events (left-wrist movements). For consistency with the FieldTrip tutorial, we will analyze 8s of recordings following each movement (from the original 10s around each trial), and split them in 1-s epochs. We will also remove the DC offset from each MEG channel.
- In the Process1 box: Drag-and-drop the pre-processed file.
Select the process Import > Import recordings > Import MEG/EEG: Events:
Subject name = Subject01
Folder name = empty
Event names = Left
Time window = 0 - 330 s
Epoch time = 0 - 8000 ms
Split recordings in time blocks = 1 s
Uncheck Create a separate folder for each event type
Check Ignore shorter epochs
Check Use CTF compensation
Check Use SSP/ICA projectors
Add the process Pre-process > Remove DC offset:
Baseline = All file
Sensor types = MEG
- Run the pipeline
|
|
|
A new folder SubjectCMC_notch_high_abs without the 'raw' indication is now created, which includes 192 individual epochs (24 trials x 8 1-s epochs each). The epochs that overlap with a "bad" event are also marked as bad, as shown with an exclamation mark in a red circle (
). These bad epochs will be automatically ignored by the Process1 and Process2 tabs, and from all further processing. 
Comparison with FieldTrip
The figures below show the EMG and MRC21 channels (a MEG sensor over the left motor-cortex) from the epoch #1.1, in Brainstorm (left), and from the FieldTrip tutorial (right).
Coherence: EMG x MEG
Let's compute the magnitude-squared coherence (MSC) between the left EMG and the MEG channels.
In the Process1 box, drag and drop the Left (192 files) trial group.
Select the process Connectivity > Coherence 1xN [2021]:
Time window = All file
The imported epochs are defined with distinct time stamps (e.g. Left#1.1: 0-1s, Left#1.2: 1-2s, Left#1.8: 7-8s), but the process tab only shows those from the first file. Select "All file" to ensure that the entire trial length is processed, regardless of its actual time stamp.Source channel = EMGlft
Do not check Include bad channels nor Remove evoke response
Magnitude squared coherence
Window length for PSD estimation = 0.5 s
Overlap for PSD estimation = 50%
Highest frequency of interest = 80 Hz
Average cross-spectra of input files (one output file)
More details on the Coherence process can be found in the Connectivity Tutorial.
Add the process File > Add tag with the following parameters:
Tag to add = MEG sensors
Select Add to file name
- Run the pipeline:
|
|
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Double-click on the resulting data node mscohere(0.6Hz,555win): EMGlft | MEG sensors to display the MSC spectra. Click on the maximum peak in the 15 to 20 Hz range, and press Enter to display the spectrum from the selected sensor in a new window. This spectrum is that of channel MRC21, and shows a prominent peak at 17.58 Hz. Use the frequency slider (under the Time panel) to explore the MSC output across frequencies.
Right-click on the spectrum and select 2D Sensor cap for a topographical representation of the magnitude of the coherence results across the sensor array. You may also use the shortcut Ctrl-T. The sensor locations can be displayed with a right-click and by selecting Channels > Display sensors from the contextual menu (shortcut Ctrl-E).
We can now average the magnitude of the MSC across the beta band (15-20 Hz).
In the Process1 box, select the new mscohere file.Run process Frequency > Group in time or frequency bands:
Select Group by frequency bands
Type cmc_band / 15, 20 / mean in the text box.
The resulting mscohere...|tfbands node contains one MSC value for each sensor (the MSC average in the 15-20 Hz band). Right-click on the file to display the 2D or 3D topography of the MSC beta-band measure.
Higher MSC values the EMG signal and MEG sensor signals map over the contralateral set of central sensors in the beta band. Sensor-level connectivity can be ambiguous to interpret anaotmically though. We will now map the magnitude of EMG-coherence across the brain (MEG sources).
Source estimation
MRI segmentation
We first need to extract the cortical surface from the T1 MRI volume we imported at the beginning of this tutorial. CAT12 is a Brainstorm pluing that will perform this task in 30-60min.
Switch back to the Anatomy view of the protocol (
). Right-click on the MRI (
) > MRI segmentation > CAT12: Number of vertices: 15000
Anatomical parcellations: Yes
Cortical maps: No
Keep the low-resolution central surface selected as the default cortex (central_15002V). This surface is the primary output of CAT12, and is shown half-way between the pial envelope and the grey-white interface (more information). The head surface was recomputed during the process and duplicates the previous surface obtained above: you can either delete one of the head surfaces or ignore this point for now.
For quality control, double-click on the head and central_15002V surfaces to visualize them in 3D.
Head models
We will perform source modeling using a distributed model approach for two different source spaces: the cortex surface and the entire MRI volume. Forward models are called head models in Brainstorm. They account for how neural electrical currents produce magnetic fields captured by sensors outside the head, considering head tissues electromagnetic properties and geometry, independently of actual empirical measurements (more information). A distinct head model is required for the cortex surface and head volume source spaces.
Cortical surface
Go back to the Functional data view of the database.
Right-click on the channel file of the imported epoch folder > Compute head model.
Comment = Overlapping spheres (surface)
Source space = Cortex surface
Forward model = MEG Overlapping spheres.
Whole-head volume
Right-click on the channel file again > Compute head model.
Comment = Overlapping spheres (volume)
Source space = MRI volume
Forward model = Overlapping spheres.
Select Regular grid and Brain
Grid resolution = 5 mm
The Overlapping spheres (volume) head model is now added to the database explorer. The green color of the name indicates this is the default head model for the current folder: you can decide to use another head model available by double clicking on its name.
Noise covariance
The recommendation for MEG is to extract basic noise statistics from empty-room recordings. When not available, as here, resting-state data can be used as proxies for MEG noise covariance. We will use a segment of the MEG recordings, away from the task and major artifacts: 18s-29s.
Right-click on the clean continuous file > Noise covariance > Compute from recordings.
Right-click on the Noise covariance (
) > Copy to other folders.
Inverse models
We will now compute three inverse models, with different source spaces: cortex surface with constrained dipole orientations (normal to the cortex), cortex surface with unconstrained orientation, and MRI volume (more information).
Cortical surface
Right-click on Overlapping spheres (surface) > Compute sources:
Minimum norm imaging
Current density map
Constrained: Normal to the cortex
Comment = MN: MEG (surface)
Repeat the previous step, but this time select Unconstrained in the Dipole orientations field.
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Volume
Right-click on the Overlapping spheres (volume) > Compute sources:
Current density map
Unconstrained
Comment = MN: MEG (volume)
Three imaging kernels (
) are now available in the database explorer. Note that each trial is associated with three source links (
). 
Coherence: EMG x Sources
We can now compute the coherence between the EMG signal and the brain source time series, for each of the source models. Let's start with the surface/constrained model.
To select the source maps we want to include in the coherence estimation, click on the Search Database button (
), and select New search. Set the parameters as shown below, and click on Search. 
- It creates a new tab in the database explorer, showing only the files that match the criteria.
Click the Process2 tab at the bottom of the main Brainstorm window.
Files A: Drag-and-drop the Left (192 files) group, select Process recordings (
). Files B: Drag-and-drop the Left (192 files) group, select Process sources (
). - Objective: Extract from the same files the EMG recordings (Files A) and the sources time series (Files B), then compute coherence between these two sets. Note that the blue labels over the file lists indicate that there are 185 "good" files (7 bad epochs).
Select the process Connectivity > Coherence AxB [2021]:
Time window = All file
Source channel (A) = EMGlft
Uncheck Use scouts (B)
Do not Remove evoked responses from each trial
Magnitude squared coherence
Window length = 0.5 s, Overlap = 50%
Highest frequency = 80 Hz
Average cross-spectra.
Add the process File > Add tag:
Tag to add = (surface)(Constr)
Select Add to file name
- Run the pipeline
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Repeat the steps above to compute the EMG-sources coherence for the other source models: surface/unconstrained and volume:
Edit the search criteria: Right-click on the search tab > Edit search.
- It updates automatically the file selection in the Process2 tab.
Select the processes: Do not forget to select again All file and update the file tag.
Close the search tab. If you don't see the 3 new connectivity files
) in the database explorer: refresh it, by pressing [F5] or clicking again on the selected button "Functional data".
Surface
Double-click the 1xN connectivity files for the two (surface) source space to show the results on the cortex. If you are not familiar with the options in the cortex figures, check Display: Cortex surface. Find the location and frequency with the highest coherence value.
In the Surface tab: Smooth=30%, Amplitude=0%.
To compare visually different cortex maps, set manually the colormap range (e.g.[0 - 0.07])
Explore with coherence spectra with the frequency slider
The highest coherence value is located at 14.65 Hz, in the right primary motor cortex (precentral gyrus). To observe the coherence spectrum at a given location: right-click on the cortex > Source: Power spectrum.
The analysis using constrained (top) and unconstrained (bottom) orientations agree in the location and frequency of the peak coherence. The main difference between these results is that unconstrained sources appear smoother, due to maximum aggregation performed across directions, explained later. These results agree with our hypothesis, previous results in the literature, and the results presented in the FieldTrip tutorial.
To get the 3D coordinates of the peak: right-click on the figure > Get coordinates. Then click on the right motor cortex with the crosshair cursor that appears. These coordinates can be useful to compare with the volume results.
Volume
Double-click the 1xN connectivity file for the (volume) source space.
- Go to 14.65 Hz, set the data transparency to 20% (Surface tab).
- Find the peak by navigating in the volume, or using the coordinates from the surface results.
Right-click on the figure > Anatomical atlas > None. This will show the coherence value under the cursor at the top-right corner, instead of an anatomical label.
Method
For constrained sources, each vertex in the source grid is associated with ONE time series, as such, when coherence is computed with the EMG signal (also one time series), the result is ONE coherence spectrum per vertex. In other words, for each frequency bin, there is a coherence brain map.
In the case of unconstrained or volume sources, each vertex in the grid is associated with THREE time series, each one corresponding to the X, Y and Z directions. Thus, when coherence is computed with the EMG signal (one time series), there are THREE coherence spectra. To be represented on the cortex, these three values need to be flattened into one, resulting in one coherence spectrum per vertex. For performing this dimension reduction, we decided to take the maximum across three directions, for each frequency bin for each vertex.
An alternative approach in the literature, to address the 3-dimensional nature of the unconstrained sources, consists in flattening the vertex X, Y and Z time series before the coherence computation; resulting in a similar case as the constrained sources. Common methods for this flattening include: PCA (only first component is kept), and (Euclidean) norm. This flattening of the time series can be performed in Brainstorm with the process: Sources > Unconstrained to flat map.
- Flattened sources are saved as full rather than recordings+kernel.
- We have tested this flattening approach with simulations and found detrimental effects on the expected results.
Coherence: EMG x Scouts
So far, we have computed coherence at the source level, thus, a coherence spectrum is computed for each of the 15002 source points. This large dimension hinders later analysis of the results. Therefore, the strategy is to reduce the dimensionality of the source space by using a surface- or volume-parcellation scheme, in Brainstorm jargon this is an atlas that is made of scouts. See the scout tutorial for detail information on atlases and scouts in Brainstorm.
Under this approach, instead of providing one result (coherence spectrum) per source vertex, one result is computed for each scout. When computing coherence (or other connectivity metrics) at the scout level, it is necessary to provide two parameters that define how the data is aggregated per scout: The scout function (mean is often used), and when the within-scout aggregation takes place (before or after the coherence computation).
Before: The scout function is applied for each direction on the vertices' source time series that make up a scout; resulting in one time series per direction per scout. Then, the scout time series are used to compute coherence with the reference signal (EMG in this tutorial), and the coherence spectra for each scout are aggregated across dimensions, as shown previously, to obtain one coherence spectrum per scout.
After: Coherence is computed between the reference signal and each direction of the vertices' source time series, as in the previous section. Then, the scout function is applied on the coherence spectra for each direction of the vertices within a scout, finally these spectra are aggregated across dimensions to obtain a coherence spectrum per scout. This option computes the coherence between the EMG and 45000 source signals, instead of a handful of times with the "before" option. The computation is therefore much longer and demanding in terms of RAM memory.
Let's here compute the coherence using scouts, using mean as scout function alongside with the Before option. We will use the Schaefer 100 parcellation atlas on the results from constrained sources.
Use Search Database (
) to select the Left trials with their respective (surface)(Constr) source maps, as shown in the previous section. In the Process2: Left trial group into both the Files A and Files B boxes. Select Process recordings (
) for Files A, and Process sources () for Files B. -
Open the Pipeline editor:
Add the process Connectivity > Coherence AxB [2021] with the following parameters:
Time window = 0 - 1000 ms or check All file
Source channel (A) = EMGlft
Check Use scouts (B)
From the menu at the right, select Schaefer_100_17net
- Select all the scouts
Scout function: Mean
When to apply the scout function: Before
Do not Remove evoked responses from each trial
Magnitude squared coherence, Window length = 0.5 s
Overlap = 50%
Highest frequency = 80 Hz
Average cross-spectra.
Add the process File > Add tag with the following parameters:
Tag to add = (surface)(Constr)
Select Add to file name
- Run the pipeline
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Open the output file by double-clicking on it. This time the coherence spectra are not displayed on the cortex, but they are plotted for each scout. Moreover, 1xN connectivity file can be shown as image.
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Note that for 14.65 Hz, the highest two peaks correspond to the SomMotA_4 R and SomMotA_2 R scouts, both located over the right primary motor cortex.
The choice of the optimal parcellation scheme for the source space is not easy, this is still an active field of research. The only recommendation we can give at the moment is to use regions of interest that are small and homogenous in size.
Additional documentation
Articles
Conway BA, Halliday DM, Farmer SF, Shahani U, Maas P, Weir AI, et al.
Synchronization between motor cortex and spinal motoneuronal pool during the performance of a maintained motor task in man.
The Journal of Physiology. 1995 Dec 15;489(3):917–24.Kilner JM, Baker SN, Salenius S, Hari R, Lemon RN.
Human Cortical Muscle Coherence Is Directly Related to Specific Motor Parameters.
J Neurosci. 2000 Dec 1;20(23):8838–45.Liu J, Sheng Y, Liu H.
Corticomuscular Coherence and Its Applications: A Review.
Front Hum Neurosci. 2019 Mar 20;13:100.Sadaghiani S, Brookes MJ, Baillet S.
Connectomics of human electrophysiology.
NeuroImage. 2022 Feb;247:118788.
Tutorials
Tutorial: Functional connectivity
Tutorial: Source estimation
Tutorial: Volume source estimation
Tutorial: Scouts
Tutorial: Connectivity graphs
Scripting
The following script from the Brainstorm distribution reproduces the analysis presented in this tutorial page: brainstorm3/toolbox/script/tutorial_coherence.m