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= Corticomuscular coherence (MEG) =
'''[TUTORIAL UNDER DEVELOPMENT: NOT READY FOR PUBLIC USE] '''

''Authors: Raymundo Cassani, Francois Tadel & 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 signal recorded from muscle activity during voluntary movement. This signal similarity is due mainly to the descending communication along corticospinal pathways between primary motor cortex (M1) and muscles. For consistency and reproducibility purposes across major software toolkits, the present tutorial replicates the processing pipeline "[[https://www.fieldtriptoolbox.org/tutorial/coherence/|Analysis of corticomuscular coherence]]" by FieldTrip.

<<TableOfContents(2,2)>>

== Background ==
[[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 cortico-muscular coherence effects in the 15–30 Hz range during maintained voluntary contractions.

IMAGE OF EXPERIMENT, SIGNALS and COHERENCE

== Dataset description ==
The dataset comprises recordings from MEG (151-channel CTF MEG system) and bipolar EMG (from left and right extensor carpi radialis longus muscles) from one participant who was tasked to lift their hand and exert 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 the left or right wrist. EOG signals were also recorded, which will be useful for detection and attenuation of ocular artifacts. We will analyze the data from the left-wrist trials in the present tutorial. Replicating the pipeline with right-wrist data is a good exercise to do next!

== Download and installation ==
 * '''Requirements''': Please make sure you have completed the [[Tutorials|get-started tutorials]] and that you have a working copy of  Brainstorm installed on your computer. In addition, you need to [[Tutorials/SegCAT12#Install_CAT12|install CAT12 plugin]] in Brainstorm. [[http://www.neuro.uni-jena.de/cat/index.html|CAT12]] will be used for MRI segmentation.
 * '''Download the dataset''':
  * Download `SubjectCMC.zip` from FieldTrip's FTP server:<<BR>> ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/SubjectCMC.zip
  * Unzip the .zip in a folder not located in any of current Brainstorm's folders (the app per se  or its database folder).
 * '''Brainstorm''':
  * Launch Brainstorm (via Matlab's command line or use Brainstorm's Matlab-free stand-alone version).
  * Select the menu '''''File > Create new protocol'''''. Name it `TutorialCMC` and select the options:<<BR>> '''No, use individual anatomy''', <<BR>> '''No, use one channel file per acquisition run'''.

The next sections describe how to import the participant's anatomical data, review raw data, manage event markers, pre-process EMG and MEG signals, epoch and import recordings for further analyzes, with a focus on computing coherence at the sensor (scalp) and brain map (sources) levels.

== Importing and processing anatomy data ==
 * Right-click on the newly created '''TutorialCMC''' node in your Brainstorm data tree then: '''''New subject > Subject01'''''.<<BR>>Keep the default options defined for the study (aka "protocol" in Brainstorm's jargon).

 * Switch to the '''Anatomy''' view of the protocol.
 * Right-click on the '''Subject01''' node then '''''Import MRI''''':
  * Select the adequate file format from the pull-down menu: '''All MRI file (subject space)'''
  * Select the file: `SubjectCMC/SubjectCMC.mri`

 * This will open the '''MRI viewer''' showing the coronal, sagittal and axial views of the MRI. In addition, [[CoordinateSystems|three anatomical fiducials]]: left and right pre-auricular points (LPA and RPA), and nasion (NAS) are automatically identifed.  These fiducials are located near the left/right ears and just above the nose respectively. Click on '''Save'''.

{{{#!wiki comment
 * Register the individual anatomy to  MNI brain space, for standardization of coordinates: in the '''MRI viewer''' click on '''Click here to compute MNI normalization''', use the '''maff8''' method. When the normalization is complete, verify that the locations of the anatomical fiducials are adequate (essentially that they are indeed near the left/right ears and right above the nose) and click on '''Save'''.
}}}
 . [[https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence?action=AttachFile&do=get&target=mri_viewer.png|{{attachment:mri_viewer.png|https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence?action=AttachFile&do=get&target=mri_viewer.png}}]]

We then need to segment the head tissues to obtain the surfaces required to derive a realistic MEG [[Tutorials/HeadModel|head model (aka "forward model")]]. Here, we will perform [[Tutorials/SegCAT12|MRI segmentation with CAT12]], this process takes between 30 to 60 minutes.

 * Right-click on the '''SubjectCMC''' MRI node, then '''''MRI segmentation > CAT12: Cortex, atlases, tissues'''''. This will prompt a series of windows to set the parameters for the MRI segmentation, use the following parameters:
  * '''Number of vertices on the cortex surface''' use `15000`
  * '''Compute anatomical parcellations?''' select `Yes`
  * '''Compute cortical maps''' select `Yes`

 . {{attachment:cat12.png||width="100%"}}

Once finished, multiple atlases or anatomical parcellations (ICON) will appear in the dataset tree alongside with surfaces for the head (head mask), white matter, cortex (pial envelope) and the midpoint between these last two. The default surfaces are indicated in green. You can display the surfaces by double-clicking on these new nodes. For further information on the anatomy files see the [[Tutorials/ExploreAnatomy|Display the anatomy tutorial]].

 . {{attachment:import_result.png||width="40%"}}

As part of the MRI segmentation pipeline with CAT12, the anatomy data was normalized in the MNI space, and several anatomical parcellations were computed. These parcellations can be used to create [[Tutorials/TutVolSource#Volume_atlases|volume]] and [[Tutorials/Scouts|surface scouts]], which will be used later in this tutorial to perform the coherence analysis in the source level.

{{{#!wiki note
Additional '''MNI parcellation templates''' to define anatomical regions of the brain can be used in Brainstorm for MNI-normalized MRI anatomy. See [[Tutorials/DefaultAnatomy#MNI_parcellations|MNI parcellations]]
}}}
== Review the MEG and EMG recordings ==
=== Link the recordings to Brainstorm's database ===
 * Switch now to the '''Functional data''' view (X button).
 * Right-click on the '''Subject01''' node then '''''Review raw file''''':
  * Select the file format of current data from the pulldown menu options: '''MEG/EEG: CTF(*.ds; *.meg4; *.res4)'''
  * Select the file: `SubjectCMC.ds`

A new folder is now created in Brainstorm's database explorer and contains:

 * '''SubjectCMC''': a folder that provides access to the MEG dataset. Note the "RAW" tag over the icon of the folder, indicating the files contain unprocessed, continuous data.
 * '''CTF channels (191)''': a node containing '''channel information''' with all channel types, names locations, etc. The number of channels available (MEG, EMG, EOG etc.) is indicated between parentheses''' (here, 191''').
 * '''Link to raw file''' provides access to '''to the original data file'''. All the relevant metadata was read from the dataset and copied inside the node itself (e.g., sampling rate, number of time samples, event markers). Note that Brainstorm's logic is not to import/duplicate the raw unprocessed data directly into the database. Instead, Brainstorm provides a link to that raw file for further review and data extraction ([[Tutorials/ChannelFile#Review_vs_Import|more information]]).

 . {{attachment:review_raw.png}} <<BR>>

=== Display MEG helmet and sensors ===
 * Right-click on the '''CTF channels (191)''' node, then select '''''Display sensors > CTF helmet''''' from the contextual menu and '''''Display sensors > MEG. '''''This will open a new display window showing the inner surface of the MEG helmet, and the lo MEG sensors respectively. Try [[Tutorials/ChannelFile#Display_the_sensors|additional display menus]].

 . {{attachment:helmet_sensors.png}}

=== Reviewing continuous recordings ===
 * Right-click on the '''Link to raw file''' node, then '''''Switch epoched/continuous''''' to convert the file to '''continuous''', a technical detail proper to CTF file formatting.
 * Right-click again on the '''Link to raw file''' node, then '''''MEG > Display time series''''' (or double-click on the node). This will open a new visualization window to explore data time series, also enabling the '''''Time''''' panel and the '''''Record''''' tab in the main Brainstorm window (see how to best use all controls in this panel and tab to [[Tutorials/ReviewRaw|explore data time series]]).
 * We will also display EMG traces by right-clicking on the '''Link to raw file''' node, then '''''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 above the data time series indicate [[Tutorials/EventMarkers|event markers]] (or triggers) saved with this dataset. The trial onset information of the left-wrist and right-wrist trials is saved in an auxiliary channel of the raw data named '''Stim'''. To add these markers, these events need to be decoded as follows:

 * While the time series figure is open, go to the '''''Record''''' tab and '''''File > Read events from channel'''''. From the options of the '''Read from channel''' process window, set '''Event channels''' = `Stim`, select '''Value''', and click '''Run'''.

 . {{attachment:read_evnt_ch.png}}

This procedure creates new event markers 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 how each of the 25 left-wrist trials had been encoded in the study. We will now delete other events of no interest, and merge the left trial events under a single event category, for convenience.

 * Delete other events: select the events to delete in the event box/list with '''Ctrl+click''', then in the menu '''''Events > Delete group''''' and confirm. Alternatively, you can selected all events with '''Ctrl+A''' and deselect the '''U1''' to '''U25''' events by clicking on them.
 * To make sure we reproduce FieldTrip's tutorial, we need to reject trial #7: Select events '''U1''' to '''U6''' and '''U8''' to '''U25''', then from the '''Events '''menu, select''' Merge group''' and type in new label ('''Left_01''') to describe this as the left-wrist condition.

 . {{attachment:left_24.png}}

These events correspond to the beginning of 10-s trials of left-wrist movements. We will compute coherence over 1-s epochs over the first 8 s of each trial. To that purpose, we will now create extra events to define these epochs.

 * Duplicate 7 times the '''Left''' events by selecting '''''Duplicate group''''' in the '''''Events''''' menu. The groups '''Left_02''' to '''Left_08''' will be created.
 * For each copy of the '''Left''' events, we will add a time offset of 1 s for '''Left02''', 2 s for '''Left03''', and so on. Select the '''Left '''event group to add a 1,000 ms time offset, by going to the menu '''''Events > Add time offset'', '''enter 1,000 in the text box. Repeat for each other group, entering 2,000, then 3,000 etc.

 . {{attachment:dup_offset.png}}

 * Once done for '''Left_08''', merge all these '''Left*''' events into a single '''Left '''category, and select '''''Save modifications''''' in the '''''File''''' menu in the '''''Record''''' tab.

 . {{attachment:left_192.png}}

{{{#!wiki comment
=== Keep relevant recordings ===
As only data for the left wrist will be analyzed, we will import only the first '''330 s''' of the original file and rewrite that segment as a binary continuous file, a raw file. This will help to optimize computation times and memory usage.

 * In the Process1 box: Drag and drop the '''Link to raw file''' node inside '''SubjectCMC'''.
 * Run process '''Import > Import recordings > Import MEG/EEG: Time''':<<BR>>
  * '''Subject name'''=`Subject01`, '''Condition name'''= `Left`, '''Time window'''=`0.0 - 330.0 s`, '''Split recordings'''=`0`, and check the three remaining options.<<BR>>
 . {{attachment:import330_process.png||width="50%"}}

 * Right-click on the '''Raw(0.00s,330.00s)''' node inside the newly created '''Left''' condition and select '''Review as raw'''. This will crate the condition '''block001''' with the link to the created raw file.

 . {{attachment:review_as_raw.png||width="50%"}}

 * To avoid any confusion later, delete the conditions '''SubjectCMC''' (which is a link to the original file), and the condition '''Left'''. Select both folders containing and press Delete (or right-click '''File > Delete''').
}}}
== Pre-process ==
{{{#!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 recordings, where the left-wrist trials were performed.
}}}
Another idiosyncrasy of the present dataset is that the CTF MEG data were saved without the desired 3-rd order gradient compensation for optimal denoising. We will now apply this compensation as follows:

 * In the '''''Process1''''' box: Drag and drop the '''Link to raw file''' node.
 * Run process '''''Artifacts > Apply SSP & CTF compensation''''':<<BR>>

 . {{attachment:pro_ctf_compensation.png||width="50%"}}

This process creates the '''SubjectCMC_clean''' folder that contains a copy of the '''channel file''' and a link to the raw file '''Raw | clean''', which points to the original data and to the fact that the 3-rd order gradient compensation will be applied. Brainstorm does not create a physical copy of the actual, large dataset at this stage.

 . {{attachment:tre_raw_clean.png||width="40%"}}

=== Removal of power line artifacts ===
We will start with identifying the spectral components of power line contamination of MEG and EMG recordings.

 * In the '''''Process1''''' box: Drag and drop the '''Raw | clean''' node.
 * 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="50%"}}

 * 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. Peaks at 50Hz and harmonics (150, 200Hz and above; European power line main and  harmonics) are clearly visible. We will use notch filters to attenuate power line contaminants at 50, 150 and 200 Hz.
 * In the '''''Process1''''' box: Drag and drop the '''Raw | clean''' node.

 * Run the process '''''Pre-processing > Notch filter''''' with: <<BR>>
  * '''Sensor types''' = `MEG, EMG`
  * '''Frequencies to remove (Hz)''' = `50, 100, 150`

 . {{attachment:pro_notch.png||width="50%"}}

A new '''raw''' folder named '''SubjectCMC_clean_notch''' is created. Estimate the PSD of these signals to appreciate the effect of the notch filters applied. As above, please remember to indicate a '''Time window''' restricted from 0 to 330 s in the options of the PSD process.

 . {{attachment:psd_after_notch.png||width="70%"}}

=== EMG pre-processing ===
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%"}}

Two new folders '''SubjectCMC_clean_notch_high''' and '''SubjectCMC_clean_notch_high_abs''' are added to Brainstorm's database explorer. We can now safely delete folders that are not needed anymore:

 * Delete '''SubjectCMC_clean_notch''' and '''SubjectCMC_clean_notch_high '''by selecting both before pressing Delete (or right-click '''''File > Delete''''').

=== MEG pre-processing ===
We need to remove more artifacts from the MEG traces via the:

 1. '''Detection and removal of stereotypical artifacts with SSP'''

 1. '''Detection of noisy (bad) data segments.'''

==== Detection and removal of artifacts with SSP (Signal Space Projection) ====
Stereotypical artifacts such eye blinks and heartbeats can be identified from their respective characteristic spatial distributions. Their contaminationn of MEG signals can then be attenuated specifically using Signal-Space Projections (SSPs). For more details, consult the dedicated tutorials 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 perform only the removal of eye blinks.

 * Display the MEG and EOG time series: Right-click on the pre-processed (for EMG) continuous file '''Raw | clean | notch(...''' (in the '''SubjectCMC_clean_notch_high_abs''' folder) then '''''MEG > Display time series''''' and '''''EOG > Display time series'''''.

 * In the '''Events''' section of the '''''Record''''' tab, select '''''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="50%"}}

 * Three categories of blink events are created. Review the traces of 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 saccade events.

 . {{attachment:blinks.png||width="70%"}}

 * To [[Tutorials/ArtifactsSsp|remove blink artifacts with SSP]] go to '''''Artifacts > SSP: Eye blinks''''', and use the parameters:
  * '''Event name'''=`blink`
  * '''Sensors'''=`MEG`
  * Check '''Compute using existing SSP/ICA projectors'''

 . {{attachment:ssp_blink_process.png||width="50%"}}

 * Display the time series and topographies of the first two (dominant) SSP components identified. In the present case, only the first SSP component can be clearly related to blinks. Select only component #1 for removal.

 . {{attachment:ssp_blink.png||width="100%"}}

 * Follow the same procedure for the other blink events ('''blink2''' and '''blink3'''). As mentioned above, none of the first two SSP components seem to be related to ocular artifacts. The figure below shows the visualization of the first two components for the '''blink2''' group.

 . {{attachment:ssp_blink2.png||width="100%"}}

 . We therefore recommend to unselect the '''blink2''' and '''blink3''' groups from the '''Select Active Projectors''' panel (see below) rather than removing spatial components which nature remains ambiguous.

 . {{attachment:ssp_active_projections.png||width="60%"}}

 * Click on the large crosshair at the top right of the main Brainstorm window to close all visualization windows.

==== 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 and 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="50%"}}

We encourage users to review and validate the segments marked using this procedure. In the present case, the segments detected as bad clearly point at contaminated MEG data segments, which we will now label these as "bad".

 * Select the '''1-7Hz''' and '''40-240Hz''' event groups and select '''Events > Mark group as bad''' from the contextual menu. Alternatively, you can also rename the events created above and append the '''bad_''' prefix to their name: 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.

== Importing data epochs ==
At this point we are finished with the pre-processing of the EMG and MEG recordings. We will now extract and import specific data segments of interest into the Brainstorm database for further derivations. We refer to these segments as '''epochs''' or '''trials'''. As mentioned previously, we will focus on the '''Left''' (wrist) category of events.

 * Right-click on the filtered continuous file '''Raw | clean | notch(...''' (in the '''SubjectCMC_clean_notch_high_abs''' condition), then '''''Import in database'''''.

 . {{attachment:import_menu.png||width="40%"}}

 * Enter the following parameter values:
  * '''Time window''' = `0 - 330 s`
  * Check '''Use events''' and highlight the '''Left(x192)''' event group
  * '''Epoch time''' = `0 - 1000 ms`
  * Check '''Apply SSP/ICA projectors'''
  * Check '''Remove DC offset''' and select '''All recordings'''

 . {{attachment:import_options.png||width="80%"}}

A new folder '''SubjectCMC_clean_notch_high_abs''' is created for '''Subject01'''. It contains a copy of the '''channel file''' from the original raw file, and individual trials tagged as '''Left '''in a new trial group. Expand the trial group and note there are trials marked with a question mark in a red circle (ICON). These indicate trials that occurred in the '''bad''' segments identified in the previous section. All the bad trials are automatically ignored for further processing, whenever dropped into the '''''Process1''''' and '''''Process2''''' tabs.

 . {{attachment:trials.png||width="40%"}}

== Coherence estimation (sensor level) ==
We will now compute the '''magnitude square coherence (MSC)''' between the '''left EMG''' signal and each of the MEG sensor data.

 * In the '''''Process1''''' box, drag and drop the '''Left (192 files)''' trial  group. Note that the number between square brackets is '''[185]''', as the 7 '''bad''' trials will be ignored by the MSC process.
 . {{attachment:dragdrop_trialgroup.png||width="40%"}}

 * Run the process '''''Connectivity > Coherence 1xN [2021]''''' with the following parameters:
  * '''Time window''' = `0 - 1000 ms` or check '''All file'''
  * '''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]].

 . {{attachment:coh_meg_emgleft.png||width="40%"}}

 * Double-click on the resulting node '''mscohere(0.6Hz,555win): EMGlft''' to display the MSC spectra. Click on the maximum peak in the 15 to 20 Hz range, and press `Enter` to plot it in a new figure. This spectrum corresponds to channel '''MRC21''', and shows a large peak at 17.58 Hz. You can also use the frequency slider (under the '''''Time''''' panel) to explore the MSC output more precisely 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 magnitude of the MSC across a frequency band of interest (15-20 Hz):

 * In the '''''Process1''''' box, drag-and-drop the '''mscohere(0.6Hz,555win): EMGlft''' node, and add the process '''''Frequency > Group in time or frequency bands''''' with the parameters:
  * Select '''Group by frequency'''
  * Type `cmc_band / 15, 20 / mean` in the text box.

 . {{attachment:pro_group_freq.png||width="40%"}}

The resulting file '''mscohere(0.6Hz,555win): EMGlft | tfbands''' has only one MSC value for each sensor (the MSC average in the 15-20 Hz band). You may visualize the topography of this MSC statistics via 3 possible representations: '''2D Sensor cap''', '''2D Sensor cap''' and '''2D Disk''', which are all accessible via a right-click over the MSC node. We clicked on sensor '''MRC21''' below; it is shown in red.

 . {{attachment:res_coh_meg_emgleft1520.png||width="100%"}}

We can observe higher MSC values between the EMG signal and MEG sensor signals over the contralateral set of central sensors in the beta band. Unfortunately, [[Tutorials/Connectivity#Sensor-level|sensor-level connectivity present the disadvantages]] of: not being interpretable, and being subject to spurious results due to volume conduction.

In the next section we will compute coherence in the source level. To do this, we first need to estimate the sources time series from the sensor data.

== Source estimation with MEG signals ==
With [[Tutorials/SourceEstimation|source estimation]] we aim to find the sources that gave origin to the signals registers in the sensors. From the diverse [[Tutorials/SourceEstimation#Method|source estimation methods available in Brainstorm]], in this tutorial the '''minimum-norm imaging''' method is used. There source grid (either cortical surface or full brain volume) is defined and the minimum-norm method estimates the current at each point in the grid to explain the recorded sensor signals favouring minimum energy (L2-norm) solutions. Before estimating the brain sources, we need to derive the sensor '''noise covariance matrix''', and the '''head model'''.

{{{#!wiki note
At each point in the source grid, the current dipole may point arbitrarily in  direction in a 3D space. '''Only for surface grids''', that orientation can be fixed to be normal to the cortical surface, this approach is based on anatomical observartions of the brain cortex. The result is then in a smaller model that is faster to compute and display. As discussion on '''constrained''' vs '''unconstrained''' sources is presented [[Tutorials/SourceEstimation#Why_does_it_look_so_noisy.3F|here]].
}}}
 
=== Noise covariance ===
The [[Tutorials/NoiseCovariance#The_case_of_MEG|recommendation for MEG]], is to extract basic noise statistics from empty-room recordings. However, when recommended empty-room recordings are not available, as with this tutorial data, resting-state data can be used as proxies for MEG noise covariance. See the [[Tutorials/NoiseCovariance|noise covariance tutorial]] for more details.

 * In the raw '''SubjectCMC_clean_notch_high_abs '''node, right-click over '''Raw | clean | notch(...'''and select '''''Noise covariance > Compute from recordings'''''. Please enter the following parameters:
  * '''Baseline:''' from `18 to 30 s`
  * Select the '''Block by block''' option.

 . {{attachment:pro_noise_cov.png||width="60%"}}

 * Copy the '''Noise covariance''' node to the '''SubjectCMC_clean_notch_high_abs''' folder. This can be done using the shortcuts `Ctrl-C` and `Ctrl-V`.

 . {{attachment:tre_covmat.png||width="50%"}}

=== Head model ===
The [[Tutorials/HeadModel|head model]], aka forward model, accounts for how neural electrical currents (in a source space) produce magnetic fields captured by sensors outside the head, considering head tissues electromagnetic properties and geometry, independently of actual empirical measurements. As the head model depends on the source space, a distinct head model is required for the surface and volume source space. Please refer to the [[Tutorials/HeadModel|head model tutorial]] for more in-depth explanations.

==== Surface ====
Instructions.

==== Volume ====
Instructions.

=== Source estimation (Surface) ===

==== Constrained ====

==== Unconstrained ====

=== Source estimation (Volume) ===

== Coherence estimation (source level) ==
=== Surface ===
 * Instructions for constrained  
 * Instructions for unconstrained

=== Volume ===
 * Instruction

=== Comparison ===
The results. Compare the 3, and the maximum point (How to find this?) Note: Unconstrained sources and volume model, the sources are 3 dimensional.  Coherence is computed between the reference signal (EMGlft) and each dimension, to plot the value of coherence is the flatted as PROCEDURE

As alternative we could flatten first the unconstrained sources, and the compute coherence, however, this is not the best approach. Show the results for the PCA.

Here we can add the results and recommendations.

As we mentioned, there is a coherence spectrum for each of the 15k sources. This is not practical. For that reason often the analysis is performed with the use of ROIs. The definition of ROIs is a current problem that is not solved here.

== Coherence estimation (Scout level) ==
Here we will be working only with the surface unconstrained data.  We will use the xxx atlas for our calculations

Place, EMGlft and sources, selected scouts, and after and before.  Explain the difference between both metrics, the advantages regarding processing. If possible add diagrams

== Connectivity NxN (connectome) ==
Here we want to write about performing NxN connectivity with the scouts. This should not be done with sources as it leads to a very big matrix that will not fit in the RAM

Also we need to define several parameters in our experiments:  - source estimation method - source estimation surface or volume - if surface constrained or unconstrained - How to select the scouts  - How to perform the aggregation across scouts (before or after) - Which function to use for the aggregation

All those are open questions that are not addressed in this tutorial nor in the literature.

<<BR>>

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== MEG source imaging ==
We will perform source modelling using a [[Tutorials/HeadModel#Dipole_fitting_vs_distributed_models|distributed model]] approach for two possible source maps:  the '''cortex surface''' and the entire '''MRI volume'''.

For the cortical source model, the locations of the sources are constrained to the cortical surface obtained from the participants anatomical MRI, as imported above. For MRI volume approach, elementary sources are uniformly distributed across the entire brain volume. Before estimating the brain sources, we need to derive a '''head model''' and estimate the '''noise covariance '''of the recordings. Note that a distinct head model is required for each source space tested here (cortical vs. volume).

=== Head modelling ===
The head model accounts 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. Please refer to the [[Tutorials/HeadModel|head model tutorial]] for more in-depth explanations.

==== Cortical surface ====
 * In the '''SubjectCMC_clean_notch_high_abs '''node, right-click over '''CTF channels (191)''' and select '''Compute head model '''from the contextual menu. Run the process with the options as indicated below:
  * '''Comment''' = `Overlapping spheres (surface)`
  * '''Source space''' = `Cortex surface`
  * '''Forward model''' = `Overlapping spheres`.

The cortical head model will be derived from each of the 15,000 sources (surface vertices) as defined when when the subject anatomy was imported.

 . {{attachment:pro_head_model_srf.png||width="40%"}}

The (ICON) '''Overlapping spheres (surface)''' head model now appears in the database explorer.

==== MRI volume source model ====
 * In the '''SubjectCMC_clean_notch_high_abs '''node, right-click over the '''CTF channels (191)''' node and select '''''Compute head model'''''. Set the option values to:
  * '''Comment''' = `Overlapping spheres (volume)`
  * '''Source space''' = `MRI volume`
  * '''Forward model''' = `Overlapping spheres`.

 . {{attachment:pro_head_model_vol.png||width="40%"}}

 * In the '''Volume source grid''' window, specify the following parameters that will produce about '''12,200''' elementary source grid points across the brain volume.
  * Select '''Regular grid''' and '''Brain'''
  * '''Grid resolution''' = `5 mm`

 . {{attachment:pro_grid_vol.png||width="50%"}}

The '''Overlapping spheres (volume)''' node is now added to the database explorer. The green color indicates this is the default head model for the current folder (this can be changed by simply double clicking over the head model  nodes.)

 . {{attachment:tre_head_models.png||width="50%"}}

=== Noise covariance ===
Basic noise statistics can be extracted (as [[Tutorials/NoiseCovariance#The_case_of_MEG|recommended]]) from empty-room recordings. However, these latter are not available from the present tutorial data. However, we will assume that data segments prior to wrist extension can be used as proxies for MEG noise covariance. See the [[Tutorials/NoiseCovariance|noise covariance tutorial]] for more details.

 * In the raw '''SubjectCMC_clean_notch_high_abs '''node, right-click over '''Raw | clean | notch(...'''and select '''''Noise covariance > Compute from recordings'''''. Please enter the following parameters:
  * '''Baseline:''' from `18 to 30 s`
  * Select the '''Block by block''' option.

 . {{attachment:pro_noise_cov.png||width="60%"}}

 * Lastly, copy the '''Noise covariance''' node to the '''SubjectCMC_clean_notch_high_abs''' folder along with the head model. This can be done using the shortcuts `Ctrl-C` and `Ctrl-V`.

 . {{attachment:tre_covmat.png||width="40%"}}

=== Source estimation ===
Now that the '''head model(s)''' and '''noise covariance''' are available, we will use the [[Tutorials/SourceEstimation#Method|minimum-norm imaging]] approach to solve the so-called '''inverse problem''' of source estimation. This will produce a large matrix called the '''imaging kernel''', that will be multiplied to the sensor data, to produce estimates of brain source time series. A different imaging kernel is derived for each of the head models we have produced above:  '''surface''' and '''volume'''. See the [[Tutorials/SourceEstimation|source estimation tutorial]] for more details.

==== Cortical surface ====
 * To compute the corresponding imaging kernel, right-click over the '''Overlapping spheres (surface)''' head model and select '''Compute sources [2018]. '''Enter the following parameters:
  * '''Minimum norm imaging'''
  * '''Current density map'''
  * '''Unconstrained'''
  * '''Comment''' = `MN: MEG (surface)`

 . {{attachment:pro_sources_srf.png||width="40%"}}

The inversion kernel (ICON) '''MN: MEG (surface)(Unconstr) 2018''' is now available in the database explorer.

==== MRI volume ====
 * Compute the corresponding imaging kernel by right-clicking over the '''Overlapping spheres (volume)''' head model and select '''Compute sources [2018], '''with the following parameters:
  * '''Minimum norm imaging'''
  * '''Current density map'''
  * '''Unconstrained'''
  * '''Comment''' = `MN: MEG (volume)`

 . {{attachment:pro_sources_vol.png||width="40%"}}

The imaging kernel (ICON) '''MN: MEG (volume)(Unconstr) 2018''' is now also available in the database explorer.

Note that now each trial is associated with '''two''' source link (ICON) nodes. One corresponds to the '''MN: MEG (surface)(Unconstr) 2018''' kernel and the other to the '''MN: MEG (volume)(Unconstr) 2018''' kernel.

 . {{attachment:gui_inverse_kernel.png||width="60%"}}

=== Defining "scouts" (regions of interest) ===
To contain computational cost, we will now restrict the computation of coherence with the left EMG signal to selected MEG source activity. We will define regions of interest, whic are known as '''scouts '''in Brainstorm. They can be defined as [[Tutorials/Scouts|surface]]or [[Tutorials/TutVolSource#Volume_scouts|volume scouts]].

==== Surface scouts ====
 * Right click over '''MN: MEG (surface)(Unconstr) 2018''' for one of the trials and select '''''Cortical activations > Display on cortex'''''. In the '''''Surface''''' tab, set the '''''Amplitude''''' slider to `100%` to hide all the sources.

 . {{attachment:fig_sources_srf.png||width="100%"}}

 * In the '''''Scout''''' tab, select from the menu '''''Atlas > From subject anatomy > AAL3 (MNI-linear)'''''. This will create the '''From volume: AAL3''' set of surface scouts. After you click on any scout label shown in the list, Brainstorm will show at the bottom the number of sources (vertices) within the region and an estimate of its surface area in cm2. Activate the (ICON) '''Show only the selected scouts''' option to shown only the scout(s) you have selected from the list.

 . {{attachment:fig_scouts_srf.png||width="90%"}}

{{{#!wiki caution
[TODO] A note, that the definition of scouts is far from perfect, but can give us a good idea of the surface projections of the MNI parcellations (described in the importing anatomy section).
}}}
 * Close the figure.

==== Volume scouts ====
 * Right click over '''MN: MEG (volume)(Unconstr) 2018''' for one of the trials and select '''''Cortical activations > Display on MRI (3D): Subject CMC'''''. In the '''''Surface''''' tab, set the '''''Amplitude''''' slider to `100%` to hide all the source map.

 . {{attachment:fig_sources_vol.png||width="100%"}}

 * In the '''''Scout''''' tab, select the menu '''''Atlas > From subject anatomy > AAL3 (MNI-linear)'''''. This will create a set of '''Volume 12203: AAL3''' volumic scouts. As with the surface scouts above, clicking on a scout in the list will show the number of elementary sources withinand its volume in cm3. Activate the (ICON) '''Show only the selected scouts''' option to show only the selected scout(s).

 . {{attachment:fig_scouts_vol.png||width="90%"}}

 * Close the figure.

== Estimating source-wise coherence ==
=== Surface scouts ===
We will use the [[Tutorials/PipelineEditor#Search_Database|search features of the Brainstorm database]] to select the source maps we want to include in the EMG-cortex coherence estimation. We will first select files related to the '''MN: MEG (surface)(Unconstr) 2018''' imaging kernel.

 * Click on the magnifying glass (ICON) above the database explorer to open the database search panel, and select '''''New search'''''.

 * Set the search parameters as shown below:

 . {{attachment:gui_search_srf.png||width="70%"}}

After pressing '''Search''', a new tab called '''''(surface)''''' appears in the database explorer. This new tab contains the data filtered through the search query above.

 . {{attachment:tre_search_srf.png||width="40%"}}

 * Click the '''Process2''' tab at the bottom of the main Brainstorm window and drag-and-drop the '''Left (192 files)''' trial group into the '''Files A box '''and repeat for the '''Files B''' '''box'''. Select '''Process recordings''' for Files A, and '''Process sources''' for Files B. The logic is that we will extract from the same files the EMG traces (Files A) and the source time series (Files B) and then compute coherence between these two sets. Note that blue labels over the '''Files A''' and the '''Files B''' boxes indicate that there are 185 "good trial" files per box.

 . {{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)'''
  * Select `From volume: AAL3` in the drop-down list (these are surface scouts)
  * Select all the scouts (shortcut `Ctrl-A`)
  * '''Scout function''' = `Mean`
  * '''When to apply''' = `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)`
  * Select '''Add to file name'''

 * Run the pipeline

 . {{attachment:pro_coh_srf.png||width="100%"}}

 * Double-click on the resulting node '''mscohere(0.6Hz,555win): Left (#1) | (surface)''' to display the coherence spectra. Open also the result node as an image with '''Display image''' from its contextual menu.

 * To visualize the location of the scouts on the cortex, double-click one of the (surface) source links for any of the trials. In the '''Surface''' tab, set the '''Amplitude''' threshold to `100%` to hide the cortical activations. Lastly, in the '''Scouts''' tab, select the `From volume: AAL3` atlas in the drop-down list, select '''Show only the selected scouts''' and the '''Show/hide the scout labels'''. Note that all visualization windows are linked depending on which scout is selected in the '''image''' representation of the coherence results.

 . {{attachment:res_coh_srf.png||width="100%"}}

The large peak at 14.65 Hz in the coherence spectra corresponds to the '''Precentral R''' scout, which encompasses the right primary motor cortex, as expected.

=== Volume scouts ===
We will repeat the same approach Similar for volume scouts. Iniate a file selection query related to the '''MN: MEG (volume)(Unconstr) 2018''' imaging kernel.

 * Click on the magnifying glass (ICON) above the database explorer to open the search panel, with the following specifications:

 . {{attachment:gui_search_vol.png||width="70%"}}

 . {{attachment:tre_search_vol.png||width="40%"}}

 * In the '''Process2''' tab, drag and drop the '''Left (192 files)''' trial group into the '''Files A '''box and repeat for the '''Files B''' box. Select the '''Process recordings''' icon for Files A, and '''Process sources''' 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)'''
  * Select `Volume 12203: AAL3` in the drop-down list (these are volume scouts)
  * Select all the scouts (shortcut `Ctrl-A`)
  * '''Scout function''' = `Mean`
  * '''When to apply''' = `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)`
  * Select '''Add to file name'''

 * Run the pipeline

 . {{attachment:pro_coh_vol.png||width="100%"}}

 * Double-click on the resulting node '''mscohere(0.6Hz,555win): Left (#1) | (volume)''' to display the coherence spectra. Open also the result node by selecting '''Display as image''' from its contextual menu.

 * Open one of the (volume) source links for any of the trials by selecting from the contextual menu '''''Display cortical activations > Display on MRI (3D): SubjectCMC '''''.  In the '''Surface''' tab, set the '''Amplitude''' threshold to `100%` to hide all the cortical activations. Lastly, in the '''Scouts''' tab, select the `Volume 12203: AAL3` atlas in the drop-down list, select the '''Show only the selected scouts''' and the '''Show/hide the scout labels'''.

 . {{attachment:res_coh_vol.png||width="100%"}}

Here too, the coherence peak at 14.65 Hz corresponds to the '''Precentral R''' scout, which encompasses the right primary motor cortex, as expected.

<<TAG(Advanced)>>

== Brain-wise coherence estimation (no scouts) ==
{{{#!wiki caution
 * We could downsample the surface and  create a more sparse volume grid
 . OR
 * Refactor the coherence process to accumulate the auto- and cross-spectra outside of the function
 . OR
}}}
=== Comparison of cortical surface with FieldTrip and CAT ===
{{{#!wiki caution
'''[TO DISCUSS among authors]''' This image and GIF are just for reference. They were obtained with all the surface sources using FieldTrip and CAT derived  surfaces.

Comparison for 14.65 Hz

{{attachment:ft_vs_cat.png||width="100%"}}

Sweeping from 0 to 80 Hz

{{attachment:ft_vs_cat.gif||width="80%"}}
}}}
<<TAG(Advanced)>>

== Script ==
{{{#!wiki caution
'''[TO DO]''' Once we agree on all the steps above.
}}}
== Additional documentation ==
==== Articles ====
 * 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.

==== Tutorials ====
 * Tutorial: [[Tutorials/TutVolSource|Volume source estimation]]
 * Tutorial: [[Tutorials/Connectivity|Functional connectivity]]

==== Forum discussions ====
{{{#!wiki caution
'''[TO DO]''' Find relevant Forum posts.
}}}
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