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| ''Authors: Francois Tadel, John C Mosher, Richard Leahy, Sylvain Baillet'' | ''Authors: Francois Tadel, Elizabeth Bock, John C Mosher, Richard Leahy, Sylvain Baillet'' |
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| The source estimation methods we use need some metrics computed from the recordings. The minimum norm solution requires an estimation of the noise level in the recordings ('''noise covariance matrix''') and the beamformers need additionally a prototype of the effect we are targetting ('''data covariance matrix'''). This first section of this tutorial shows how to compute a noise covariance matrix from the MEG empty room recordings. The details that follow can be skipped if you are not interested. | Modeling and measuring certain characteristics of the noise contaminating the data is beneficial to source estimation. For instance, minimum norm estimators can integrate second-order sample statistics of sensor noise (summarized into a '''noise covariance matrix''', see below). Beamformers further require similar sample statistics for the data portion of interest (summarized into a '''data covariance matrix'''). This first section of this tutorial explains how to obtain a noise covariance estimate from MEG empty room recordings. |
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| == Compute the noise covariance == Ideally, we want to represent only the noise of the sensors. In MEG, this is easy to obtain with a few minutes of empty room measurements. The only constrain is to use noise recordings that have been acquired the same day as the subject's recordings (if possible just before) and pre-processed in the same way (same sampling rate and frequency filters). In this study we have already prepared a segment of 2min of noise recordings, we will estimate the noise covariance based on it. |
== Noise covariance == Instrumental noise ("sensor noise") can be readily captured in MEG using two or more minutes of empty room measurements. We encourage the use of noise recordings collected the same day as the subject's recordings (if possible just before the session) and pre-processed in the same manner (with same sampling rate and same frequency filters applied) as the participant data. In this study we have already prepared a 2-min segment of noise recordings that we will use to estimate noise covariance sample statistics. |
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| Right-click on the link to the '''noise recordings''' '''> Noise covariance'''. Available menus: | Right-click on the entry for '''noise recordings''' '''> Noise covariance'''. Available menus: |
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| * '''Import from file''': Use a matrix that was computed previously using the MNE software. * '''Import from Matlab''': Import from any [nChannels x nChannels] matrix from the Matlab workspace. * '''Compute from recordings''': Use the selected recordings to estimate the noise covariance. * '''No noise modeling''': Use an identity matrix as the noise noise covariance. Useful when you don't have access to noise recordings (eg. ongoing EEG activity or simulations). <<BR>><<BR>> {{attachment:noisecov_popup.gif||height="267",width="474"}} |
* '''Compute from recordings''': Use the selected recordings to estimate noise covariance statistics. * '''No noise modeling''': Use an identity matrix as noise covariance. This option is useful when no noise recording is available (e.g. ongoing EEG without any baseline of no interest). * '''Import from file''': Use noise covariance statistics available from another source (e.g., obtained using the MNE software.) * '''Import from Matlab''': Import any [Nchannels x Nchannels] matrix as noise covariance matrix from the Matlab workspace. <<BR>><<BR>> {{attachment:noisecov_popup.gif||width="408",height="231"}} |
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| * '''Data selection''': The top part of this window shows a summary of the files that have been selected to estimate the noise: 1 file of 120s at 600Hz. Total number of time samples: 72,000. We can chose to use only a part of this file with the option "baseline". The large chunks of continuous files are split in blocks of a maximum of '''10,000 samples''', that are then processed as different files. | * '''Files''': The top part of this window shows a summary of the files that have been selected to estimate the noise: 1 file of 120s at 600Hz. Total number of time samples in selected file: 72,000. We can also choose to use only a portion of this file, with the option "baseline". The large continuous files are split in blocks of a maximum of '''10,000 samples''' that are then processed as different files. |
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| * '''Remove DC offset''': All the selected blocks of data are baseline corrected and concatenated to form a large matrix "F". There are two options for the baseline correction:<<BR>>'''Block by block''': The average value is subtracted from each block before the concatenation. <<BR>>If Fi is the recordings corresponding to block #i: F = Concatenate[Fi - mean(Fi)].<<BR>>'''Global''': The average value is removed after concatenation (same correction for all blocks). <<BR>>F = Concatenate[Fi] - mean(Concatenate[Fi]). | * '''Remove DC offset''': All the selected blocks of data are baseline corrected and concatenated to form a large matrix "F". There are two options for baseline correction: * '''Block by block''': The average value of each channel is subtracted from each block before concatenating files together. Let Fi contain data from block #i: <<BR>>F = Concatenate[Fi - mean(Fi)]. |
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| * The noise covariance is computed from this concatenated matrix: '''NoiseCov = F * F' / Nsamples''' | * '''Global''': The average value of each channel is removed after concatenation (same correction for all blocks): F = Concatenate[Fi] - mean(Concatenate[Fi]). |
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| * '''Output''': Compute either a full noise covariance (best option) or just a diagonal matrix (only the variances of the channels). The second option is only useful if you do not have enough time samples to estimate the covariance properly. Always keep the default selection unless you know exactly what you are doing, Brainstorm detects what the preferred option is for every case. <<BR>><<BR>> {{attachment:noisecov_options.gif||height="378",width="375"}} | * The sample noise covariance is computed from F: '''NoiseCov = F * F' / Nsamples''' <<BR>><<BR>> {{attachment:noisecov_options.gif||width="346",height="278"}} |
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| Keep the default options and click on ['''OK''']. | For this tutorial, keep the default options and click on ['''OK''']. |
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| * One new file appears in the noise dataset, next to the channel file. Description of the popup menus: | * One new file is created and appears under the noise data folder, next to the channel file. The corresponding contextual menus are: |
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| * '''Display as image''': Shows the noise covariance matrix as an indexed image. This can be useful to quickly check the quality of the recordings: noisier channels appear in red. You can display the noise covariance for all the sensors at once, or for each sensor type separately. Double-clicking on the file displays all the sensors. * '''Copy to other conditions''': Copy this file to all the other folders of the same subject. |
* '''Display as image''': Opens a display of the noise covariance matrix as an indexed image (same as double-click on file). This can be useful to quickly control the quality of the recordings: for instance, noisier channels appear as rows/columns marked in red. * '''Copy to other conditions''': Copy the file obtained to all the other folders of the same subject, to avoid re-computing the noise covariance statistics again for each folder from the same session. |
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| * You can also copy a noise covariance file to another folder just like any other file: <<BR>>Right-click > File > Copy/Paste, or keyboard shortcuts Ctrl+C/Ctrl+V. <<BR>><<BR>> {{attachment:noisecov_file.gif||height="139",width="378"}} {{attachment:noisecov_display.gif||height="170",width="148"}} | * You can also copy a noise covariance file to another folder just like any other file: <<BR>>Right-click > File > Copy/Paste, or keyboard shortcuts Ctrl+C/Ctrl+V. <<BR>><<BR>> {{attachment:noisecov_file.gif||width="315",height="141"}} {{attachment:noisecov_display.gif||width="148",height="170"}} |
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| Right-click on the the noise covariance file > '''Copy to other folders''': We need this file in the two folders where the epochs were imported, in order to estimate the sources for them. | Right-click on the the noise covariance file > '''Copy to other folders''': We need this file in the two folders where the epochs were imported before we compute the respective source models. |
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| . {{attachment:noisecov_copy.gif||height="225",width="212"}} | . {{attachment:noisecov_copy.gif||width="212",height="225"}} |
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| == Other scenarios == Computationally speaking, this noise covariance matrix is very easy to calculate, the Brainstorm interface offers a lot of flexibility to select the files and time windows you want to use. The real difficulty is to define what "noise" means. The ideal is to use segments of recordings that contain only the noise of the sensors, or segments of recordings that do not contain any of the brain signals of interest. This section is not directly useful for the current tutorial, but can be used as a reference for selecting the appropriate method in another experiment. |
== Variations on how to estimate sample noise covariance == The sample noise covariance matrix is straightforward to obtain. Brainstorm's interface features a lot of flexibility to select the files and time windows used to calculate the sample statistics. You need to have a clear understanding of the concept of "noise" to pick the best possible option. We support the notion that noise covariance accounts for contaminants that remain present in the data after preprocessing is complete. Hence it is not meant to account for eye blinks, heartbeats, muscle artifacts, flat or bad channels and noisy segments: all these the above need to be taken care of during previous preprocessing steps, as show in previous tutorial sections. The noise covariance entry is to account for remaining and stationary instrumental, sensor and environmental noise components. For this reason, the ideal scenario is to use segments of recordings that contain exclusively this type of contaminant, or segments of recordings deemed not to contain any of brain signals of interest. This section is advanced reading material that can be used as a reference in a different experimental context. |
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| ==== MEG ==== '''Empty room''': The MEG case is usually easier because we have access to real noise measurements, the MEG room just has to be empty. Record a few minutes right before bringing the subject in the MEG, or after the experiment is done. This would isolate only the noise from the sensors, which is what we are interested in most cases.<<BR>>If you acquire several runs successively and your MEG system is relatively stable, you can assume that the state of the sensors doesn't change much over the time. Therefore, you can re-use the same noise recordings and noise covariance matrix for several runs and subjects acquired during the same day. |
==== The case of MEG ==== '''From empty-room recordings''': actual noise measurements (due to the instrument, environment) using empty-room conditions (no subject under the MEG helmet) are possible in MEG. We recommend you obtain 2 to more minutes of empty-room data right before bringing the subject in the MEG room, or right after the experiment is finished. <<BR>>You can verify quantitatively how stable and reproducible is the noise covariance estimated (e.g., during the day/week). The MEG system may be located in a "quiet environment", allowing that you re-use the same noise recordings and therefore, noise covariance matrix, for all runs and subjects acquired on the same day. |
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| '''Resting baseline''': Alternatively, when studying evoked responses (aka event-related responses), you can use a few minutes of recordings where the subject is resting, ie. not performing the task. Record those resting segments before or after the experiment, or before/after each run. This approach considers the resting brain activity as "noise", the sources estimated for the evoked response are going to be preferentially the ones that were not activated during the resting period. | '''From resting-state segments''': When studying evoked responses (aka event-related responses), you may want to collect a few minutes of recordings where the subject is resting, i.e. not performing the task. Using these segments to obtain the noise covariance estimates implies that resting brain activity will be assumed as "noise", which we know now is not the case. We therefore encourage MEG users to acquire short empty-room runs instead. |
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| '''Pre-stimulation baseline''': It can also be a valid approach to use the pre-stimulation baseline of the individual trials to estimate the noise covariance. But keep in mind that in this case, everything in your pre-stimulation baseline is going to be attenuated in the source reconstruction, noise and brain activity. Therefore, your stimuli have to be distant enough in time so that the response to a stimulus is not recorded in the "baseline" of the following one. For repetitive stimuli, randomized delays between stimuli can help avoiding expectation effects in the baseline. | '''From pre-stimulus baseline''': Using concatenated pre-stimulation baseline segments from individual trials is in principle similar to the previous scenario, hence has similar limitations: regions prominently active during pre-stimulation baseline will tend to be attenuated by source analysis. |
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| ==== EEG ==== The EEG case is typically more complicated. It is not possible to estimate the noise of the sensors only. Only the two other approaches described for the MEG are still valid: <<BR>>'''resting baseline''' and '''pre-stimulation baseline'''. |
==== The case of EEG ==== It is less straightforward to estimate sensor noise from EEG data, because the electrodes need to be attached to a conductive medium (i.e. the scalp) to produce signals. Therefore only the last two options shown above in the MEG section are possible in EEG: <<BR>>'''resting baseline''' and '''pre-stimulation baseline'''. |
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| The noise level of the electrodes recordings depends primarily on the quality of the connection with the skin, which varies a lot from a subject to another, or even during the acquisition of one single subject. The conductive gel or solution used on the electrodes tends to dry, and the electrode cap can move. Therefore, it is very important to use one channel file per subject, hence one noise covariance per subject. In some specific cases, if the quality of the recordings varies a lot over the time, it can be interesting to split long recordings in different runs, with different noise covariance matrices too. | EEG noise levels depend on the quality of the electrode connection with the skin. It varies considerably between subjects, and during acquisition. Indeed, the conductive gel/paste/solution used for contact tends to dry up, which affects impedance. The electrode cap/locations can also move slightly, depending on how cooperative the participants. To account for variable noise levels between subjects, it is therefore preferrable to use one channel file per subject, because it allows the definition of one noise covariance entry per participant. In some specific cases, if the quality of the recordings varies a lot over time, it is preferrable to segment long recordings into shorter runs, and obtain different noise covariance matrices for each. |
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| ==== EEG and resting state ==== When studying the resting brain, you cannot use resting recordings as a noise baseline. For MEG the best choice is to use empty room measurements. For '''EEG''', you can chose between two different approaches: using the sensors variance, or not using any noise information.<<BR>>'''Option #1''': Calculate the covariance over a long segment of the resting recordings, but save only the diagonal, ie. the variance of the sensors. To do so from the interface: just check the box "Diagonal matrix" in the options window.<<BR>>'''Option #2''': Select "No noise modeling" in the popup menu. This would use an identity matrix instead of a noise covariance matrix (equal, unit variance of noise on every sensor). In the inverse modeling, this is equivalent to the assumption that the noise in the recordings is homoskedastic, and equivalent for all the sensors. The problem with this approach is that an electrode with a higher level of noise is going to be interpreted as a lot of activity in its region of the brain. |
==== EEG in resting-state conditions ==== If the target brain activity to your experiment is resting, resting segments cannot be used to obtain noise statistics. For MEG, use empty-room measurements as explained above. For '''EEG''', there are possible options: use sensor variance estimates, or avoid estimating empirical noise statistics.<<BR>>'''Option #1''': Calculate noise covariance over a long segment of resting recordings, but save only the diagonal elements, i.e. the variance measured at each sensor. This option is available in Brainstorm's advanced options of source computation: select the option "Diagonal noise covariance".<<BR>>'''Option #2''': Select "No noise modeling" in the contextual menu. This option uses the identity matrix as noise covariance matrix, and therefore assumes equal, unit variance of noise on every sensor. In inverse modeling, this is equivalent to assuming that noise is homoskedastic, and equivalent on all sensors. With this latter option, if data quality is not even on all electrodes, a higher noise level on some sensors may be explained with stronger, spurious source activity. |
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| ==== Noise and epilepsy ==== Analyzing a single interictal spike, using either EEG and MEG data, we are faced with a similar problem in defining what is noise. The brain activity before and after the spike can even be very informative about the spike's generation, particularly if it is part of a sequence of interictal activity that precedes ictal (seizure) onset. Defining a segment of time adjacent the spike as "background" may not be practical. In practice, however, we often can find a temporal region of spontaneous brain activity in the recordings that appears adequate for declaring as background, even in the epileptic patient. As discussed above, MEG has the additional option of using empty room data as a baseline, an option not available in EEG. |
==== Epilepsy ==== Interictal spikes as often considered as events of interest in epilepsy studies. In that respect, they can be considered as a form of brain activity evoked by the epileptogenic process, very much like a stimulus-related response. For this reason, one shall be cautious about how to define noise conditions from ongoing EEG or MEG recordings to study epilepsy. Defining a segment of time adjacent to the spike as "background noise" is certainly not justified. In practice, however, one often uses a data segment clear from visible interictal activity. As discussed above, MEG has the additional, preferred option of using empty-room data as a baseline - an option not available with EEG. |
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| We thus have the same options as above:<<BR>>'''Option #1a''': Compute the noise covariance statistics from blocks of recordings away from the peak of any identified interictal spike, and keep only the diagonal (the variance of the sensors).<<BR>>'''Option #1b:''' If a large period of time is available, calculate the full noise covariance.<<BR>>'''Option #2(MEG): '''Use empty room data as the baseline.<<BR>>'''Option #3''': Select "No noise modeling" in the popup menu (identity matrix, unit variance of noise on every sensor). | The same options as above are available to the epilepsy researcher:<<BR>>'''Option #1a''': Estimate noise covariance statistics from blocks of recordings away from the peak of any identified interictal spike, and keep only the diagonal (the variance of each sensor time series).<<BR>>'''Option #1b:''' If a large period of time clear of visible interictal events is available, use this latter to estimate the full noise covariance array.<<BR>>'''Option #2(MEG): '''Use empty-room data as baseline.<<BR>>'''Option #3''': Select "No noise modeling" in the popup menu (identity matrix, unit variance of noise on every sensor). |
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| * '''Long noise recordings''': In order to get a good estimation of the noise covariance, we need a significant number of time samples, at least '''N*(N+1)/2''', where N is the number of sensors. This means about 40s for CTF275 recordings at 1000Hz, or 20s for 128-channel EEG at 500Hz. Always try to use as much data as possible for estimating this noise covariance. * '''Do not import averages''': For this reason, you should never compute the noise covariance matrix from averaged responses. If you want to import recordings that you have fully pre-processed with another program, we recommend you import the individual trials and use them to compute the noise covariance. If you can only import the averaged responses in the Brainstorm database, you have to be aware that you may get poor results in the source estimation. |
* '''Long noise recordings''': In order to obtain a more accurate estimation of the noise covariance, a sufficiently large number of time samples is required: at least '''N*(N+1)/2''' samples, (N is the number of sensors.) This amounts to 40s of data for CTF275 recordings at 1000Hz, or 20s for 128-channel EEG at 500Hz. Remember to always use as much data as possible to estimate noise covariance statistics. * '''Do not use signal averages''': For this reason, you should never compute the noise covariance matrix from averaged responses. If you want to import recordings that you have fully pre-processed with another program, we recommend you import the individual trials and use them to estimate noise covariance. If you can only import the averaged responses in Brainstorm, please be aware that you may under estimate noise levels and bias source results. |
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| * '''Use single trials''': If you want to use the pre-stimulation baseline of the single trials, first import the trials in the database, then select all the groups of imported trials at once, right-click on one of them > Noise covariance > Compute from recordings, and inally copy the noise covariance to the other folders. * '''Using multiple continuous blocks''': This is similar to the single trial case. Import all the blocks you consider as a quiet resting baseline in the database, then select all the imported blocks in the database explorer > Noise covariance > Compute from recordings. |
* '''Use single trials''': If you want to use the pre-stimulation baseline from single trials, first import the trials in the database, then select all the groups of imported trials at once, right-click on one of them > Noise covariance > Compute from recordings, and finally copy the file to the other folders. * '''Using multiple continuous blocks''': This is similar to the single trial case. Import in the database all the blocks you consider as quiet resting baselines, then select all the imported blocks in the database explorer > Noise covariance > Compute from recordings. |
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| == Data covariance matrix == The computation of a data covariance matrix is very similar to a noise covariance matrix, except that you need to target the segments of recordings of interest instead of the noise. In the case of an event-related study, you can consider all the recordings in a range of latencies after the stimulation corresponding to the effect you want to localize in the brain. |
== Data covariance [TODO] == Beamforming source mapping further requires the estimation of data covariance statistics. The LMCV beamformer uses an estimated data covariance matrix to compute spatial filters that define the beamformer. It is important that this covariance matrix contains contributions from all sources that contribute to the data over the time window to be analyzed (signal + noise). |
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| * For '''run#01''', select '''all the trials''', right-click > '''Data covariance > Compute from recordings'''. <<BR>><<BR>> {{attachment:datacov_popup.gif||height="199",width="370"}} * We need to specify the time window of interest in these recordings. If want to image the activity during the primary response, we can for instance consider the segment '''[50,150]ms''' post-stimulus. <<BR>><<BR>> {{attachment:datacov_options.gif||height="356",width="363"}} {{attachment:datacov_timewindow.gif||height="105",width="238"}} * Repeat the operation for '''run#02'''. <<BR>><<BR>> {{attachment:datacov_files.gif||height="257",width="225"}} |
We have found, as have others, that it is important to use a relatively long time window for robust beamformer performance. This also helps to avoid numerical instability when inverting the data covariance, as required in computing the beamformer kernel matrix. Our recommendations: * '''Evoked responses''': Use a window that spans prestim through the end of the response of interest, with a minimum of 500ms total duration. * '''Spontaneous data''': Use the full time window to be analyzed, with a minimum of 30s of data. The procedure to compute the data covariance is very similar to the noise covariance: * For '''run#01''', select '''all the trials''', right-click > '''Data covariance > Compute from recordings'''. <<BR>><<BR>> {{attachment:datacov_popup.gif||width="407",height="180"}} * We need to specify two time windows:<<BR>>'''Baseline''': Pre-stimulus time, used for DC offset correction (subtracts the baseline mean).<<BR>>'''Data''': Time segment of interest (let's use all the time available post-stimulus in this tutorial example).<<BR>><<BR>> {{attachment:datacov_options.gif||width="365",height="329"}} * Repeat the same steps for '''run#02'''. <<BR>><<BR>> {{attachment:datacov_files.gif||width="208",height="238"}} |
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| . {{attachment:noisecov_contents.gif||height="175",width="487"}} | . {{attachment:noisecov_contents.gif||width="487",height="175"}} |
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| ==== Structure of the noise/data covariance files ==== | ==== Structure of the noise/data covariance files: noisecov_*.mat / ndatacov_*.mat ==== |
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| * '''FourthMoment''': [nChannels x nChannels] fourth order moments: '''F.<<HTML(^)>>2 * F'.<<HTML(^)>>2 ./ (nSamples-1)''' * '''nSamples''': [nChannels x nChannels] number of time samples that were used for each pair of sensors. This is not necessarily the same value everywhere, some channels can be bad only for a few trials. |
* '''FourthMoment''': [nChannels x nChannels] fourth order moments: '''F.<<HTML(^)>>2 * F'.<<HTML(^)>>2 ./ (nSamples-1) ''' * '''nSamples''': [nChannels x nChannels] number of time samples that were used for each pair of sensors. This is not necessarily the same value everywhere, some channels can be declared as bad only for a few trials. |
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| * bst_noisecov.m * panel_noisecov.m |
* '''process_noisecov'''.m: Function for process "Sources > Compute covariance (noise or data)" * '''bst_noisecov'''.m: Computes the data/noise covariance matrices. * '''panel_noisecov'''.m: Options panel. |
Tutorial 21: Noise and data covariance matrices
Authors: Francois Tadel, Elizabeth Bock, John C Mosher, Richard Leahy, Sylvain Baillet
Modeling and measuring certain characteristics of the noise contaminating the data is beneficial to source estimation. For instance, minimum norm estimators can integrate second-order sample statistics of sensor noise (summarized into a noise covariance matrix, see below). Beamformers further require similar sample statistics for the data portion of interest (summarized into a data covariance matrix). This first section of this tutorial explains how to obtain a noise covariance estimate from MEG empty room recordings.
Contents
Noise covariance
Instrumental noise ("sensor noise") can be readily captured in MEG using two or more minutes of empty room measurements. We encourage the use of noise recordings collected the same day as the subject's recordings (if possible just before the session) and pre-processed in the same manner (with same sampling rate and same frequency filters applied) as the participant data. In this study we have already prepared a 2-min segment of noise recordings that we will use to estimate noise covariance sample statistics.
Right-click on the entry for noise recordings > Noise covariance. Available menus:
Compute from recordings: Use the selected recordings to estimate noise covariance statistics.
No noise modeling: Use an identity matrix as noise covariance. This option is useful when no noise recording is available (e.g. ongoing EEG without any baseline of no interest).
Import from file: Use noise covariance statistics available from another source (e.g., obtained using the MNE software.)
Import from Matlab: Import any [Nchannels x Nchannels] matrix as noise covariance matrix from the Matlab workspace.
Select the menu Noise covariance > Compute from recordings. Available options:
Files: The top part of this window shows a summary of the files that have been selected to estimate the noise: 1 file of 120s at 600Hz. Total number of time samples in selected file: 72,000. We can also choose to use only a portion of this file, with the option "baseline". The large continuous files are split in blocks of a maximum of 10,000 samples that are then processed as different files.
Remove DC offset: All the selected blocks of data are baseline corrected and concatenated to form a large matrix "F". There are two options for baseline correction:
Block by block: The average value of each channel is subtracted from each block before concatenating files together. Let Fi contain data from block #i:
F = Concatenate[Fi - mean(Fi)].Global: The average value of each channel is removed after concatenation (same correction for all blocks): F = Concatenate[Fi] - mean(Concatenate[Fi]).
The sample noise covariance is computed from F: NoiseCov = F * F' / Nsamples
For this tutorial, keep the default options and click on [OK].
- One new file is created and appears under the noise data folder, next to the channel file. The corresponding contextual menus are:
Display as image: Opens a display of the noise covariance matrix as an indexed image (same as double-click on file). This can be useful to quickly control the quality of the recordings: for instance, noisier channels appear as rows/columns marked in red.
Copy to other conditions: Copy the file obtained to all the other folders of the same subject, to avoid re-computing the noise covariance statistics again for each folder from the same session.
Copy to other subjects: Copy this file to all the folders of all the subjects in the protocol.
You can also copy a noise covariance file to another folder just like any other file:
Right-click > File > Copy/Paste, or keyboard shortcuts Ctrl+C/Ctrl+V.
Right-click on the the noise covariance file > Copy to other folders: We need this file in the two folders where the epochs were imported before we compute the respective source models.
Variations on how to estimate sample noise covariance
The sample noise covariance matrix is straightforward to obtain. Brainstorm's interface features a lot of flexibility to select the files and time windows used to calculate the sample statistics. You need to have a clear understanding of the concept of "noise" to pick the best possible option. We support the notion that noise covariance accounts for contaminants that remain present in the data after preprocessing is complete. Hence it is not meant to account for eye blinks, heartbeats, muscle artifacts, flat or bad channels and noisy segments: all these the above need to be taken care of during previous preprocessing steps, as show in previous tutorial sections. The noise covariance entry is to account for remaining and stationary instrumental, sensor and environmental noise components. For this reason, the ideal scenario is to use segments of recordings that contain exclusively this type of contaminant, or segments of recordings deemed not to contain any of brain signals of interest. This section is advanced reading material that can be used as a reference in a different experimental context.
The case of MEG
From empty-room recordings: actual noise measurements (due to the instrument, environment) using empty-room conditions (no subject under the MEG helmet) are possible in MEG. We recommend you obtain 2 to more minutes of empty-room data right before bringing the subject in the MEG room, or right after the experiment is finished.
You can verify quantitatively how stable and reproducible is the noise covariance estimated (e.g., during the day/week). The MEG system may be located in a "quiet environment", allowing that you re-use the same noise recordings and therefore, noise covariance matrix, for all runs and subjects acquired on the same day.
From resting-state segments: When studying evoked responses (aka event-related responses), you may want to collect a few minutes of recordings where the subject is resting, i.e. not performing the task. Using these segments to obtain the noise covariance estimates implies that resting brain activity will be assumed as "noise", which we know now is not the case. We therefore encourage MEG users to acquire short empty-room runs instead.
From pre-stimulus baseline: Using concatenated pre-stimulation baseline segments from individual trials is in principle similar to the previous scenario, hence has similar limitations: regions prominently active during pre-stimulation baseline will tend to be attenuated by source analysis.
The case of EEG
It is less straightforward to estimate sensor noise from EEG data, because the electrodes need to be attached to a conductive medium (i.e. the scalp) to produce signals. Therefore only the last two options shown above in the MEG section are possible in EEG:
resting baseline and pre-stimulation baseline.
EEG noise levels depend on the quality of the electrode connection with the skin. It varies considerably between subjects, and during acquisition. Indeed, the conductive gel/paste/solution used for contact tends to dry up, which affects impedance. The electrode cap/locations can also move slightly, depending on how cooperative the participants. To account for variable noise levels between subjects, it is therefore preferrable to use one channel file per subject, because it allows the definition of one noise covariance entry per participant. In some specific cases, if the quality of the recordings varies a lot over time, it is preferrable to segment long recordings into shorter runs, and obtain different noise covariance matrices for each.
EEG in resting-state conditions
If the target brain activity to your experiment is resting, resting segments cannot be used to obtain noise statistics. For MEG, use empty-room measurements as explained above. For EEG, there are possible options: use sensor variance estimates, or avoid estimating empirical noise statistics.
Option #1: Calculate noise covariance over a long segment of resting recordings, but save only the diagonal elements, i.e. the variance measured at each sensor. This option is available in Brainstorm's advanced options of source computation: select the option "Diagonal noise covariance".
Option #2: Select "No noise modeling" in the contextual menu. This option uses the identity matrix as noise covariance matrix, and therefore assumes equal, unit variance of noise on every sensor. In inverse modeling, this is equivalent to assuming that noise is homoskedastic, and equivalent on all sensors. With this latter option, if data quality is not even on all electrodes, a higher noise level on some sensors may be explained with stronger, spurious source activity.
Epilepsy
Interictal spikes as often considered as events of interest in epilepsy studies. In that respect, they can be considered as a form of brain activity evoked by the epileptogenic process, very much like a stimulus-related response. For this reason, one shall be cautious about how to define noise conditions from ongoing EEG or MEG recordings to study epilepsy. Defining a segment of time adjacent to the spike as "background noise" is certainly not justified. In practice, however, one often uses a data segment clear from visible interictal activity. As discussed above, MEG has the additional, preferred option of using empty-room data as a baseline - an option not available with EEG.
The same options as above are available to the epilepsy researcher:
Option #1a: Estimate noise covariance statistics from blocks of recordings away from the peak of any identified interictal spike, and keep only the diagonal (the variance of each sensor time series).
Option #1b: If a large period of time clear of visible interictal events is available, use this latter to estimate the full noise covariance array.
Option #2(MEG): Use empty-room data as baseline.
Option #3: Select "No noise modeling" in the popup menu (identity matrix, unit variance of noise on every sensor).
Recommendations
Long noise recordings: In order to obtain a more accurate estimation of the noise covariance, a sufficiently large number of time samples is required: at least N*(N+1)/2 samples, (N is the number of sensors.) This amounts to 40s of data for CTF275 recordings at 1000Hz, or 20s for 128-channel EEG at 500Hz. Remember to always use as much data as possible to estimate noise covariance statistics.
Do not use signal averages: For this reason, you should never compute the noise covariance matrix from averaged responses. If you want to import recordings that you have fully pre-processed with another program, we recommend you import the individual trials and use them to estimate noise covariance. If you can only import the averaged responses in Brainstorm, please be aware that you may under estimate noise levels and bias source results.
Using one block: If you want to use a segment of "quiet" recordings in a continuous file: right-click on the continuous file > Noise covariance > Compute from recordings, then copy the noise covariance to the other folders. This is the case described in this tutorial.
Use single trials: If you want to use the pre-stimulation baseline from single trials, first import the trials in the database, then select all the groups of imported trials at once, right-click on one of them > Noise covariance > Compute from recordings, and finally copy the file to the other folders.
Using multiple continuous blocks: This is similar to the single trial case. Import in the database all the blocks you consider as quiet resting baselines, then select all the imported blocks in the database explorer > Noise covariance > Compute from recordings.
Data covariance [TODO]
Beamforming source mapping further requires the estimation of data covariance statistics. The LMCV beamformer uses an estimated data covariance matrix to compute spatial filters that define the beamformer. It is important that this covariance matrix contains contributions from all sources that contribute to the data over the time window to be analyzed (signal + noise).
We have found, as have others, that it is important to use a relatively long time window for robust beamformer performance. This also helps to avoid numerical instability when inverting the data covariance, as required in computing the beamformer kernel matrix. Our recommendations:
Evoked responses: Use a window that spans prestim through the end of the response of interest, with a minimum of 500ms total duration.
Spontaneous data: Use the full time window to be analyzed, with a minimum of 30s of data.
The procedure to compute the data covariance is very similar to the noise covariance:
For run#01, select all the trials, right-click > Data covariance > Compute from recordings.
We need to specify two time windows:
Baseline: Pre-stimulus time, used for DC offset correction (subtracts the baseline mean).
Data: Time segment of interest (let's use all the time available post-stimulus in this tutorial example).
Repeat the same steps for run#02.
On the hard drive
Right-click on any noise covariance file > File > View file contents:
Structure of the noise/data covariance files: noisecov_*.mat / ndatacov_*.mat
Comment: String displayed in the database explorer to represent this file.
NoiseCov: [nChannels x nChannels] noise covariance: F * F' ./ (nSamples-1)
Unknown values are set to zero.FourthMoment: [nChannels x nChannels] fourth order moments: F.^2 * F'.^2 ./ (nSamples-1)
nSamples: [nChannels x nChannels] number of time samples that were used for each pair of sensors. This is not necessarily the same value everywhere, some channels can be declared as bad only for a few trials.
Related functions
process_noisecov.m: Function for process "Sources > Compute covariance (noise or data)"
bst_noisecov.m: Computes the data/noise covariance matrices.
panel_noisecov.m: Options panel.
Additional documentation
Forum: EEG reference: http://neuroimage.usc.edu/forums/showthread.php?1525#post6718