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BEP042 surface electromyography (HDsEMG/EMG) #1371
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Good day, |
Hi @neuromechanist et al.! Nice to hear that you find BIDS valuable and want to implement support for EMG. These are busy days, so I don't expect much to happen until early next year (including a more thorough pass by me and some questions / recommendations). However I can already tell you that you'll be able to reach a much larger audience by cross-posting and advertising this issue on some of our BIDS channels such as
Once we discussed some more (soon), we can also advertise via Twitter/Mastodon and hopefully get more EMG researchers involved. I could very well imagine that there are already some people working with BIDS who also work with EMG, and it'd be valuable to get their input on what's needed in BIDS to become "nice" for EMG. |
Thanks @sappelhoff, a lot for the introduction and instructions. Of course. I will cross-post to make sure that the message reaches interested researchers. Just to clarify, This BEP is not about EMG but about high-density surface EMG (HDsEMG). HDsEMG is recording from a single muscle (or a group of closely positioned muscles) with multiple electrodes (usually 32 or 64) to find the spatial distribution of the electrical activity over the muscle and to potentially recover motor-unit activity using convolutive ICA. The practice, data collection, sensor placement, analysis, and use cases of HDsEMG can differ considerably from EMG. For example, while EMG is usually collected from multiple sites on the body and is bipolar, HDsEMG is mainly collected from one or two single muscles, and the collection is monopolar (i.e., reference is on the bone). Also, as much with the EEG ICA, it turns out the decomposing HDsEMG to the motor units provides good accuracy compared to intramuscular EMG (iEMG):
I believe that EMG is already included as a part of BIDS-EEG. I think this setup (i.e., EEG and EMG being together) makes sense for the brain-body recordings and makes the analysis straightforward. However, I believe that an extension of BIDS is necessary for pure EMG setups (i.e., not including EEG), biomechanics, physical therapy, and others. Still, this is out of the scope of the current HDsEMG issue 🙈. Having said that, I am interested in BIDS-EMG, but as you said, I also believe it requires a large-scale collaborative effort from researchers across many disciplines. On the other hand, HDsEMG is rapidly on the rise but is not yet a fully streamlined and widely-used modality. So, it might be just the right time to extend BIDS to HDsEMG. Happy holidays and see you in 2023! |
Hi Seyed, Let me shortly chime in here - also to ensure I get notified of new activity on this issue. Thanks for sending the email to the google group, that is what got me here. I did my PhD research in the group of Dick Stegeman and was involved in some of the HD-sEMG research, for example this, this, and this. I think I still have a decent understanding of HD-sEMG recordings and how the data is analyzed - although I have not kept up to date with more recent work. I also happen to have a good understanding of BIDS and BEPs ;-) Perhaps you have been contacted by others with interest in a HD-sEMG-BEP. I think it would be good to plan an online meeting to get to know each other and make some initial plans how to tackle this. best regards, |
Some time ago I already had a go with data2bids to convert an EMG dataset to something that resembles BIDS. See https://www.fieldtriptoolbox.org/example/bids_emg/. Note that that example is conventional EMG, not high-density. I don't know whether I still have some of our own HD-sEMG recordings in my backups/archive. If so, those could be a starting point for a better draft example. If not, I could ask the EMG colleagues with whom I did it back then. |
Hi Robert, Thanks a lot for your input. I actually have an email going out to you and @CPernet this morning (8 am ET) about this BEP. I think I need to revise it now a little 😅. The papers are super great and helpful, especially regarding the setup and demonstrating how HDsEMG can also help with intricate musucalr structure in the face and neck area; thanks for sharing. Yes, probably a short startup meeting is needed at this stage. I will share the starting draft and the working group chat here in the next couple of days. I will also reach you and others via email (and also the group chat). We have access to a good amount of HDsEMG data, including public datasets. But, most (if not all) are from OTB instruments. It would be great if we can also provide datasets from other instruments to ensure the efforts would work on as many files and datasets as possible. All the best |
tagging @GiacomoBert from BEP37NIBS for which Shokoofeh and Joona will work on an hdEMG + TMS dataset -- as a general rule, we want as much overlap with any electrophysiology if there is a way to have EMG and hd-EMG that's a plus. |
Thanks, @CPernet, for adding potentially interested researchers. I believe having EMG and HDsEMG together, or separately can make a perfect topic for the first workgroup meeting. |
Hello back, Here is also the BIDS-HDsEMG working group invitation to the Element/Matrix platform. I have just created it, as we need to retire the Slack group and migrate to an open-source and free platform. Hopefully, the members of the Slack channel will join soon as well 😊: |
The call for the first meeting is up now. Looking forward to seeing you there. |
Good day everyone, The inaugural meeting for BIDS-HDsEMG will be on Monday, Jan 30th, 2023, 9 am ET, 3 pm CET. You can join the meeting using this link: https://ucsd.zoom.us/j/97533232141 I hope to see you all on Monday. |
To provide an update and resume discussion, the first meeting was held on Jan 30th, 2023, and we need to address the following questions:
PS: Apologies for the pause in the efforts; an extended sick leave, a major grant submission, and a transcontinental move happened all in this period. |
@robertoostenveld kindly converted the sample HDsEMG (and bipolar) EMG datasets to BIDS format which is available in this BIDS folders under mne-tools/mne-bids#1129. Here are a summary of the contents of each folder under the BIDS folders. I agree that the main issue is to make the data FAIR; otherwise, electrical signals are electrical signals: BIDS1: Delsys Trigno Mini EMG recordings
BIDS2: Delsys Galileo HDsEMG recordings
BIDS3: g.tec Pangolin
BIDS4: OTB Sessantaquattro
One thing common across all files is a need for grouping the electrodes/channels within an array or sensor. Each system can contain multiple arrays, which can have different features, including location, size, and IED. Also, several other pieces of information are missing beyond the sensor location/muscle or recording mode (bi/monopolar) and reference. They include the relative position of the electrode to the muscle innervation zone, how the innervation zone is determined, which muscles are covered by the arrays, etc. I'll try to summarize them in the Google Doc under item 3 above. |
Regarding "On a separate note, should IMU channels be recorded with EMG?", I would say yes. That aligns with how we deal with auxiliary channels in MEG, EEG, etc. However, in an XXX dataset (with XXX being MEG, EEG, NIRS, iEEG, EMG) the XXX channels are required. The optional auxiliary channels are to be sampled with the same equipment. If it were data from a different device, it should be stored as its own modality. |
In the case of the Galileo and Pangolin the electrodes have a fixed arrangement, similar to "grids" and "strips" in the iEEG specification. For the Pangolin I would say that
The identifiers The anatomical locations might be too imprecise but can be made better (medical/anatomical terminology is not my expertise). This does not specify the orientation yet, I don't directly have an idea for that other than free-text in |
For the 4th example it would be for example with this HD04MM1305
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For your information, I have updated the examples here on https://drive.google.com/drive/folders/1k-PNBejOYi4JCE8iLxYhQ6R7L1kWuAbD?usp=sharing such that they use the |
Thank you @robertoostenveld for adding the EMG-specific fields to the GDrive folder. Querying hd-sEMG on PubMed for 2022 and 2023 results in 148 papers. After sorting by year and examining 40 of them, 6 did not include EMG data. from the rest 34, 23 studies were done using OTB systems (~68%), 4 using TMSi (12%), 2 using custom amplifiers and grids, and 1 using each of LSiN, Intan, and Delsys systems. A recent paper lists the potential requirements for hd-sEMG experiment designs, including the parameters that should be taken into account in designing the protocol, sensor placement, reporting, and analysis. Surprisingly, most studies reported IED and electrode diameter or mentioned the electrode part number. Several also provided their use of EMG problems to find the innervation zones and placement of the sensors. Here are a couple of points that would need further exploring:
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Had a quick look at this issue and the google doc. Maybe I am wrong but it seems that having a single BEP for sEMG and hdsEMG still makes sense. I suspect both methods would still share a lot common points in terms metadata, auxiliary files... And that filenames could still make it explicit which methods was used. |
@agramfort recently showed interest in this, so he might want to chime in. |
Indeed. I think it will be great to have a standard way of sharing / organizing sEMG data. Meta CTLR team should soon open source large datasets and using bids is to me the best way of doing it. I am currently consulting a few people to see what is the best course of action. Please reach out to me if you want to push this effort forward.
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Thanks, @Remi-Gau, for looking into the BEP proposal (and for the earlier chat at the BIDS maintainers meeting). Yes, the suffix (modality) still can be different while the data type is the same (suffix: One critical metadata difference between HDsEMG and EMG is the sensor placement. @JuliusWelzel, @sjeung, and I are converging, after almost a year, on a draft standard for sensor placement that would work very well for this purpose. @agramfort, yes, please. We want to push this forward, Thanks. I will also reach out to some academic contributors for potential interest. |
In the BEP Google Doc, we originally had this idea of single-subject datasets/tar files that manufacturer stakeholders can use to generate their data (we called it HDsEMG .BIDS file structure). During my conversation with @yarikoptic, it turns out that this is pretty much inline with an issue in BIDS 2.0 development: So, it might be best to separate the efforts, dedicate this BEP to EMG-BIDS, and later work on the small-dataset BIDS structure. I edited the issue title accordingly and am more than happy to remove the related parts from the BEP Google Doc. I appreciate your comments. Edit 4/14: BIDS file structure is removed from EMG-BIDS BEP. |
@neuromechanist I am arriving a bit late in the conversation. I will start with a few naive question to see where we are.
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@agramfort, it is still early. Given that the formats and metadata structure for human electrophysiology, the EMG-BIDS BEP has a huge headstart. Yet, the EMG community is very diverse and passionate about EMG-specific phenomena and potential solutions (for example, cross-talk and using single or double differential sensors to avoid it, See Koh 1993)
Definitely EDF/BDF (16-bit, 24bit). Bioelecttronica seems to have potential since (1) It is open source, and (2) ~70% of the HDsEMG data is being done with their instruments. I think a major issue is major EMG non-opensource formats, namely Delsys and Noraxon.
One advantage is potentially faster convergence; engaging sEMG, HDsEMG, and iEMG communities might be a significant undertaking. Still, with the recent convo with BIDS maintainers, we'll work toward integrating the modalities and inviting different communities to provide input.
Sensor locations are a major concern for FAIR EMG data distribution (as it is for BIDS-Motion). The EEG logic for electrode location is pretty good. We are extending a similar format for surface anatomy with the BIDS-Motion Devs. However, there are several other metadata needed for EMG as well. I tried to summarize the currently missing metadata in the Necassary Terms Google Doc |
@agramfort you may be interested in following the discussion in #197 regarding file formats for tabular data, including physio and stim. |
@bids-maintenance Can you perhaps comment on the status/checks needed to proceed. Seems like a group of people is getting excited to move this forward? Whether hdEMG and EMG should be in the same file or separate files/formats can then be flushed out in more detail. |
@dorahermes |
While it is a little belated, happy to announce that the EMG-BIDS BEP is now officially BEP-042 🎉. |
Together with Motion-BIDS maintainers (@sjeung and @JuliusWelzel) we are developing a unified sensor placement specification. The main goal of this specification is to properly annotate sensor locations under a specified accuracy. We believe that this specification will increase data transparency and reusability for both Motion-BIDS and EMG-BIDS. Annotaing sensor locations precisely is crucial for EMG, especially as the muscle composition varies across people signficantly. Also, we are working with the HED working group (@VisLab) to implement a version of this specification in HED as a partnered schema. Please let me know if you are interested in collaboration. |
Good day all, Thanks for sticking to this BEP. We will try to have a kick-off meeting to work on the specs more regularly. Meetings will be tentatively biweekly, on Wednesdays at 8 am PT / 11 am ET / 5 pm CET, with the start the next week, Sept. 11, 2024. Please reach out if this time will not work for you and if you plan to participate actively. We will try to make it work for everyone. I will share the meeting links on our Element Group under the main discussion and email the invite to everyone mentioned in this issue. Please feel free to decline, and please feel free to extend the invitation to anyone interested in contributing. Since no specs are good without tools, I'd like to invite @arnodelorme, @drammock, and @larsoner for their support in developing import/export tools for Matlab/EEGLAB and MNE-Python. |
Although belated, the kickoff meeting was held last week with @arnodelorme, @robertoostenveld, @larsoner, @drammock, Lena Ting, Janna Protzak, and Mario Braklin, and me. We went over the definitions, briefly discussed sensor/electrode location metadata, and compared electrode locations in Please reach out if you want to join the call so I can send you the invite. |
In the zoom meeting just now we touched upon the 80/20 rule and a discussion was brought up whether high-density or regular EMG is more commonly used. I therefore revisited the query that @neuromechanist posted above for pubmed with I also searched for publications in Psychophysiology with In Muscle and Nerve the fractions appear to be similar. Based on these, regular EMG seems to be much more commonly reported upon, with a factor of 100x or so. However, the level of detail recorded in high-density EMG is much higher, investments are larger, and therefore the value of sharing EMG data is probably larger for HDsEMG researchers. I therefore hope that we can create a BIDS extension that works for both. |
The 9/25 meeting was held with @arnodelorme, @robertoostenveld, @larsoner, @drammock, Tjreed, Raul Simpetru, and me present. We discussed the common metadata fields from EEG. The issue of anatomical landmarks and how the electrode placement and channel locations was raised. We also discussed electrode placement and channel description of example one in the EMG-specific metadata document. We also briefly discussed the need for annotating reference electrodes in bipolar and monopolar EMG recordings.
Thank you, @robertoostenveld. I agree that hdsEMG is far less used and support Robert's rationale for including it. I would also like to add to the rationale that the ratio of shared hdsEMG datasets to all hdsEMG research papers is much greater than the ratio of shared EMG datasets to all EMG papers. So, it seems the relatively small community using hdsEMG is more inclined to share their data than the researchers using EMG. I hope this will change with our efforts. The 80/20 rule during this week's Zoom, in case it did not get across correctly, was about EMG examples in the EMG-specific document (not high-density) that we were discussing. I raised the point that most EMG research is carried out with EMG-specific instruments. The first example, getting most of the meeting time, had several shortcomings: a Raspberry Pi with a general-purpose ADC converter, generic electrodes with undefined function of each electrode, and unclear electrode placement, Link to the paper in discussion. I do not think this example represents EMG recordings, so I raised the 80/20 concern. Still, since this example had a very generic structure, I believe that we could generalize the electrode and channel description quite well. The next meeting will be in Four weeks on 10/23, to avoid conflicts with SfN. |
at the EMG-BIDS meeting on Nov 6th, @arnodelorme, @robertoostenveld, @larsoner, @drammock, and Tjreed discussed Many-to-Many mapping and Localizer concepts. Many-to-Many mapping indicates that one or more EMG channels can target (and record) one or more muscles. It seems that our examples contain all combinations (1-M, M-1, 1-1, M-M). We also discussed different localization methods, namely functional localizers (i.e., annotating sensor locations based on muscle function, such as specific contractions or movements) and anatomical localizers (i.e., annotating sensor locations based on measuring distance from anatomical landmarks). We are still at Example 3. I'd be grateful if we can work on Examples 3, 4, and 5 by adding their comments in a single paragraph for each examples, so that we can discuss all comments in the next meeting on 11/20. |
UPDATE April 12, 2024,
Important Links for faster access:
BEP Google Doc
List of HDsEMG/EMG-specific terms
HDsEMG/EMG Element group
Pros and cons of having HDsEMG/EMG as a single BEP
Good day,
Based on the BIDS Extension Proposal Guideline, I want to start the discussion to extend the BIDS to include HDsEMG.
HDsEMG involves recording multiple streams of electrical activity from the skin surface above a muscle or a group of muscles and provides a spatial representation of the muscle activity as seen on the surface (i.e., the skin).
There is a rapidly growing interest in the HDsEMG domain, especially as several blind-source separation techniques can decompose the signal array to motor-unit spike trains.
Source: Pubmed, retrieved 12/08/2022 from a search query including the phrase "high-density electromyography" and "HDsEMG"
Also, at least three independent and public datasets are available with extensive multi-task and multi-session recordings, but they are not in the BIDS format. See Malešević et al., Sci Data 2019, Matran-Fernandez et al., Sci Data 2019, and Jiang et al., 2021 IEEE TNSRE.
HDsEMG findings closely connect to brain imaging and mobile Brain/Body Imaging by providing insights about muscular activity at the motor-unit level. Also, this modality can become easily integrated into other brain imaging studies as a standalone modality that informs about the efferent pathways or with functional connectivity to the other brain imaging methods. A great tutorial describing the basics of the HDsEMG and its decomposition is available at Del Vecchio, et al., J Electromyogr Kinesiology 2020
On the instrument/hardware side, the sooner the events, data files, and the recording information convert to the BIDS format, the less possibility for error and much greater savings in the researcher’s time. OT Bioelettronica (OTB) and its esteemed technical team, one of the leading companies in manufacturing HDsEMG instruments, expressed their interest in adopting the BIDS standard for single-subject implementation at the recording time. We hope to be able to implement a transparent recording and dataset scheme that starts with data collection.
The motor unit activations, spike trains, and the derived metrics from this information are derivatives of HDsEMG, and are usually computed using blind source separation (BSS) methods such as Convolutive Independent Component Analysis (ICA). However, the HDsEMG BSS process, much like all BSS in the biosignal domain, has many assumptions and requires tuning several hyperparameters. We hope this proposal extend the proposed guidelines in BEP021, Common Electrophysiological Derivatives to HDsEMG, and also provides transparency on the reported and provided BSS results (as reported in the derivative directory) both when the BSS is performed at the data-collection point for a single subject (by the instrument software) and when it is done as a post-processing step by the researcher.
We appreciate your comments and contribution to this potential proposal. We look forward riot hearing from you, and in the coming days, we will also reach out to the authors of the public data to request their help in this effort. If you have any questions, please do not hestiate to conact me, Simone Posella (OTB, @SPosella), or Fabio Bolognesi (OTB, @FabioOT).
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