Hello,
I have read an EDF file. The EEG values are in Volt.
For the visualization purposes, how can I convert them to uV/mm?
Thank you!
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Does raw.plot() not produce a correctly scaled plot (it should)?
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In MNE, it is mentioned:
For example, the default scaling of 20e-6 (20µV) for EEG signals means that the visualized range will be 40 µV (20 µV in the positive direction and 20 µV in the negative direction).
Is it the same with sensitivity (uV/mm)?
I don’t understand what you mean by sensitivity? You can see the scaling as a purple scale bar in the top left corner of each channel type group. We don’t use mm because this depends on the size and resolution of your monitor.
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Is there any way to scale (use the gain/sensitivity) in mV/mm?
For instance: The EEG amplitude scale ranges from 1 microvolt/mm to 5 millivolt/mm.
Neither @cbrnr nor I have any idea how you imagine to get values in that unit, so I’m afraid we cannot help unless you provide additional information. EEG data is in voltage, not voltage per distance…
There is a software for the visualization of EEGs, called Natus NeuroWorks EEG software.
You can find further information about sensitivity (mV/mm) in page 97 (https://partners.natus.com/asset/resource/file/neuro/asset/2020-06/013017_Rev07_NeuroWorks%208%20Reference%20Manual.pdf).
Hope it helps.
My understanding is that they simply try to determine the physical dimensions of each pixel of your computer screen and then scale the displayed signal such that one mm of screen height corresponds to a certain signal amplitude.
MNE has no support for such functionality, sorry.
What would be the use case?
@marsipu I believe it should be possible to add this to mne-qt-browser but I’m not sure we actually want to have this …
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With pressing x on the keyboard you can activate a cursor where you can see the ampltitude of a signal at the cursor in the status-bar. Would that get you the same kind of information you need?
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I think this is mainly about convention. In certain areas, people are used to e.g. 5 µV corresponding to e.g. 5 mm. We don’t provide this functionality currently, but it would be possible (with a decent amount of effort I could imagine). However, this is the first time someone has requested such a feature, so I’m not sure how common it is.
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I could imagine this to be important in certain medical settings, where imaging data is also only visualized on specially calibrated display devices.
We can trivially get the DPI of a monitor and do the conversion. But like @cbrnr said, it’s unclear whether we should do it if only few people will ever need this.
Hence, @LoukasIlias if you could provide some further input as to why this is needed and just how common this requirement is, it would help us make a decision.
Thanks a lot for the answers and sorry for the delayed response!
Actually, two things are needed:
-
The plot of duration (time in seconds) is not enough for clinical purposes. We need to have cm/s. It would be really helpful, if we could choose 3 cm/s, 6 cm/s, etc.
-
Regarding the scaling of the EEG: We want to have uV/mm. In this way, we can see specific patterns in terms of the EEG activity.
The following will be helpful, where one can choose the sensitivity and the timebase.
It would be really helpful if these changes can be incorporated in the MNE library.
Thank you in advance!
Best regards,
Loukas
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Can you fill in the “etc” here? I can’t guarantee we’ll be able to implement this, but we definitely can’t do it if we don’t know which sensitivity and timebase choices are standardly used in clinical practice. (e.g. your screenshot shows 7 uV/mm and 30 mm/s… what other choices are offered in those dropdown menus? are these standard values that all manufacturers implement, or does it vary by manufacturer?)
The values are usually the same across all suppliers, the only thing that can vary are the units.
The standard for display is Sensitivity 7 uV/mm and Timebase 30 mm/sec. We may adjust them according to the signal we are looking at. You can see the choices offered on the drop boxes below. I have included in red the ones that are used more commonly (this is referring to EEG signals only).
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thanks! I’ve opened a feature enhancement request: support "sensitivity" and "timebase" style scaling in raw data browsers · Issue #10888 · mne-tools/mne-python · GitHub
Thank you!
If you need further clarifications, do not hesitate to contact me.
I am also looking for the timebase function. I have a question to better understand it. I saw also “mm/sec” used interchangeably with “sec/page”. Quoting from a research paper “…with a paper speed setting of 15 mm/sec or a screen display of 20 sec/page…”. So it is about how many seconds we display on the screen? It could be easier to develop in this way?
Hello guys,
I have started working on this project as part of my diploma thesis.
I aim to enhance both amplitude and time scaling settings, as well as the monitor sensitivity mentioned before.
My only concern for the time being are the values of the dropboxes, which you claim to be standardised.
I can agree for the time related ones, but what about the amplitude dropboxes? I saw the screenshots for EEG, but what about the other types of channels?
My approach would be to use the already used Inverted Norm and populate the dropboxes with standard items, around that norm.
If not, i guess it would require some kind of dictionary with the commonly used items for every type, as well as a valid source for all this information.
Anyways, please feel free to contact me for any information needed.
@Grifunf I’ve answered your question on the GitHub issue, let’s move our discussion of implementation details there from now on (more MNE devs are likely to see it over there). @LoukasIlias please have a look and feel free to weigh in about what API would be most useful for you.