[FieldTrip] Pre-whitening/Denoising Elekta/Neuromag Resting State Data

[Schoffelen, J.M. (Jan Mathijs)]

Hi Sarah,

I am glad that the beamformer paper is useful to you.

Unfortunately, spatial prewhitening resting state data can only be done with empty room recordings. If you were to prewhiten the data using (other) resting state data, you will throw away the baby with the bathwater. In your case, there is nothing to be done w.r.t. prewhitening. But no worries, also without prewhitening the beamformer may perform well enough.

Best wishes,

Jan-Mathijs


On 16 May 2024, at 23:18, Sarah via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hello Fieldtrippers!

I’ve recently learned from this wonderful paper by our very own Fieldtrip developers “A unified view on beamformers for M/EEG source reconstruction” (https://www.sciencedirect.com/science/article/pii/S1053811921010612<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS1053811921010612&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Ce9f6abc431e64e20d92e08dc795a46a0%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638518675832320835%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=PaHFGOIO%2F%2Bw2fnfU992cx3N57lZrnD%2FC%2BAaz6pCS6pQ%3D&reserved=0>) that - when working with the Elekta/Neuromag system, if SSS is applied through the MEGIN software for cleaning (ex. MaxFilter), regularization alone is not sufficient for good beam former performance. Instead, one recommendation was pre-whitening in combination with using a truncated pseudo-inverse.

Since I also have MEG data acquired from an Elekta with SSS applied, I am interested in applying this pre-whitening step on Fieldtrip, particularly to my resting state data. For pre-whitening of this data, one recommendation from the paper is using an empty room recording as the inputted noise data to the pre-whiten function. However, in my case, unfortunately I do not have these to accompany each of my resting state recordings.

I was wondering if anyone may have any recommendations on how I may still follow through with pre-whitening to ensure good beam former performance in my case. Are there any potential alternatives to the input noise data to the prewhiten function in Fieldtrip suitable for resting state data (ex. Something that potentially makes use of the resting state recordings)?

If, on the contrary, it seems that the pre-whiten function is not something I could use in my case, I would also appreciate any alternate functions/methods/steps that I could take to still ensure the unwanted effects of the SSS by the MEGIN software are minimized (ie rank deficiency).

Thanks and I would greatly appreciate any thoughts or suggestions,
Sarah
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https://doi.org/10.1371/journal.pcbi.1002202

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