<div dir="ltr"><div>Hi Jan-Mathijs, <br></div><div><br></div><div>Thank you for your response!<br></div><div><br></div><div>Yes, I agree that using other resting state data may throw away the baby with the bathwater as you say. I suppose what I was thinking when writing my message and mentioned to "make use of the resting state recordings" was potentially using "a part" of the resting state data as a way to estimate the noise data - that is, preprocessing and filtering the RS data in the upper most range, ex. 150Hz+ - upper limit Hz, to use as the estimate of the noise data in the pre-whitening function. (This freq range I'm guessing may more likely contain less physiologic data and more noise). </div><div><br></div><div>I guess maybe this still might slightly throw away the baby with the bathwater, but nevertheless was just trying to think about solutions to improve beamforming in cases where it is maybe more necessary (ex.connectivity/cross-frequency coupling analyses). <br></div><div><br></div><div>Nevertheless, thanks again for your help!</div><div>Sarah<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, May 16, 2024 at 5:18 PM Sarah <<a href="mailto:s83728498@gmail.com">s83728498@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">





<p style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:"Helvetica Neue"">Hello Fieldtrippers!</p>
<p style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:"Helvetica Neue";min-height:15px"><br></p>
<p style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:"Helvetica Neue"">I’ve recently learned from this wonderful paper by our very own Fieldtrip developers “A unified view on beamformers for M/EEG source reconstruction” (<a href="https://www.sciencedirect.com/science/article/pii/S1053811921010612" target="_blank"><span style="color:rgb(220,161,13)">https://www.sciencedirect.com/science/article/pii/S1053811921010612</span></a>) 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.<span> </span></p>
<p style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:"Helvetica Neue";min-height:15px"><br></p>
<p style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:"Helvetica Neue"">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.<span> </span></p>
<p style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:"Helvetica Neue";min-height:15px"><br></p>
<p style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:"Helvetica Neue"">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)?</p>
<p style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:"Helvetica Neue";min-height:15px"><br></p>
<p style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:"Helvetica Neue"">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).<span> </span></p>
<p style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:"Helvetica Neue";min-height:15px"><br></p>
<p style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:"Helvetica Neue"">Thanks and I would greatly appreciate any thoughts or suggestions,<span> </span></p>
<p style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:"Helvetica Neue"">Sarah</p></div>
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