<div dir="ltr">Also, I think mne_analyze baseline corrects from -0.2 to 0 by default, which might not happen in the MATLAB code. This could introduce a vertical shift.<div><br></div><div>Eric</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Oct 13, 2015 at 1:22 PM, dgw <span dir="ltr"><<a href="mailto:dgwakeman@gmail.com" target="_blank">dgwakeman@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Cody,<br>
<br>
Can you tell us exactly how the numbers differ? : click on a point get<br>
the value in mne_analyze, then extract that same timepoint in matlab<br>
get the value, and tell us what the difference is (for a few points).<br>
Judging just from the y-axis is difficult.<br>
<br>
Thanks,<br>
d<br>
<br>
On Tue, Oct 13, 2015 at 1:11 PM, Cushing, Cody<br>
<div class="HOEnZb"><div class="h5"><<a href="mailto:CCUSHING1@mgh.harvard.edu">CCUSHING1@mgh.harvard.edu</a>> wrote:<br>
> Hi Alex,<br>
><br>
> So this strategy worked great, but it has caused me to run into a new problem that I wasn't sure if you'd be able to help me with. When I try to produce stc files then extract from label files made in mne_analyze from the data processed using the strategy below, the data appears to become shifted on the y-axis across my subjects. The shape of the waveform itself is fine and is what is to be expected, but they are all shifted up or down on the y-axis (e.g. some start at -2, -6, 4, etc.). This is not how they appear in mne_analyze and I am using dSPM values across the board, but when I extract the stc data from the label files in the matlab toolbox I encounter the problem. Thanks for any help.<br>
><br>
> Cheers,<br>
> Cody<br>
><br>
> ________________________________________<br>
> From: <a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu">mne_analysis-bounces@nmr.mgh.harvard.edu</a> [<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu">mne_analysis-bounces@nmr.mgh.harvard.edu</a>] on behalf of Alexandre Gramfort [<a href="mailto:alexandre.gramfort@telecom-paristech.fr">alexandre.gramfort@telecom-paristech.fr</a>]<br>
> Sent: Tuesday, October 06, 2015 11:43 AM<br>
> To: Discussion and support forum for the users of MNE Software<br>
> Subject: Re: [Mne_analysis] Mne_analyze SNR estimate<br>
><br>
> hi Cody,<br>
><br>
> to me you hit a problem I have seen a few times that the stats of the<br>
> baseline differs from the stats of the end of your epochs. As you<br>
> estimate the noise cov from baseline it generates what you describe.<br>
><br>
> A way around this I have seen working is to highpass the data and<br>
> don't do any extra baselining. The difficulty here is that you might<br>
> distort the ERP/ERF by highpass filtering.<br>
><br>
> makes sense?<br>
><br>
> Alex<br>
><br>
> On Tue, Oct 6, 2015 at 4:18 PM, Cushing, Cody <<a href="mailto:CCUSHING1@mgh.harvard.edu">CCUSHING1@mgh.harvard.edu</a>> wrote:<br>
>> Hi all,<br>
>><br>
>> This is likely a naive question, but I couldn't find much help for myself<br>
>> either in the manual or browsing the mne_analysis archives. So, if I<br>
>> understand correctly, in mne_analyze, the SNR estimate display window shows<br>
>> what the data is expected to be with the red line and then shows the<br>
>> mismatch between the actual data and expected data with the green line (so<br>
>> the high amplitude difference between the green and red lines is bad yes?).<br>
>> Fairly unanimously, all of my subjects start off with both lines hugging<br>
>> each other pretty tight, but on some of my participants, the green line<br>
>> rises pretty sharply towards the end of the epoch. My trial length is<br>
>> relatively long, but nothing absurd (about 1s). My question is, what<br>
>> factors go in to computing this mismatch? Is it something in the<br>
>> computation of the noise covariance matrix or the inverse solution that I<br>
>> can tweak parameters on to try and improve the apparent mismatch? Or does<br>
>> this just represent subjects that aren't able to stay still and end up<br>
>> fidgeting or blinking or something towards the end of the trial? Thanks for<br>
>> any help, and I am of course happy to supply any further info that would<br>
>> help answer my question.<br>
>><br>
>> Cheers,<br>
>> Cody Cushing<br>
>><br>
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