[Mne_analysis] Mne_analyze SNR estimate

[dgw]

Hi Cody,

Can you tell us exactly how the numbers differ? : click on a point get
the value in mne_analyze, then extract that same timepoint in matlab
get the value, and tell us what the difference is (for a few points).
Judging just from the y-axis is difficult.

Thanks,
d

On Tue, Oct 13, 2015 at 1:11 PM, Cushing, Cody
<CCUSHING1 at mgh.harvard.edu> wrote:
> Hi Alex,
>
> 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.
>
> Cheers,
> Cody
>
> ________________________________________
> From: mne_analysis-bounces at nmr.mgh.harvard.edu [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Alexandre Gramfort [alexandre.gramfort at telecom-paristech.fr]
> Sent: Tuesday, October 06, 2015 11:43 AM
> To: Discussion and support forum for the users of MNE Software
> Subject: Re: [Mne_analysis] Mne_analyze SNR estimate
>
> hi Cody,
>
> to me you hit a problem I have seen a few times that the stats of the
> baseline differs from the stats of the end of your epochs. As you
> estimate the noise cov from baseline it generates what you describe.
>
> A way around this I have seen working is to highpass the data and
> don't do any extra baselining. The difficulty here is that you might
> distort the ERP/ERF by highpass filtering.
>
> makes sense?
>
> Alex
>
> On Tue, Oct 6, 2015 at 4:18 PM, Cushing, Cody <CCUSHING1 at mgh.harvard.edu> wrote:
>> Hi all,
>>
>> This is likely a naive question, but I couldn't find much help for myself
>> either in the manual or browsing the mne_analysis archives.  So, if I
>> understand correctly, in mne_analyze, the SNR estimate display window shows
>> what the data is expected to be with the red line and then shows the
>> mismatch between the actual data and expected data with the green line (so
>> the high amplitude difference between the green and red lines is bad yes?).
>> Fairly unanimously, all of my subjects start off with both lines hugging
>> each other pretty tight, but on some of my participants, the green line
>> rises pretty sharply towards the end of the epoch.  My trial length is
>> relatively long, but nothing absurd (about 1s).  My question is, what
>> factors go in to computing this mismatch?  Is it something in the
>> computation of the noise covariance matrix or the inverse solution that I
>> can tweak parameters on to try and improve the apparent mismatch?  Or does
>> this just represent subjects that aren't able to stay still and end up
>> fidgeting or blinking or something towards the end of the trial?  Thanks for
>> any help, and I am of course happy to supply any further info that would
>> help answer my question.
>>
>> Cheers,
>> Cody Cushing
>>
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