[Mne_analysis] Mne_analyze SNR estimate

[Eric Larson]

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.

Eric


On Tue, Oct 13, 2015 at 1:22 PM, dgw <dgwakeman at gmail.com> wrote:

> 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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