[Mne_analysis] Mne_analyze SNR estimate

Cushing, Cody CCUSHING1 at mgh.harvard.edu
Tue Oct 13 15:49:11 EDT 2015
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When I produced some stc files using bmin of -200 and bmax of 0, they did match (up to the tenths place at least).  So perhaps this is the issue here, but really this just reverts me back to the same issue I had at the beginning of this thread.  I'll try averaging from the beginning with a baseline of -200 rather than -500 ms and see if that improves the mismatch in the SNR estimate display.  

Cheers,
Cody
________________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman at gmail.com]
Sent: Tuesday, October 13, 2015 3:10 PM
To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] Mne_analyze SNR estimate

so you were able to get the same values when you use the same baseline?



On Tue, Oct 13, 2015 at 2:49 PM, Cushing, Cody
<CCUSHING1 at mgh.harvard.edu> wrote:
> Hi,
>
> Thanks. So for the values I got from mne_analyze:
> t(ms)             dspm
> 133.2             2.40
> 153.6             2.23
> 185.9             1.43
> 219.9             2.72
>
> and from matlab:
> t(ms)             dspm
> 133.2              3.0192
> 153.6             1.6635
> 185.9             .9090
> 219.9             2.6229
>
> I would imagine that as Eric was getting at, it is a baseline correction issue somewhere since the only difference between how I processed this set of data compared to how I traditionally do was the removal of the baseline from everything.
>
> Hope that helps to clarify things.
>
> Cheers,
> Cody
> ________________________________________
> From: mne_analysis-bounces at nmr.mgh.harvard.edu [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman at gmail.com]
> Sent: Tuesday, October 13, 2015 2:22 PM
> To: Discussion and support forum for the users of MNE Software
> Subject: Re: [Mne_analysis] Mne_analyze SNR estimate
>
> when you load an stc file in matlab it is a structure with four fields:
> tmin
> tstep
> vertices
> data
>
> You need to look up the vertex number used in mne-analyze to match it
> to the row of the data matrix.
>
> The reason for this is MNE preserves the original FreeSurfer vertex
> numbers (this makes many subsequent steps easier).
>
> hth
> d
>
> On Tue, Oct 13, 2015 at 2:06 PM, Cushing, Cody
> <CCUSHING1 at mgh.harvard.edu> wrote:
>> Hi,
>>
>> I'm trying to do what you asked, but I got a noobie question for you.  Is there a way to either have mne_analyze display the average dspm value for a label you've drawn? Or vice versa, I'm having trouble matching up the vertex number from mne_analyze in matlab to directly compare the numerical values.  When I use mne_read_stc_file in matlab, it shows 6360 vertices, but the vertex number I'm looking for from mne_analyze is much higher (I was trying to find vertex # 11967 for example).  I tried just dropping the first digit, but that wasn't yielding a meaningful comparison. Am I approaching how to do this comparison all wrong? Sorry for the naivete
>>
>> Cheers,
>> Cody
>> ________________________________________
>> From: mne_analysis-bounces at nmr.mgh.harvard.edu [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of dgw [dgwakeman at gmail.com]
>> Sent: Tuesday, October 13, 2015 1:22 PM
>> To: Discussion and support forum for the users of MNE Software
>> Subject: Re: [Mne_analysis] Mne_analyze SNR estimate
>>
>> 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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