[Mne_analysis] Mne_analyze SNR estimate

Cushing, Cody CCUSHING1 at mgh.harvard.edu
Tue Oct 13 14:49:06 EDT 2015
Search archives:

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
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>>> error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis



More information about the Mne_analysis mailing list