[Mne_analysis] source localizing frequency bands

Wed Dec 2 16:01:19 EST 2009

Hi Gus,
   The noise covariance should ideally be the covariance of whatever is
considered as noise in the signal that you are applying the inverse
operator on. For example, if you are filtering the data between 0.1 and
40Hz and using empty room to calculate the noise covariance, you should
also filter your empty room between 0.1 and 40Hz. This is because the 
signal on which you are going to use the inverse operator has noise
only in the 0.1-40Hz range.

It is true that this or any other filtering will cause noise to be
correlated in time (which it anyway might be), but its usually considered
OK unless the filtering is very extensive such as say 7-12Hz for alpha. Of
course there is no one best way to do this. That noise is uncorrelated in
time is a required assumption for MNE which may or may not hold depending
on what the noise is. My take would be to just not violate it extremely.

The other thing to keep in mind is that filtering can change your SNR and
that has strong effects on the MNE estimates. For example, if there is
some artifact at 50-55 Hz, filtering between 0.1-40Hz will improve the SNR
a lot and that should be recognized when calculating the inverse operator
and the inverse solution.

Hope that helps.

Regards,
Hari

On Wed, December 2, 2009 3:25 pm, Gustavo Sudre wrote:
> Hari,
>
> That makes sense. In other words, the better way to do this would be
> to calculate the noise covariance with unfiltered data, and also do
> source localization with unfiltered data. Then, look for sources that
> have the oscillation of interest? Keep in mind that I'm talking about
> raw data, and not averaged responses. Also, noise covariance would be
> estimated with empty room measurements (or subjecting relaxing, but
> regardless, raw data).
>
> And that brings up another question. Based on this discussion, any
> type of band-pass filtering of the data (be it to single out a narrow
> band, or to filter out likely noise - e.g .1 to 40Hz filtering)
> introduces temporal correlation to the noise, which hurts MNE
> estimates because of its initial assumptions. In that case, would you
> say that making estimates based on the signal prior to any filtering
> is the safest thing to do?
>
> Thanks,
>
> Gus
>
> On Dec 2, 2009, at 3:05 PM, Hari Bharadwaj wrote:
>
>> Hi Gus,
>>  Your intuition that all the estimates should be similar is correct
>> when
>> is no noise. But when there is noise, we have to go back to the math
>> and
>> see what the sources you are looking at actually represent for each of
>> the different kinds of estimates (MNE,MCE, dipole fits, DICS etc.).
>> This
>> is exactly the reason why filtering ahead is different from filtering
>> the MNE solution: The noise which one is trying to avoid when
>> estimating
>> the sources is different in the 2 cases though the underlying 10Hz
>> alpha
>> might be the same.
>>
>> Regards,
>> Hari
>>
>>
>> On Wed, December 2, 2009 2:48 pm, Gustavo Sudre wrote:
>>> Thank you for all the responses. Elli did get to the heart of the
>>> question, and my gut feeling said the same (i.e. that they would not
>>> result in the same thing). It's good to see that the following
>>> answers
>>> seem to provide explanations for it.
>>>
>>> However, if we abstract ourselves from the details of the math behind
>>> it, shouldn't these processes be the same? For example, let's say we
>>> recorded raw MEG signal with a strong 10Hz component to it.
>>>
>>> 1) If I run MCE/DICS in this 10Hz activity, I should get some source
>>> activity that caused it.
>>> 2) If I band-pass the signal to 10Hz and run MNE on it, I will get
>>> some source activity that caused it.
>>> 3) If I run MNE on the signal prior to any filtering, band-pass the
>>> activity in all sources estimates to 10Hz, and focus on the sources
>>> with highest power in 10Hz.
>>>
>>> In all 3 cases, I'm looking for the sources that caused the 10Hz
>>> activity I see in the MEG signal. Then, shouldn't the results of
>>> all 3
>>> methods above agree to a certain degree?
>>>
>>> Before I end this e-mail, I realize that "abstracting from the math"
>>> is not a luxury we can have, since they're the heart of every source
>>> localization technique. But maybe one technique or the other would be
>>> more in accordance with the intuition above?
>>>
>>> Thanks,
>>>
>>> Gus
>>>
>>> On Dec 2, 2009, at 2:36 PM, Hari Bharadwaj wrote:
>>>
>>>> Hi Kanal,
>>>>  You are right, they are are not the same. The reason they are not
>>>> the
>>>> same practically is that the noise covariance when generated after
>>>> bandpass  filtering the signal first can be very very different (in
>>>> scale and possibly also in the spatial structure) and hence the
>>>> inverse
>>>> operator is different.
>>>>
>>>> I would vouch for computing one inverse operator with the entire
>>>> band of
>>>> interest (0-100Hz for example) and then looking at narrower bands
>>>> once the
>>>> data is in source space. My reason for that would be to not impose
>>>> too
>>>> much temporal correlation in the noise by band-pass filtering in
>>>> sensor
>>>> space. MNE as such is equivalent to a maximum aposteriori
>>>> probability
>>>> (MAP) estimate of the source space activity only under the
>>>> assumption that
>>>> the noise is uncorrelated in time. It is robust to violations of the
>>>> assumption to a large extent (correct me if I'm wrong here) but
>>>> filtering
>>>> around 7Hz, for instance to look at alpha makes the noise heavily
>>>> different from its assumed no temporal correlation behaviour.
>>>>
>>>> Having said that, if its an event related paradigm and you have
>>>> enough
>>>> trials and excellent SNR, doing it either way should not make a
>>>> difference.
>>>>
>>>> Regards,
>>>> Hari
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Wed, December 2, 2009 2:11 pm, Kanal Eliezer wrote:
>>>>> Just a few thoughts...
>>>>>
>>>>> I'm not familiar enough to comment on the DICS method, but the MNE
>>>>> method
>>>>> returns a distribution based on the provided sensor waveforms. It
>>>>> would
>>>>> seem intuitive to me that performing a restrictive (say, only alpha
>>>>> activity) bandpass on the sensor waveform prior to performing MNE
>>>>> would
>>>>> significantly change the topology of the waveform, and thus
>>>>> significantly
>>>>> affect how the sources are localized.
>>>>>
>>>>> The real question being asked is whether the steps are commutative;
>>>>> i.e.,
>>>>> do the following two analysis streams produce identical results:
>>>>> 1) bandpass, MNE
>>>>> 2) MNE, bandpass
>>>>> My gut intuition is that they are NOT, since the first method
>>>>> performs the
>>>>> bandpass on the raw MEG data, so to speak, while the second one
>>>>> performs
>>>>> the bandpass on reconstructed data. However, I can't prove this,
>>>>> and it
>>>>> bears further investigation. Anyone else have any thoughts?
>>>>>
>>>>> Elli Kanal
>>>>>
>>>>>
>>>>>
>>>>> On Nov 30, 2009, at 5:20 PM, Gustavo Sudre wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I have a generic question about source localization. From what
>>>>>> I've
>>>>>> seen so far, when the goal is to localize the activity in certain
>>>>>> frequency bands, it's common to use methods such as DICS or the
>>>>>> variant of MCE for frequency bands. I was wondering if it is also
>>>>>> correct to do source localization using a different method (e.g.
>>>>>> MNE)
>>>>>> with the whole signal (i.e. prior to band-pass filtering to
>>>>>> specific
>>>>>> bands) and then convert the signal in the localized sources to
>>>>>> frequency domain. Another alternative would be to band-pass the
>>>>>> signal
>>>>>> to a certain frequency band in source space, and then run a
>>>>>> different
>>>>>> source localization method on it (e.g. MNE).
>>>>>>
>>>>>> Could anyone elaborate on the advantages / disadvantages ( /
>>>>>> validity)
>>>>>> of these two methods?
>>>>>>
>>>>>> Thank you,
>>>>>>
>>>>>> Gus
>>>>>>
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>>>>>
>>>>>
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>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Hari Bharadwaj
>>>
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>>>
>>
>>
>> --
>> Hari Bharadwaj
>
>
>

-- 
Hari Bharadwaj