[Mne_analysis] source estimate stc files and current source density estimates

Thu Apr 10 11:58:43 EDT 2014

Yes, in mne_analyze.

HTH,
D

On Thu, Apr 10, 2014 at 11:52 AM, David Leitman
<leitman at mail.med.upenn.edu> wrote:
>
> Thanks for the clarification Please see below:
> Sent from my iPhone
>
>> On Apr 10, 2014, at 11:32 AM, dgw <dgwakeman at gmail.com> wrote:
>>
>> Hi David,
>>
>> Please see my replies in text
>>
>> On Thu, Apr 10, 2014 at 11:21 AM, David I Leitman
>> <leitman at mail.med.upenn.edu> wrote:
>>> Hi D,
>>>
>>> To be clear: the " dSPM value "units reported on  the y axis of figures such
>>> as plot_compute_mne_inverse.py are real and by "Am" do you mean micro
>>> Amperes?
>>
>> No this is not true for dSPM only for the L2 solutions (both can be
>> calculated by mne).
> Is this done by selecting method "MNE"  instead of "dSPM"
>> . By Am, I mean Ampere meters:
>> https://en.wikipedia.org/wiki/Ampere-meter.
>>
>> HTH,
>> D
>>
>>>
>>> if so I am then really confused by the MNE manual(6.2): in the section on
>>> Minimum norm estimates : It really suggests that the dSPM output is a stat
>>> because of the noise normalization procedure conducted: see below:
>>>
>>> Noise normalization
>>>
>>> The noise-normalized linear estimates introduced by Dale et al. require
>>> division of the expected current amplitude by its variance. Noise normal-
>>> ization serves three purposes:
>>>
>>> It converts the expected current value into a dimensionless statistical test
>>> variable. Thus the resulting time and location dependent values are often
>>> referred to as dynamic statistical parameter maps (dSPM).
>>>
>>> It reduces the location bias of the estimates. In particular, the tendency
>>> of the MNE to prefer superficial currents is eliminated.
>>>
>>> The width of the point-spread function becomes less dependent on the source
>>> location on the cortical mantle. The point-spread is defined as the MNE
>>> resulting from the signals coming from a point current source (a current
>>> dipole) located at a certain point on the cortex.
>>>
>>> In practice, noise normalization requires the computation of the diagonal
>>> elements of the matrix
>>>
>>> M C M T = M ̃ M ̃ T .
>>> With help of the singular-value decomposition approach we see directly
>>>
>>> that
>>>
>>> M ̃ M ̃ T = V Γ 2 V T .
>>>
>>> Under the conditions expressed at the end of Section 6.2.5, it follows that
>>> the t-statistic values associated with fixed-orientation sources) are thus
>>> proportional to L while the F-statistic employed with free-orientation
>>> sources is proportional to L , correspondingly.
>>>
>>> Note: A section discussing statistical considerations related to the noise
>>> normalization procedure will be added to this manual in one of the subse-
>>> quent releases.
>>>
>>> Note: The MNE software usually computes the square roots of the F-sta-
>>> tistic to be displayed on the inflated cortical surfaces. These are also
>>> pro- portional to L .
>>>
>>> On Apr 9, 2014, at 10:23 PM, dgw wrote:
>>>
>>> Hi David
>>> The l2 results are in "real units" Am.
>>>
>>> For the second question, you could ( though it would only make some sense to
>>> do with the l2 ( for the above reason). But it is not likely to provide you
>>> with different information if running it on averaged data(epochs may be
>>> interesting though). As for the other details the units would depend on what
>>> analysis you ran. There are examples in mne-python of several available
>>> functions. As for the normality question some support for permutation
>>> testing is implemented,but obviously choosing the right statistic will
>>> depend on your particular question and data.
>>> Hth
>>> D
>>>
>>> David I Leitman <leitman at mail.med.upenn.edu> wrote:
>>>>
>>>> HI all,
>>>>
>>>> I have been trying to figure out how to get a measure of current source
>>>> density from the l2 min-norm source model. It seems that both methods dSPM
>>>> and MNE that I use, yield  arbitrary or r  statistical values (MNe manual
>>>> 6.2.6). From what i can tell this is do to the noise normalization step as
>>>> described in the MNE manual is there any way to get a CSD measure in
>>>> microamps or something real?
>>>>
>>>> My second question is if I pass my epoched or evoked data through the mne
>>>> L2 min-norm source model using  mne or dSPM as the method, Can the resulting
>>>> time-series data comprising these MNE or dSPM values be submitted to
>>>> temporo-spectral analysis? If so how is power at a particular frequency
>>>> calculated? and if you can only get db change, how do wavelet or FFT
>>>> procedure used to measure oscillations conform to statistical distributions
>>>> like the f distribution in-terms of their non-normality and tendency to be
>>>> skewed? I sho uld say I am not a statistician ... so this latter point may
>>>> be a non-starter:)
>>>>
>>>> Finally, is the above a problem for the beamforming routines detailed in
>>>> MNE python? I do not know much about this approach.
>>>>
>>>> thanks so much
>>>>
>>>> david
>>>>
>>>>
>>>> David I. Leitman PhD
>>>>
>>>> Research Assistant Professor
>>>> Department of Psychiatry-
>>>> Neuropsychiatry program
>>>> Perelman School of Medicine
>>>> University of Pennsylvania
>>>> Gates Pavilion 10th floor room 1042
>>>> 3400 Spruce St
>>>> Philadelphia, PA 19104-4283
>>>> P: (215) 662-7389
>>>> F: (215) 662-7903
>>>> E: leitman at mail.med.upenn.edu
>>>> Faculty page:
>>>> http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343
>>>> Lab website:
>>>> http://davidileitman.com
>>>>
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>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>> David I. Leitman PhD
>>>
>>> Research Assistant Professor
>>> Department of Psychiatry-
>>> Neuropsychiatry program
>>> Perelman School of Medicine
>>> University of Pennsylvania
>>> Gates Pavilion 10th floor room 1042
>>> 3400 Spruce St
>>> Philadelphia, PA 19104-4283
>>> P: (215) 662-7389
>>> F: (215) 662-7903
>>> E: leitman at mail.med.upenn.edu
>>> Faculty page: http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343
>>> Lab website:
>>> http://davidileitman.com
>>>
>>> The information contained in this e-mail message is intended only for the
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