[Mne_analysis] group dSPM?

[Hari Bharadwaj]

Hi Alex,

  If you combine using A = x^2 + y^2 + z^2 (i.e without the square root or
square what MNE gives you) and if x,y,z are *after noise normalization*,
then it is reasonable to assume that A is chi2 as long as the noise
covariance was computed using a large number of points, I wouldn't be
concerned about variances being different since each has approximately
variance 1 in the null...

The maps we have gotten from running long permutation tests at the group
level and then thresholding using this transformation look very similar.
So our current practice is to use this transform and run the usual
parametric analyses and invest time in running permutations as
confirmation once we see something we like.

Regards,
Hari



On Fri, June 8, 2012 11:38 am, Alexandre Gramfort wrote:
> hi,
>
> MNE assembles orientation with sqrt(x^2 + y^2 + z^2)
> The problem that can happen is that since you're likely to use loose
> orientation the variance of x, y and z component will be different
> but also the number of trials for each subject will vary causing
> amplitude differences in dSPM values.
>
> @hari : do you agree? From your experience does your chi2->T
> transformation
> somehow reduces the problem?
>
> Alex
>
> On Fri, Jun 8, 2012 at 5:30 PM, Hari Bharadwaj <hari at nmr.mgh.harvard.edu>
> wrote:
>> Hi Elena,
>>  If you are using a fixed orientation solution, then the dSPMs are z
>> scores and can be combined in group studies using t-stats etc..
>>
>> If you are using a free orientation solution, then depending on how you
>> combine the compnents you end up with an F or a chi2.. Atleast as a
>> first
>> pass, you could compute group stats using a transform such as that goes
>> from chi2 (with 3 dof) to Z such as:
>>   y = (x/3)^(1/3)
>> y is then approximately distributed normally with mean (1 - 2/27)and
>> variance (2/27)
>>
>> See: Wilson, E.B.; Hilferty, M.M. (1931) "The distribution of
>> chi-squared". Proceedings of the National Academy of Sciences,
>> Washington,
>> 17, 684–688.
>>
>>
>> We have usually dSPM scores non-parametrically (i.e using permutation
>> type
>> tests) at the group level which might be the cleanest way of doing it
>> but
>> very slow.
>> See: http://www.ncbi.nlm.nih.gov/pubmed/11747097
>>
>>
>> Regards,
>> Hari
>>
>>
>>
>>
>> On Fri, June 8, 2012 10:22 am, Alexandre Gramfort wrote:
>>> Hello Elena,
>>>
>>> there is one way that would consist is keeping track on the noise
>>> normalization
>>> used for each subject dSPM, then morph the noise normalization values
>>> too
>>> and then do the maths to average MNE estimates and divide by the mean
>>> noise normalization.
>>>
>>> Unfortunately there is build in way to do this currently...
>>>
>>> Alex
>>>
>>> On Fri, Jun 8, 2012 at 11:55 AM, Elena Orekhova
>>> <Elena.Orekhova at neuro.gu.se> wrote:
>>>> Dear MNE community,
>>>>
>>>>
>>>>
>>>> I would like to estimate reliability of the MNE activations on a group
>>>> level.  dSPM, that give us F values, can be performed in a single
>>>> subjects,
>>>> but what is about GROUP dSPM?
>>>>
>>>>
>>>>
>>>> I have seen the presentation by Daniel Goldenholz, where he speculates
>>>> on
>>>> possibility of the ‘group dSPM’ and I have seen the post by Marina
>>>> Papoutsi
>>>> (from February 18, 2009), where she tried to implement this analysis.
>>>> However, there was no news on this topic since then.  Does anybody use
>>>> the
>>>> ‘group dSPM’ and/or has any practical hints on that?
>>>>
>>>>
>>>>
>>>> Elena
>>>>
>>>>
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>>
>>
>> --
>> Hari Bharadwaj
>> PhD Candidate, Biomedical Engineering,
>> Boston University
>> 677 Beacon St.,
>> Boston, MA 02215
>>
>> Martinos Center for Biomedical Imaging,
>> Massachusetts General Hospital
>> 149 Thirteenth Street,
>> Charlestown, MA 02129
>>
>> hari at nmr.mgh.harvard.edu
>> Ph: 734-883-5954
>>
>>
>
>
>


-- 
Hari Bharadwaj
PhD Candidate, Biomedical Engineering,
Boston University
677 Beacon St.,
Boston, MA 02215

Martinos Center for Biomedical Imaging,
Massachusetts General Hospital
149 Thirteenth Street,
Charlestown, MA 02129

hari at nmr.mgh.harvard.edu
Ph: 734-883-5954