[FieldTrip] LCMV giving conflicting results vs SAM and DICS

Eelke Spaak eelke.spaak at donders.ru.nl
Thu Nov 28 11:22:04 CET 2013 

Hi Haris,

Sorry for the slow reply, I had other stuff to do for a while. It
seems that you have indeed stumbled on a bug, unfortunately. Let's
move the discussion over to bugzilla:
http://bugzilla.fcdonders.nl/show_bug.cgi?id=2395 Feel free to
contribute anything there if you like (you can create an account if
you don't have one yet). Hopefully we will be able to fix this soon.

Best,
Eelke

On 29 October 2013 00:02, Charidimos Tzagarakis <haristz at gmail.com> wrote:
> Hi Eelke,
> I have now run a test which I think does what you describe.
> cfg.keeptrials='yes'  for the calls to ft_timelockanalysis and
> ft_sourcenalysis that generate the filter.
> cfg.keeptrials='no' for all the other calls to these 2 functions (those that
> generate the 2 conditions to be compared).
> The result is still the same (ie not what I would call the 'correct' one,
> but rather what seems to be based on an evoked response covariance matrix).
> I should stress again that how I set keeptrials in ft_timelockanalysis is
> also how I set it for the "matched" call to ft_sourceanalysis (It didn't
> seem to me that this matters anyway as unless cfg.rawtrial='yes',
> ft_sourceanalysis handles both cases so that what is used further down is
> the same but I may be wrong in this) .
> Best,
> Haris
>
>
> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>
>
>
>
> On 28 October 2013 05:26, Eelke Spaak <eelke.spaak at donders.ru.nl> wrote:
>>
>> Hi Charidimos,
>>
>> If I understand you correctly, you specified cfg.keeptrials = 'no' in
>> the calls to ft_timelockanalysis prior to the *first* call of
>> ft_sourceanalysis, right? Could you try what happens when you specify
>> it in ft_timelockanalysis prior to the second call to
>> ft_sourceanalysis (so the step where the precomputed filter is
>> applied)?
>>
>> Thanks,
>> Eelke
>>
>> On 25 October 2013 01:06, Charidimos Tzagarakis <haristz at gmail.com> wrote:
>> > Hi Eelke,
>> > Thank you for looking into this!
>> > The piece of code I commented out is indeed [790:836] (changing line 784
>> > accordingly or alternatively adding a copy of 785-789 after 790).
>> > I did try running ft_timelockanalysis with keeptrials='no' for all 3
>> > calls
>> > and that resulted in the same behaviour as before for LCMV (ie not the
>> > "correct" one). I also tried it   setting keeptrials='no' in
>> > ft_sourceanalysis at the same time (ie keeptrials='no' for both
>> > ft_timelockanalysis and ft_sourceanalysis) which had the same outcome (I
>> > actually had run these tests before posting but wanted to 2ble check).
>> > I may however be confused here because there are some other possible
>> > combinations with keeptrials since for each subject there is a total of
>> > 6
>> > calls to functions that accept it as an input and the filter is
>> > estimated
>> > with only 2 of them.
>> > Do let me know if there is another combination I should run and I will
>> > do
>> > that.
>> > Best,
>> > Haris
>> >
>> > Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
>> > University of Minnesota Dept of Neuroscience and Brain Sciences Center
>> >
>> >
>> > On 24 October 2013 03:08, Eelke Spaak <eelke.spaak at donders.ru.nl> wrote:
>> >>
>> >> Hi Charidimos,
>> >>
>> >> Thanks for your elaborate e-mail. We discussed this issue in
>> >> yesterday's FieldTrip meeting. It is very reasonable that you expect
>> >> the three methods to produce the same results, and the code/interface
>> >> indeed suggests that this would be the case. In other words, we need
>> >> to clean up this part of the code to produce consistent results;
>> >> however, this might take a while.
>> >>
>> >> We believe the discrepancy is caused by the fact that you compute the
>> >> covariance while specifying cfg.keeptrials = 'yes', which is
>> >> unnecessary while computing the filter. This results in a covariance
>> >> matrix with dimensions trial X channel X channel, which then is
>> >> subsequently averaged over trials during ft_sourceanalysis. Likely the
>> >> filter is still in fact computed on the averaged covariance, as it
>> >> should be. However, the subsequent projection of data through the
>> >> filter will not first average the covariance, and will in essence only
>> >> project the first trial through the filter. (This is because the dip{}
>> >> fields will be struct arrays of dimension nTrial X 1, and in an
>> >> assignment a(1).b = 2; a(2).b = 3; x = a; then x will be 2, so
>> >> everything but the first element of a struct array is ignored in an
>> >> assignment statement.)
>> >>
>> >> Could you try to compute the covariance with cfg.keeptrials = 'no' and
>> >> then run LCMV again? This will still compute the covariance on the raw
>> >> traces, not on the average. If our hunch is right, you should get the
>> >> correct results then.
>> >>
>> >> As said, this is indeed messy and unclear, our apologies for that.
>> >>
>> >> Finally, could you tell us what part of the code you commented out to
>> >> make the results consistent? We suspect it will be between lines 790
>> >> and 835, but it would be helpful to know for sure.
>> >>
>> >> Best,
>> >> Eelke
>> >>
>> >>
>> >> On 23 October 2013 21:43, Charidimos Tzagarakis <haristz at gmail.com>
>> >> wrote:
>> >> > Hi Don,
>> >> > Thanks for your reply. I do agree that some of these beamformers
>> >> > are probably better suited than others to study beta
>> >> > desynchronisation,
>> >> > or
>> >> > generally questions in the frequency domain. I in fact started from
>> >> > DICS.
>> >> > The reason I looked at LCMV and SAM is to be sure that I get
>> >> > consistent
>> >> > results (and also because my experiment can also address some
>> >> > additional
>> >> > time domain questions, so I wanted to see what happens when my data
>> >> > goes
>> >> > from one to the other). I therefore tried to set them up so I that
>> >> > the
>> >> > results from all 3 are similar. So you are correct in pointing out
>> >> > that
>> >> > my
>> >> > question is why SAM and LCMV produce different results. Based on
>> >> > their
>> >> > description within the fieldtrip website and mailing list (if I have
>> >> > interpreted these correctly) they should be treating the covariance
>> >> > matrix
>> >> > in the same way (to get a true evoked response covariance matrix you
>> >> > would
>> >> > normally need the extra call to ft_timelockanalysis that I show at
>> >> > the
>> >> > last
>> >> > piece of code in my post). Also , if the covariance matrix is indeed
>> >> > the
>> >> > issue, it seems that the change in how it is treated in the
>> >> > ft_sourceanalysis code (based on the "hack" I described) is unique to
>> >> > LCMV
>> >> > (none of the other beamformer options share that piece of code) and
>> >> > is
>> >> > active only when LCMV is given a precomputed filter which is (I
>> >> > think)
>> >> > unusual.
>> >> > Hence my question!
>> >> > Best,
>> >> > Haris
>> >> >
>> >> > Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
>> >> > University of Minnesota Dept of Neuroscience and Brain Sciences
>> >> > Center
>> >> >
>> >> >
>> >> >
>> >> > On 23 October 2013 13:31, Rojas, Don <Don.Rojas at ucdenver.edu> wrote:
>> >> >>
>> >> >> Haris,
>> >> >>
>> >> >> Sorry - In my last post, I mistakenly put DICS and the Fieldtrip
>> >> >> implementation of SAM into the same frequency domain category. In
>> >> >> Fieldtrip,
>> >> >> SAM is a time-domain technique and is not the same as the
>> >> >> implementation of
>> >> >> SAM that has been used in the published literature for beta ERD. So,
>> >> >> are you
>> >> >> then wondering why the two time-domain approaches produce differing
>> >> >> results?
>> >> >> That probably does depend on how the covariance matrix is
>> >> >> calculated.
>> >> >> Although I still think it is a bad idea to use a time-domain
>> >> >> beamformer
>> >> >> on
>> >> >> motor beta ERD/ERS.
>> >> >>
>> >> >> Best,
>> >> >>
>> >> >> Don
>> >> >>
>> >> >>
>> >> >>
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>> >> >
>> >> >
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