[Eeglablist] Fwd: SIFT toolbox

Makoto Miyakoshi mmiyakoshi at ucsd.edu
Thu Jul 11 17:00:29 PDT 2019


Dear Akiterini and Matt,

I found an error in SIFT model order validation part. The SIFT function and
the SIFT manual uses [number of channels/component]^2 in the numerator, but
according to the original references it is NOT square. I mentioned it in my
wiki page. See step 18. I have already talked to Tim, and he said he would
do something for this soon.
https://sccn.ucsd.edu/wiki/Makoto's_preprocessing_pipeline#Dependency_across_the_preprocessing_stages_.2807.2F05.2F2019_updated.29


Makoto

On Mon, Jul 8, 2019 at 6:59 AM AIKATERINI LYMPERIDOU <
med1p1040133 at med.uoc.gr> wrote:

> Thank you very much for your time and your answer!
> That was really helpful for me!
>
>
> Quoting Matt Gerhold <matt.gerhold at gmail.com>:
>
> > If the residuals aren't white, that means not all the information in the
> > timeseries has been absorbed into the coefficient matrix.
> >
> >
> >
> > In terms of the math, if you look at the equations for the VAR model, the
> > modelling procedure should extract the coefficient matrices upto a given
> > lag/model order, added to this is a noise component. The noise component
> is
> > by definition, gaussian and white: all the observations are independent
> > from each other, across time and across channels. So, if you have
> > successfully modelled the data, then the residuals should be white. If
> you
> > have one or two models across time that don't fit this, i.e. 96.5% of
> > models are white, then that is alright as well.
> >
> >
> >
> > So, you have to go back to the pre-processing stage and tend to your
> > datasets to ensure you get all the information out of the data and into
> the
> > model coefficients. It all has to do with careful pre-processing. They
> are
> > not the easiest models to fit, so you have to proceed with a certain
> level
> > of determination.
> >
> >
> > On Mon, Jul 8, 2019 at 1:52 PM AIKATERINI LYMPERIDOU <
> > med1p1040133 at med.uoc.gr> wrote:
> >
> >> Thank you for the answer Matthew.
> >>
> >> The thing is that my model pass the "percent consistency test" and the
> >> "stability index test" but did not pass the "Residual whiteness test".
> >> Is that an important issue as well?
> >>
> >> Quoting Matt Gerhold <matt.gerhold at gmail.com>:
> >>
> >> > Aikaterini:
> >> >
> >> > You do need to validate your model(s). Reviewers and examiners will
> >> request
> >> > validation statistics. This should include:
> >> >
> >> >    - Whiteness of residuals
> >> >    - Test for model stability
> >> >    - A check if the residuals are Gaussian (optional for some)
> >> >
> >> > This tells us whether the modelling procedure has been successfully
> >> applied
> >> > to the data. Window length in relation to model order can contribute
> to
> >> > estimation bias, so these parameters have to be chosen carefully.
> Often,
> >> > one has to pre-process cautiously and iterate through a few models in
> >> order
> >> > to get a good final model that satisfies the criteria.
> >> >
> >> > Rgds,
> >> >
> >> > Matthew
> >> >
> >> >
> >> >
> >> > On Mon, Jul 8, 2019 at 12:51 PM AIKATERINI LYMPERIDOU <
> >> > med1p1040133 at med.uoc.gr> wrote:
> >> >
> >> >>
> >> >> I just noticed that I can compute the connectivity measures
> >> >> successfully even my model does not pass the Validation Tests. So if
> >> >> you are facing the same problem, just go the next step without
> >> >> bothering a lot. The most important things are Model Order selection,
> >> >> the selection of the window step and the window length.
> >> >>
> >> >> Hope you the very best!
> >> >>
> >> >>
> >> >>
> >> >> Quoting AIKATERINI LYMPERIDOU <med1p1040133 at med.uoc.gr>:
> >> >>
> >> >> > Please note that the window for the "Model Validation Results"
> >> >> > appears but none of the windows pass the "Residual Whiteness Test"
> >> >> > and the graph for the "Whiteness Significance" does not appear.
> >> >> >
> >> >> > I cannot understand if this is a problem of preprocessing or I am
> >> >> > missing something.
> >> >> >
> >> >> >
> >> >> >
> >> >> > Quoting AIKATERINI LYMPERIDOU <med1p1040133 at med.uoc.gr>:
> >> >> >
> >> >> >> Hello to everyone!
> >> >> >>
> >> >> >> I am using the SIFT toolbox (EEGLAB-compatible toolbox for
> analysis
> >> >> >> and visualization of multivariate causality).
> >> >> >>
> >> >> >> My data are task-related (button pushed when the subject realize
> if
> >> >> >> he see a figure inside the context of the whole pictue ). I used
> >> >> >> filtering (bandpass filter (2:65), hamming window) and
> >> >> >> preprocessing and the other steps the group of SIFT recommends for
> >> >> >> analysis in their "SIFT_Practicum"
> >> >> >> (https://sccn.ucsd.edu/wiki/SIFT) for a sample dataset.
> >> >> >>
> >> >> >>
> >> >> >> Unfortunately, in the step of "Validate Model" I get this error.
> >> >> >>
> >> >> >> Warning: defaultParallelConfig will be removed in a future
> release.
> >> Use
> >> >> >> parallel.defaultClusterProfile instead.
> >> >> >> WARNING: The MVAR algorithm 'BSBL L1' depends on BSBL_L1_noise.m,
> >> >> >> which cannot be located on the path. This algorithm will not be
> >> >> >> available.
> >> >> >> Constant detrending each window...
> >> >> >> done.
> >> >> >> Done.
> >> >> >> WARNING: The MVAR algorithm 'BSBL L1' depends on BSBL_L1_noise.m,
> >> >> >> which cannot be located on the path. This algorithm will not be
> >> >> >> available.
> >> >> >> Warning: defaultParallelConfig will be removed in a future
> release.
> >> Use
> >> >> >> parallel.defaultClusterProfile instead.
> >> >> >> Constant detrending each window...
> >> >> >> done.
> >> >> >> Done.
> >> >> >> Undefined function or variable "f".
> >> >> >>
> >> >> >> Error in findobjuser (line 45)
> >> >> >> h = h(f);
> >> >> >> Error in PropertyGrid/FindPropertyGrid (line 409)
> >> >> >>            h = findobjuser(@(userdata) userdata.(member) == obj,
> >> >> >> '__PropertyGrid__');
> >> >> >>
> >> >> >> Error in PropertyGrid.OnPropertyChange (line 428)
> >> >> >>            self = PropertyGrid.FindPropertyGrid(obj, 'Model');
> >> >> >>
> >> >> >> Done.
> >> >> >>
> >> >> >>
> >> >> >> Could anyone face the same error as me?
> >> >> >> I would really appreciate it if you have any idea why this is
> >> happening.
> >> >> >>
> >> >> >> Thank you,
> >> >> >> Katerina
> >> >> >>
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> >> >> >
> >> >> >
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>
>
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-- 
Makoto Miyakoshi
Assistant Project Scientist, Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego


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