[Eeglablist] Fwd: SIFT toolbox

Makoto Miyakoshi mmiyakoshi at ucsd.edu
Tue Aug 6 18:18:15 PDT 2019


Dear Aikaterini,

> Do you think it will be possible to be released before September?

I have no idea about the schedule, it's up to the developer of the plugin.
I would rather suggest that you make a tiny modification on the original
SIFT code, which is much easier for us for the time being.
I made an update for you in my Wiki page. Please follow the instruction
here and fix the problem. Also, please follow my explanation carefully, and
stay as conservative as possible after making the change.
https://sccn.ucsd.edu/wiki/Makoto%27s_preprocessing_pipeline#SIFT_tips_.2808.2F06.2F2019_updated.29

Makoto


On Fri, Aug 2, 2019 at 7:34 AM AIKATERINI LYMPERIDOU <
med1p1040133 at med.uoc.gr> wrote:

> Thank you for your kindness to reply and help us with this.
> It will be great for me to have the corrected "SIFT toolbox" and use
> it for my Master thesis.
> Do you think it will be possible to be released before September?
> (if not, I can use the solution you mentioned in your preprocessing
> pipeline)
>
> Thank you again,
> Aikaterini Lymperidou
>
>
>
> Quoting Makoto Miyakoshi <mmiyakoshi at ucsd.edu>:
>
> > 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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> >> >>
> >> >>
> >> >>
> >>
> >>
> >>
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> >
> >
> > --
> > Makoto Miyakoshi
> > Assistant Project Scientist, Swartz Center for Computational Neuroscience
> > Institute for Neural Computation, University of California San Diego
>
>
>
>

-- 
Makoto Miyakoshi
Assistant Project Scientist, Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego


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