[Eeglablist] AMICA

[Samran]

Hi Lina,

For the error message, try removing spaces from the path of directories
which contain the data and EEGLAB, e.g.
for eeglab it can be something like C:\user\eeglab\plugins\amica
and for data: D:\data_EEG\subject_1\eeg_1.set

You can use the following line of code to extract the marked ICs
reject_IC_components = EEG.reject.gcompreject;

later, to reject the marked components
EEG = pop_subcomp(EEG, find(reject_IC_components == 1), 0);

Amount of ICs to reject: You can look at the thread which also has some
references:
https://sccn.ucsd.edu/pipermail/eeglablist/2018/013964.html

Samran.

On Mon, May 11, 2020 at 9:00 PM <eeglablist-request at sccn.ucsd.edu> wrote:

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> Today's Topics:
>
>    1. Re: Double precision (Rogene Eichler West, Ph.D.)
>    2. Re: From Unipolar to Bipolar Montages (Dr. Michael Villanueva)
>    3. AMICA (Lina Ismail)
>    4. analysis of resting-state eeg data from brain vision
>       (elnaz ensafi)
>    5. ERD/ERS: log ratio with negative std_erspplot values (Carmen Dang)
>    6. Fw: bilateral dipole and SASICA error (Lina Ismail)
>
>
>
> ---------- Forwarded message ----------
> From: "Rogene Eichler West, Ph.D." <rogene at brainhealthnorthwest.com>
> To: Stephen Friedberg <friedberg.stephen at gmail.com>, Lina Ismail <
> linaelsherif at knights.ucf.edu>
> Cc: "eeglablist at sccn.ucsd.edu" <eeglablist at sccn.ucsd.edu>
> Bcc:
> Date: Sun, 10 May 2020 17:09:16 +0000
> Subject: Re: [Eeglablist] Double precision
>
> I use both NeuroGuide and BrainAvatar in private practice. Are you asking
> about clinical outcomes?
>
> On 5/10/20, 12:41 AM, "eeglablist on behalf of Stephen Friedberg" <
> eeglablist-bounces at sccn.ucsd.edu on behalf of friedberg.stephen at gmail.com>
> wrote:
>
>     Do people here have experience using ANI’s swloretta application for
> training purposes? Hoping to hear if that has been generally helpful /
> positive. I’m curious what the experience has been for those using
> BrainMaster’s sloretta application as well.
>
>     Warm regards,
>     Stephen
>
>
>     > On May 4, 2020, at 1:14 AM, Lina Ismail <
> linaelsherif at knights.ucf.edu> wrote:
>     >
>     > Dear all,
>     > Following makotos Pipeline, the first step is to ensure double
> precision for ICA purpose. I have downloaded the latest version V2019.1  in
> which there is no "File' -> 'Memory and other options' -> 'If set, use
> single precision under...' uncheck it." as the old version does.
>     > _______________________________________________
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>
> ---------- Forwarded message ----------
> From: "Dr. Michael Villanueva" <mvillanueva at alphathetacenter.com>
> To: "eeglablist at sccn.ucsd.edu" <eeglablist at sccn.ucsd.edu>
> Cc:
> Bcc:
> Date: Sun, 10 May 2020 22:23:01 +0000
> Subject: Re: [Eeglablist] From Unipolar to Bipolar Montages
> Hello Massimo
>
> There a few free EDF viewers available on the net if you do a search.
> Maybe one of them would work for you?  You can freely use WinEEG software
> as it allows you to open .EEG files for free; however, you cannot import
> .EDF files unless you purchase the software. Please understand do not want
> to discourage you from using or experimenting with EEGLAB, just be aware of
> your (our) initial and unspoken bias towards visualization.
>
> I am curious: What amp / software do you use to acquire your EEG data?
>
> Michael Villanueva
>
>
> From: Massimo Valerio <massimo.valerio at unito.it>
> Sent: Sunday, May 10, 2020 7:14 AM
> To: Dr. Michael Villanueva <mvillanueva at alphathetacenter.com>;
> eeglablist at sccn.ucsd.edu
> Subject: Re: [Eeglablist] From Unipolar to Bipolar Montages
>
> Dear Colleague, what could I add?
>
> Your experience will be a milestone for me in my training towards the
> knowledge of an instrument like EEGLAB. As you write well, clinical and
> engineering are not always able to find solutions that are good for both. I
> think the collaboration between these two worlds will benefit science and
> health. I have been working with engineers for a while and continue to have
> the same problems that you describe. I am only in difficulty because I do
> not yet have the economic possibilities for purchasing more suitable
> solutions for the clinic that often require a lot of money. I was hoping
> that an experimental and open to research tool like EEGLAB would do it but
> as you have explained to me very well it is not like that. I will use
> EEGLAB for analysis and for everything that will develop and I will also
> contribute as far as possible to its success. However, I ask you if you can
> recommend a free tool that helps me (EEGwin is a commercial product).
>
> Thanks again for your availability, your knowledge and your advices.
>
> Many thanks also to the other colleagues, I will try their solutions as
> soon as possible. In this period I am very busy learning the basics of
> programming to be able to have some freedom in knowledge in the use of
> these powerful means of science.
>
> Massimo Valerio
>
> Il giorno dom 10 mag 2020 alle ore 01:12 Dr. Michael Villanueva <
> mvillanueva at alphathetacenter.com<mailto:mvillanueva at alphathetacenter.com>>
> ha scritto:
> Believe me Massimo, I had the very same question: Back In 2016 I went to
> my first EEGLAB workshop, and asked: "How do you rearrange the channel
> order so to look at the EEG in different montages?"  The next 5-10 minutes
> of conversation with an  SCCN engineer were nearly nonsensical: He was
> utterly flummoxed, asking several times over "Why would you want to do
> that?" The more I explained the why and how we (in neurofeedback land)
> routinely reordered montages against various references, the more
> non-sensical we became to each other.  In hindsight it was singularly the
> most illuminating conversation I have ever had with a neuroscientist.
>
> EEGLAB is designed for source space, not scalp space. Whereas tools like
> WinEEG are great for visual clinical analysis of EEG in scalp space,
> statistical and numerical analysis are the correct (and only viable) tools
> in source space.  EEGLAB is a clinical research tool that relies on
> statistical and numerical computation to understand brain function; as a
> research tool rooted in source space, it does not readily lend itself to
> forming visually-based clinical diagnostic impressions extracted from the
> raw channel EEG.  Using learning to pilot an aircraft as a metaphor might
> be helpful to you:  When you learn to pilot an aircraft, you are trained to
> fly by visual rules, commonly called "VFR" (Visual Flight Rules); however,
> as you advance, you learn to fly only by use of  your cockpit instruments,
> commonly called IFR (Instrument Flight Rules).  You can think of
> neuroscientists who use EEGLAB are using IFR to statistically and
> numerically navigate brain sources; while clinicians like
> electro-neurophysiologists, neurologists, and neurofeedback providers use
> VFR to connect observable pathology to the individual EEG.  Both groups
> operate in "EEG Space" but one specializes in Source Space and the other in
> Scalp Space.
>
> Even if you took the time using MATLAB to code various montages as Arnaud
> suggested, EEGLAB would still be less than adequate.  First, the resultant
> re-montaged raw EEG would not have the channel EEG visual resolution a
> commercial program like WinEEG already has. Secondly, using Plot > Channel
> data (scroll) would be painfully slow, and, as such, scanning for transient
> discharges or watching shifting vigilance states in different montages
> would be hellish. Thirdly, there is no clinically suitable channel based
> Power Spectrum Density function in EEGLAB.  While Tools >  Channel spectra
> and maps is ok, the frequency resolution combined with the default log
> power scale occults the variances in power-squared clinical frequency
> information most useful to us. Could you make a better power spectra graph
> and maps visual tool in MATLAB?  Given enough time and training, yes;
> however, if you are just starting in MATLAB as you say you are, it would be
> a rough ride.
>
> In her native source space, EEGLAB is nimble, agile, and powerful; in
> scalp space, she is hobbled and painfully slow.
>
> For 4 years now, we use WinEEG and ICA in our clinical practice for rapid
> visual-based clinical examination of the raw in accordance with standard
> electroencephalography.  We do think EEGLAB has untapped and unexplored
> clinical strengths in several areas, notably multiple model AMICA, however
> (for us) at this time there is no easy co-existence between source and
> scalp space. There is simply too much we do not know about the brain.
>
> My advice to you after this lengthy discussion is to forget about forcing
> EEGLAB into visual clinical work: such efforts are a distraction and a Red
> Herring. Instead, combine EEGLAB source space strengths with free or
> commercial programs designed for clinical electrophysiology analysis and
> simply observe. Personally,  I think the hours spent learning how to code
> and develop work arounds in MATLAB would be far, far better spent learning
> the clinical applications of AMICA and ERPs and how to create peer
> survivable research study designs,
>
> Once you intuitively grasp EEGLAB is all about source space and not scalp
> space, once you understand (or believe) the time series data recorded at
> each channel location is a linear sum of all biological and environmental
> electrical activity, your learning will accelerate: you will make intuitive
> use of ICA and ERPs in your future clinical formulations, your questions
> will be more intelligible to the engineers who will help guide you, and
> your research contributions will be firmly rooted in neuroscience.
>
> Best of luck
>
> Michael Villanueva
>
> -----Original Message-----
> From: eeglablist <eeglablist-bounces at sccn.ucsd.edu<mailto:
> eeglablist-bounces at sccn.ucsd.edu>> On Behalf Of Massimo Valerio
> Sent: Sunday, May 3, 2020 2:09 AM
> To: Scott Makeig <smakeig at ucsd.edu<mailto:smakeig at ucsd.edu>>
> Cc: eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>
> Subject: Re: [Eeglablist] From Unipolar to Bipolar Montages
>
> Dear Scott Smakeig,
> I see the EEG in bipolar mode during my clinical activity. I learned
> almost exclusively to report the EEG in this way. I work in a pediatric
> hospital and I use several different bipolar montages. I'm new also in
> matlab coding. I will try to follow your advice but I was hoping to find a
> tool.
> Thanks for your help. Massimo Valerio
>
> Il giorno sab 2 mag 2020 alle ore 22:58 Scott Makeig <smakeig at ucsd.edu
> <mailto:smakeig at ucsd.edu>> ha
> scritto:
>
> > Massimo -
> >
> > I have not heard such a request before, and do not believe there is an
> > EEGLAB tool dedicated to doing this, though a function or script for
> > doing this in a fixed way should not be difficult to write.
> >
> > Scott Makeig
> >
> > On Fri, Apr 24, 2020 at 11:30 AM Massimo Valerio
> > <massimo.valerio at unito.it<mailto:massimo.valerio at unito.it>>
> > wrote:
> >
> >> Hi, I'm newuser of EEGLab.
> >> Please, could you give me information about to visualize through Plot
> >> > Channel Data (scroll) the EEG in unipolar montage to bipolar
> >> (example, longitudinal montage). I tried to look for extensions and
> >> plugin in EEGLab without success. Thanks and regards.
> >> Massimo Valerio
> >>
> >> <
> >> https://urldefense.com/v3/__https://www.avast.com/sig-email?utm_mediu<
> https://urldefense.com/v3/__https:/www.avast.com/sig-email?utm_mediu>
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> >> Mail
> >> priva di virus.
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> >> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >> _______________________________________________
> >> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
> >> To unsubscribe, send an empty email to
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> >> eeglablist-request at sccn.ucsd.edu<mailto:
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> >>
> >
> >
> > --
> > Scott Makeig, Research Scientist and Director, Swartz Center for
> > Computational Neuroscience, Institute for Neural Computation,
> > University of California San Diego, La Jolla CA 92093-0961,
> > http://sccn.ucsd.edu/~scott
> >
> _______________________________________________
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>
>
> ---------- Forwarded message ----------
> From: Lina Ismail <linaelsherif at knights.ucf.edu>
> To: "eeglablist at sccn.ucsd.edu" <eeglablist at sccn.ucsd.edu>
> Cc:
> Bcc:
> Date: Sun, 10 May 2020 23:05:07 +0000
> Subject: [Eeglablist] AMICA
> Dear all,
> Its my first time data cleaning for EEG data. I would like you  to help me
> to know what is the acceptable number of IC to reject in 64 components to
> decide whether this participant will be skipped from analysis or no?
>
> For example, having to reject 32 out of 64 components. Is this data must
> be rejected?
>
> Another question, After running AMICA we should manually save the file.
> What about saving the "selected  rejected labels" without removing them
> from the data set. How can I save the selected IC labels that I selected to
> reject, but I want to remove them later!
>
>
>
>
> ---------- Forwarded message ----------
> From: elnaz ensafi <elnazensafi89 at gmail.com>
> To: eeglablist at sccn.ucsd.edu
> Cc:
> Bcc:
> Date: Sun, 10 May 2020 18:25:34 -0600
> Subject: [Eeglablist] analysis of resting-state eeg data from brain vision
> Hi everyone,
>
> I'm new user of EEGLAB. can anyone help me how can I pre-process the
> resting-state EEG and then how can I check the alpha asymmetry on frontal
> electrode?
> I have this type of dataset from brain vision  (.vhdr , .vmrk, .eeg, .ehst2
> /hfinf2), and I don't know which on contain the resting-state EEG.
>
> Thanks and regards,
> elnaz
>
>
>
>
> ---------- Forwarded message ----------
> From: Carmen Dang <c1dang at psych.ryerson.ca>
> To: "eeglablist at sccn.ucsd.edu" <eeglablist at sccn.ucsd.edu>
> Cc:
> Bcc:
> Date: Mon, 11 May 2020 01:29:08 +0000
> Subject: [Eeglablist] ERD/ERS: log ratio with negative std_erspplot values
> Dear eeglablist,
>
> I'd like to calculate the ERD/ERS of a frequency band with the following
> formula: log(A/R) where A is the power in the frequency band of interest in
> the period after the event and R is the power in the preceding baseline or
> reference period?. I'm using the values obtained from [STUDY erspdata] =
> std_erspplot(STUDY,ALLEEG,'channels', {'C4' 'Cz' 'C3'});, but some of these
> values are negative so I cannot take the logarithm of the ratio. Is there a
> transformation I should apply to the data (e.g. add a constant to all
> values)? Has 'erspdata' from std_erspplot been transformed similar to this
> post https://sccn.ucsd.edu/pipermail/eeglablist/2012/004755.html??
>
> Thank you,
> Carmen
>
>
>
>
> ---------- Forwarded message ----------
> From: Lina Ismail <linaelsherif at knights.ucf.edu>
> To: "eeglablist at sccn.ucsd.edu" <eeglablist at sccn.ucsd.edu>
> Cc:
> Bcc:
> Date: Mon, 11 May 2020 07:54:25 +0000
> Subject: [Eeglablist] Fw: bilateral dipole and SASICA error
>
> Dear all,
>
>
>   1.  I am following Makoto's preprocessing pipeline but when I plot IC
> label there is only one single dipole althought I followed all steps
> carefully and applied twodipole plugin using large rectangular region with
> threshold 35% having the following error:
>
> "Local minimum possible.
>
> fminunc stopped because the size of the current step is less than
> the value of the step size tolerance.
>
> <stopping criteria details>
> found minimum after non-linear optimization for topography 1 on [-27.2688
> -31.7784 -55.0945; 27.2688 -31.7784 -55.0945]
> the call to "ft_dipolefitting" took 1 seconds
> No MRI file given as input. Looking up one.
> Done.
> Warning: Adding folders named 'resources' to the path is not supported:
> C:\EEG_data\eeglab14_1_2b\eeglab14_1_2b\functions\resources
> > In path (line 109)
>   In addpath (line 86)
>   In eeglab>addpathifnotinlist (line 2059)
>   In eeglab>myaddpath (line 2088)
>   In eeglab (line 293) "
>
> 2. Could you please help me to fix the current error for running SASICA
>
> "Error in eeg_SASICA (line 289)
>         myact =sort(abs(zscore(range(icaacts,2),[],3)),3,'descend'); %
> sorts standardized range of trial activity
>
> Error in SASICA>push_ok_Callback (line 594)
>     [EEG, cfg] = eeg_SASICA(EEG,cfg);
>
> Error in gui_mainfcn (line 95)
>         feval(varargin{:});
>
> Error in SASICA (line 108)
>     gui_mainfcn(gui_State, varargin{:});
>
> Error in
>
> matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)SASICA('push_ok_Callback',hObject,eventdata,guidata(hObject))
> Error while evaluating UIControl Callback. "
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