[Eeglablist] AMICA
Lina Ismail
linaelsherif at Knights.ucf.edu
Thu May 14 20:19:36 PDT 2020
Thank you samran
Now it worked
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________________________________
From: Samran <samranasghar at gmail.com>
Sent: Thursday, May 14, 2020 7:46:29 PM
To: Lina Ismail <linaelsherif at Knights.ucf.edu>
Cc: eeglablist <eeglablist at sccn.ucsd.edu>
Subject: Re: AMICA
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<https://urldefense.com/v3/__https://nam02.safelinks.protection.outlook.com/?url=https*3A*2F*2Fsccn.ucsd.edu*2Fpipermail*2Feeglablist*2F2018*2F013964.html&data=02*7C01*7Clinaelsherif*40knights.ucf.edu*7C6e0a3c21b5a44261c06308d7f8610e0b*7C5b16e18278b3412c919668342689eeb7*7C0*7C0*7C637250968048713635&sdata=JrRZJvqg60skk8fJ8UDGV3py2FQ7zX*2BzJcAjXqs3cCc*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSU!!Mih3wA!SbudWU-REGTwXKFkIVk0WgVKQ-1wL9tUDHP3bug2XWUvc-irPuUwpLdx76f5Erhcl2XetQ$ >
Samran.
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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<mailto:rogene at brainhealthnorthwest.com>>
To: Stephen Friedberg <friedberg.stephen at gmail.com<mailto:friedberg.stephen at gmail.com>>, Lina Ismail <linaelsherif at knights.ucf.edu<mailto:linaelsherif at knights.ucf.edu>>
Cc: "eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>" <eeglablist at sccn.ucsd.edu<mailto: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<mailto:eeglablist-bounces at sccn.ucsd.edu> on behalf of friedberg.stephen at gmail.com<mailto: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<mailto: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<mailto:mvillanueva at alphathetacenter.com>>
To: "eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>" <eeglablist at sccn.ucsd.edu<mailto: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<mailto:massimo.valerio at unito.it>>
Sent: Sunday, May 10, 2020 7:14 AM
To: Dr. Michael Villanueva <mvillanueva at alphathetacenter.com<mailto:mvillanueva at alphathetacenter.com>>; eeglablist at sccn.ucsd.edu<mailto: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><mailto: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><mailto: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><mailto:smakeig at ucsd.edu<mailto:smakeig at ucsd.edu>>>
Cc: eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu><mailto: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><mailto: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><mailto: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
>>
>> <
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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<https://urldefense.com/v3/__https://nam02.safelinks.protection.outlook.com/?url=http:*2F*2Fsccn.ucsd.edu*2F*scott&data=02*7C01*7Clinaelsherif*40knights.ucf.edu*7C6e0a3c21b5a44261c06308d7f8610e0b*7C5b16e18278b3412c919668342689eeb7*7C0*7C0*7C637250968048753465&sdata=WB1mECXtqIzCl8rXAanbT*2BnDCHV8dLSwrQZZfYNZIE4*3D&reserved=0__;JSUlfiUlJSUlJSUlJSU!!Mih3wA!SbudWU-REGTwXKFkIVk0WgVKQ-1wL9tUDHP3bug2XWUvc-irPuUwpLdx76f5ErjQ1PTYjQ$ >
>
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---------- Forwarded message ----------
From: Lina Ismail <linaelsherif at knights.ucf.edu<mailto:linaelsherif at knights.ucf.edu>>
To: "eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>" <eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>>
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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<mailto:elnazensafi89 at gmail.com>>
To: eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>
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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<mailto:c1dang at psych.ryerson.ca>>
To: "eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>" <eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>>
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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<https://urldefense.com/v3/__https://nam02.safelinks.protection.outlook.com/?url=https*3A*2F*2Fsccn.ucsd.edu*2Fpipermail*2Feeglablist*2F2012*2F004755.html&data=02*7C01*7Clinaelsherif*40knights.ucf.edu*7C6e0a3c21b5a44261c06308d7f8610e0b*7C5b16e18278b3412c919668342689eeb7*7C0*7C0*7C637250968048763426&sdata=*2BX1lLziat5HGW2XDXGX*2B6UOPh2*2BNcytq1yJLOV0cmng*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!SbudWU-REGTwXKFkIVk0WgVKQ-1wL9tUDHP3bug2XWUvc-irPuUwpLdx76f5ErjY4zKPfw$ >??
Thank you,
Carmen
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From: Lina Ismail <linaelsherif at knights.ucf.edu<mailto:linaelsherif at knights.ucf.edu>>
To: "eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>" <eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>>
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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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