[Eeglablist] Paper on skull conductivity estimation

[James Jones-Rounds]

Thank you Zeynep! When will SCALE be a functional toolbox for EEGLAB? And
to be clear, it does require a structural MR scan of each subject, correct?

James

On Wed, Aug 12, 2015 at 3:00 PM, <eeglablist-request at sccn.ucsd.edu> wrote:

> Send eeglablist mailing list submissions to
>         eeglablist at sccn.ucsd.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://sccn.ucsd.edu/mailman/listinfo/eeglablist
> or, via email, send a message with subject or body 'help' to
>         eeglablist-request at sccn.ucsd.edu
>
> You can reach the person managing the list at
>         eeglablist-owner at sccn.ucsd.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of eeglablist digest..."
>
> Today's Topics:
>
>    1. how can i fix bem_metrix.exe its cusses my matlab to crush
>       due to runtime problem (Yair Massury)
>    2. Subjects head radius in DIPFIT2 (Mostafa IR)
>    3. Why do I have to duplicate the labels used in     classification
>       process? (Sahar Selim)
>    4. Re: Topography maps of continuous data (Stephen Politzer-Ahles)
>    5. Re: Couldn't able to load channel location file
>       (Stephen Politzer-Ahles)
>    6. Re: Topography maps of continuous data (Stephen Politzer-Ahles)
>    7. Paper on skull conductivity estimation (Zeynep Akalin Acar)
>    8. Re: How to determine the type of events in the dataset
>       (Stephen Politzer-Ahles)
>
>
> ---------- Forwarded message ----------
> From: Yair Massury <massury at gmail.com>
> To: <eeglablist at sccn.ucsd.edu>
> Cc:
> Date: Tue, 11 Aug 2015 15:06:59 +0300
> Subject: [Eeglablist] how can i fix bem_metrix.exe its cusses my matlab to
> crush due to runtime problem
> I am running matlab R2014b on windows 10 OS.
> it's seem that the problem originated from the bem_matrix.exe which compiled
> with cygwin.
>
> I hope that compile bem_matrix.exe with Visual Studio will solve the problem but i don't have the source code.
>
> "*This application has requested the Runtime to terminate it in an unusual
> way.
> Please contact the application's support team for more information."*
>
> is anybody else encounter this problem? and if so how did you solve that.
>
> i have tried a few suggestions on line, but with no help.
>
>
>
>
> ---------- Forwarded message ----------
> From: Mostafa IR <mostafa.rouzbahani at gmail.com>
> To: EEGLAB List <eeglablist at sccn.ucsd.edu>
> Cc:
> Date: Tue, 11 Aug 2015 13:17:01 +0430
> Subject: [Eeglablist] Subjects head radius in DIPFIT2
> Hi eeglab
>
>  I have questions about different subject heads radius. I used
> >>pop_chanedit to set subjects head radius on my owns. These radius are
> less than 85.In DIPFIT2 head model and settings, I used BESA head model
> which have 85 spherical head radius. Then I manually co-register the
> channels. After that I used the auto-fit for locating the dipoles. I check
> the option to remove dipoles outside the heads. After fitting, all of my
> dipoles removed because all of them located outside the head. If I fitting
> the dipoles location without remove outside head option, I can have them
> all.
> Are you think this is because of my head radius? If yes Is there any way
> to decrease the head size in DIPFIT2 to my owns?
>
> Thanks
> Mostafa Rouzbahani
>
>
> ---------- Forwarded message ----------
> From: Sahar Selim <sahar.soussa at gmail.com>
> To: undisclosed-recipients:;
> Cc:
> Date: Wed, 12 Aug 2015 11:32:19 +0200
> Subject: [Eeglablist] Why do I have to duplicate the labels used in
> classification process?
> Dear All,
>
> I'm using the BCI Competition dataset IV 2a. I'm working on Left & right
> hand movement.  I extracted data of channels (Fz,Cz,Pz).
> I filtered data [8-30], then normalized it. Then, I calculated the common
> spatial patterns of the training dataset using the CSP.m of the Biosig
> toolbox
> I want to use the "train_sc" to classify my data.
>
> My question is why do I need to duplicate the labels of each event?
>
> ex:
> for each right hand event (750 samples) I must have 750 label = 1
> for each left  hand event (750 samples) I must have 750 label = 2
>
> labels = repmat(classlabel’,n,1)’;   %where n is the number of
> samples/event
> CC = train_sc(features,labels,'LDA');
>
> Does that mean that classification is done on samples rather than events?
> Is each sample classified independently?!!!
>
> The results I got are very disappointing. I've tried many classifiers but
> the best accuracy I got was 0.5
> I need to know what I'm doing wrong.
>
> I've read too much on CSP feature extraction & classification of the eeg
> signals, but still I feel that I'm missing many things :(
> Any help please.
>
> Best Regards,
> Sahar Selim
>
>
> ---------- Forwarded message ----------
> From: Stephen Politzer-Ahles <spa268 at nyu.edu>
> To: Hoori Sa <hoorisa33 at gmail.com>
> Cc: eeglablist <eeglablist at sccn.ucsd.edu>
> Date: Mon, 10 Aug 2015 22:55:51 +0100
> Subject: Re: [Eeglablist] Topography maps of continuous data
> Hello Hoori,
>
> Do you mean to plot a topomap of a specific timepoint or time range in
> continuous data? I'm not sure if it's possible from the GUI, but it should
> be possible from the command line using the topoplot() function. That
> function just needs a vector of values (for instance, if your EEG data has
> 32 channels, then you give topoplot() a 32x1 vector of voltages), so you
> could easily use a point in continuous data (or an average over a range of
> timepoints) to do this.
>
> Best,
> Steve
>
>
>
> Stephen Politzer-Ahles
> New York University, Abu Dhabi
> Neuroscience of Language Lab
> http://www.nyu.edu/projects/politzer-ahles/
>
> On Fri, Aug 7, 2015 at 9:32 AM, Hoori Sa <hoorisa33 at gmail.com> wrote:
>
>> Hi
>>
>> Is there anyway to plot topo map of continuous data? In tutorials I just
>> can find ERP topo plotting.
>>
>> Thanks in advance.
>>
>> Best,
>> Hoorisa
>>
>> _______________________________________________
>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
>> To unsubscribe, send an empty email to
>> eeglablist-unsubscribe at sccn.ucsd.edu
>> For digest mode, send an email with the subject "set digest mime" to
>> eeglablist-request at sccn.ucsd.edu
>>
>
>
>
> ---------- Forwarded message ----------
> From: Stephen Politzer-Ahles <spa268 at nyu.edu>
> To: Edward Wiskers <edwardwiskers at gmail.com>
> Cc: eeglablist <eeglablist at sccn.ucsd.edu>
> Date: Mon, 10 Aug 2015 22:57:12 +0100
> Subject: Re: [Eeglablist] Couldn't able to load channel location file
> Hello Edward,
>
> This is a common issue, see
> https://sccn.ucsd.edu/bugzilla/show_bug.cgi?id=1722 for discussion and
> for a fix.
>
> Best,
> Steve
>
>
>
> Stephen Politzer-Ahles
> New York University, Abu Dhabi
> Neuroscience of Language Lab
> http://www.nyu.edu/projects/politzer-ahles/
>
> On Mon, Aug 10, 2015 at 1:44 PM, Edward Wiskers <edwardwiskers at gmail.com>
> wrote:
>
>> Dear all,
>>
>>
>>
>> I have an edf file, after loading it into EEGLAB, I tried directly to
>> load the channel location file through edit -> Channel location.
>> Unfortunately, I could not do that, I had the following error message
>> displayed in Matlab:
>>
>>
>>
>> *??? Operands to the || and && operators must be convertible to logical
>> scalar values.*
>>
>>
>>
>> *Error in ==> pop_chanedit at 163*
>>
>> *if isempty(chans) || ~ishandle(chans)*
>>
>>
>>
>> *Error in ==> pop_chanedit at 225*
>>
>> *        [chans chaninfo urchans com] = pop_chanedit(chans, chaninfo,
>> 'lookupgui', []);*
>>
>>
>>
>> *??? Error while evaluating uimenu Callback*
>>
>>
>>
>> Did I miss anything? What should I do to fix this problem.
>>
>>
>>
>> Thank you.
>>
>> Edward
>>
>>
>>
>> _______________________________________________
>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
>> To unsubscribe, send an empty email to
>> eeglablist-unsubscribe at sccn.ucsd.edu
>> For digest mode, send an email with the subject "set digest mime" to
>> eeglablist-request at sccn.ucsd.edu
>>
>
>
>
> ---------- Forwarded message ----------
> From: Stephen Politzer-Ahles <spa268 at nyu.edu>
> To: Hoori Sa <hoorisa33 at gmail.com>
> Cc: EEGLAB List <eeglablist at sccn.ucsd.edu>
> Date: Wed, 12 Aug 2015 09:49:33 +0100
> Subject: Re: [Eeglablist] Topography maps of continuous data
> This is still doable with topoplot. Something along the lines of:
>
> topoplot( mean(EEG.data,2), EEG.chanlocs )
>
>
>
>
>
> Stephen Politzer-Ahles
> New York University, Abu Dhabi
> Neuroscience of Language Lab
> http://www.nyu.edu/projects/politzer-ahles/
>
> On Wed, Aug 12, 2015 at 9:26 AM, Hoori Sa <hoorisa33 at gmail.com> wrote:
>
>> Hi
>>
>> Thanks for your reply!
>>
>> I meant plotting the whole time of my continuous data which is about 100
>> s.
>>
>> Anyway, I'll try topoplot.
>>
>> Best,
>> Hoori
>>
>> On 11 August 2015 at 09:32, Makoto Miyakoshi <mmiyakoshi at ucsd.edu> wrote:
>>
>>> Dear Hoori,
>>>
>>> Probably you need to use topoplot() function. Type 'help topoplot' in
>>> the command line to check how it should be used.
>>>
>>> Makoto
>>>
>>> On Fri, Aug 7, 2015 at 1:32 AM, Hoori Sa <hoorisa33 at gmail.com> wrote:
>>>
>>>> Hi
>>>>
>>>> Is there anyway to plot topo map of continuous data? In tutorials I
>>>> just can find ERP topo plotting.
>>>>
>>>> Thanks in advance.
>>>>
>>>> Best,
>>>> Hoorisa
>>>>
>>>> _______________________________________________
>>>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
>>>> To unsubscribe, send an empty email to
>>>> eeglablist-unsubscribe at sccn.ucsd.edu
>>>> For digest mode, send an email with the subject "set digest mime" to
>>>> eeglablist-request at sccn.ucsd.edu
>>>>
>>>
>>>
>>>
>>> --
>>> Makoto Miyakoshi
>>> Swartz Center for Computational Neuroscience
>>> Institute for Neural Computation, University of California San Diego
>>>
>>
>>
>
>
> ---------- Forwarded message ----------
> From: Zeynep Akalin Acar <zeynep at sccn.ucsd.edu>
> To: EEGLAB List <eeglablist at sccn.ucsd.edu>
> Cc:
> Date: Tue, 11 Aug 2015 20:40:29 -0700
> Subject: [Eeglablist] Paper on skull conductivity estimation
> Dear EEGLAB users,
>
> I'm happy to announce that our recent paper on skull conductivity
> estimation is now accepted for publication in Neuroimage.
>
> You can find the accepted version at:
>
> Preprint of the accepted version
> <http://sccn.ucsd.edu/%7Escott/pdf/AkalinAcar_SCALE_NeuroImage_in_press_0815.pdf>
>
> *Title*: Simultaneous head tissue conductivity and EEG source location
> estimation
>
> *Authors*: Z. Akalin Acar, C. Acar, S. Makeig
>
> *Abstract*:
> Accurate electroencephalographic (EEG) source localization requires an
> electrical head model incorporating accurate geometries and conductivity
> values for the major head tissues. While consistent conductivity values
> have been reported for scalp, brain, and cerebrospinal fluid, measured
> brain-to- skull conductivity ratio (BSCR) estimates have varied between 8
> and 80, likely reflecting both inter-subject and measurement method
> differences. In simulations, mis-estimation of skull conductivity can
> produce source local- ization errors as large as 3 cm. Here, we describe an
> iterative gradient-based approach to Simultaneous tissue Conductivity And
> source Location Estima- tion (SCALE). The scalp projection maps used by
> SCALE are obtained from near-dipolar effective EEG sources found by
> adequate independent compo- nent analysis (ICA) decomposition of sufficient
> high-density EEG data. We applied SCALE to simulated scalp projections of
> 15 cm2-scale cortical patch sources in an MR image-based electrical head
> model with simulated BSCR of 30. Initialized either with a BSCR of 80 or
> 20, SCALE estimated BSCR as 32.6. In Adaptive Mixture ICA (AMICA)
> decompositions of (45-min, 128-channel) EEG data from two young adults we
> identified sets of 13 in- dependent components having near-dipolar scalp
> maps compatible with a single cortical source patch. Again initialized with
> either BSCR 80 or 25, SCALE gave BSCR estimates of 34 and 54 for the two
> subjects respectively. The ability to accurately estimate skull
> conductivity non-invasively from any well-recorded EEG data in combination
> with a stable and non-invasively ac- quired MR imaging-derived electrical
> head model could remove a critical barrier to using EEG as a sub-cm2-scale
> accurate 3-D functional cortical imaging modality.
>
> Thank you,
> Zeynep Akalin Acar
>
>
> ---------- Forwarded message ----------
> From: Stephen Politzer-Ahles <spa268 at nyu.edu>
> To: Andria Lan <andrialan108 at gmail.com>
> Cc: eeglablist <eeglablist at sccn.ucsd.edu>
> Date: Wed, 12 Aug 2015 19:04:17 +0100
> Subject: Re: [Eeglablist] How to determine the type of events in the
> dataset
> Hi Andria,
>
> In the EEGLAB GUI, you can select "Tools", then "Extract Epochs", then
> click the button next to "Time-locking event types", and you will see the
> list of event types that are present in the dataset.
>
> Best,
> Steve
>
>
>
> Stephen Politzer-Ahles
> New York University, Abu Dhabi
> Neuroscience of Language Lab
> http://www.nyu.edu/projects/politzer-ahles/
>
> On Tue, Aug 11, 2015 at 4:34 AM, Andria Lan <andrialan108 at gmail.com>
> wrote:
>
>> Hi everyone,
>>
>> My question is about the fininding type of event in the dataset.
>>
>> In the eeglab dataset (dedicated by eeglab), for instance, the event
>> types are "square" and "rt". Thus, how to determine them (square and rt)?
>> What are the necessary steps for this?
>>
>> Thanks in advance.
>>
>> Andria
>>
>> _______________________________________________
>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
>> To unsubscribe, send an empty email to
>> eeglablist-unsubscribe at sccn.ucsd.edu
>> For digest mode, send an email with the subject "set digest mime" to
>> eeglablist-request at sccn.ucsd.edu
>>
>
>
> _______________________________________________
> eeglablist mailing list eeglablist at sccn.ucsd.edu
> Eeglablist page: http://www.sccn.ucsd.edu/eeglab/eeglabmail.html
> To unsubscribe, send an empty email to eeglablist-unsub at sccn.ucsd.edu
> To switch to non-digest mode, send an empty email to
> eeglablist-nodigest at sccn.ucsd.edu
>



-- 
James Jones-Rounds
Laboratory Manager
Human Development EEG and Psychophysiology (HEP) Laboratory,
Department of Human Development,
--------------------------------------------
Cornell University | Ithaca, NY
607-255-9883
eeg at cornell.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://sccn.ucsd.edu/pipermail/eeglablist/attachments/20150812/4b9cf0d5/attachment.html>