[FieldTrip] 'rule of thumb' for defining how many independent components to analyze for EEG?

Eleanor Harding harding at cbs.mpg.de
Wed Nov 7 11:37:21 CET 2012 

Dear Arno and Eelke,

Thanks for the information. I also received the following code suggestion from J.Obleser in house

cfg.runica.pca  =rank(your_number_of_channels)

which I am trying out right now.

Cheers,
Ellie

----- Original Message -----
From: fieldtrip-request at science.ru.nl
To: fieldtrip at science.ru.nl
Sent: Tuesday, November 6, 2012 6:34:47 PM
Subject: fieldtrip Digest, Vol 24, Issue 5

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Today's Topics:

   1. subspace projection (Jan.Hirschmann at med.uni-duesseldorf.de)
   2. Re: subspace projection (jan-mathijs schoffelen)
   3. Re: co registration of the mesh points to the atlas (Luke Bloy)
   4. 'rule of thumb' for defining how many independent components
      to analyze for EEG? (Eleanor Harding)
   5. Re: opposite to the ft_appenddata (Nenad Polomac)


----------------------------------------------------------------------

Message: 1
Date: Tue, 6 Nov 2012 14:34:53 +0100
From: <Jan.Hirschmann at med.uni-duesseldorf.de>
To: <fieldtrip at science.ru.nl>
Subject: [FieldTrip] subspace projection
Message-ID:
	<72E993C35FB11743B79FF9286E5B6D8B048E4A8B at Mail2-UKD.VMED.UKD>
Content-Type: text/plain; charset="iso-8859-1"

Dear fieldtrip community,

 

In LCMV beamforming there is an option cfg.lcmv.subspace=X. Does anyone have experience or recommendations regarding this option? Is there a publication in which the rationale is described? From looking at the code it seems that data and lead field are projected onto a subspace spanned by the first X singular vectors of the covariance matrix (correct me if I'm wrong). Seems helpful in my case but I am hesitant to use it without knowing anything about it.

 

Thanks for any comment!

Jan

 

--

Jan Hirschmann

MSc Neuroscience

Institute of Clinical Neuroscience and Medical Psychology

Heinrich Heine University D?sseldorf

Universit?tsstr. 1

40225 D?sseldorf

Germany

Tel: +49 (0)211 81 18415

Fax: +49 (0)211 81 19033

 

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Message: 2
Date: Tue, 6 Nov 2012 14:49:36 +0100
From: jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] subspace projection
Message-ID: <0E290E21-72BD-4E44-A6CE-ADADD1886432 at donders.ru.nl>
Content-Type: text/plain; charset="windows-1252"

Hi Jan,

You can look up the rationale in the work of Kensuke Sekihara. Look for 'eigenspace beamformer'. The implementation in FieldTrip is along these lines (but slightly differently implemented).

Best wishes,

Jan-Mathijs

On Nov 6, 2012, at 2:34 PM, <Jan.Hirschmann at med.uni-duesseldorf.de> <Jan.Hirschmann at med.uni-duesseldorf.de> wrote:

> Dear fieldtrip community,
>  
> In LCMV beamforming there is an option cfg.lcmv.subspace=X. Does anyone have experience or recommendations regarding this option? Is there a publication in which the rationale is described? From looking at the code it seems that data and lead field are projected onto a subspace spanned by the first X singular vectors of the covariance matrix (correct me if I?m wrong). Seems helpful in my case but I am hesitant to use it without knowing anything about it.
>  
> Thanks for any comment!
> Jan
>  
> --
> Jan Hirschmann
> MSc Neuroscience
> Institute of Clinical Neuroscience and Medical Psychology
> Heinrich Heine University D?sseldorf
> Universit?tsstr. 1
> 40225 D?sseldorf
> Germany
> Tel: +49 (0)211 81 18415
> Fax: +49 (0)211 81 19033
>  
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

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Message: 3
Date: Tue, 6 Nov 2012 10:36:48 -0500
From: "Luke Bloy" <luke.bloy at gmail.com>
To: "'FieldTrip discussion list'" <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] co registration of the mesh points to the
	atlas
Message-ID: <50992e91.0347e00a.5ced.6484 at mx.google.com>
Content-Type: text/plain;	charset="iso-8859-1"

Hi Qi,

I'm not sure if this is what you are looking for but take a look at the
--morph option to mne_setup_source_space. It should let you create
corresponding source grids in each of your subjects.

-Luke

-----Original Message-----
From: fieldtrip-bounces at science.ru.nl
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of qi li
Sent: Wednesday, October 31, 2012 5:39 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] co registration of the mesh points to the atlas

Hi J?rn,

Thanks a lot! This link is very helpful for my question.

Actually, I followed the tutorial of source reconstruction of event-related
fields using MNE which clearly states 'recon-all -surfreg -subjid Subject01'
this already co-registered the original surface to the standard atlas
sphere. So for each individual, their cortical surfaces are aligned at this
step. The confusion is when down-sampling by using 'mne_setup_source_space
--ico -6', what is exactly done(algorithm) to down-sample from 20,000 nodes
to only 8196?
This might be crucial for a group analysis so I seek a clarification.

Thanks!

Qi



On Tue, Oct 30, 2012 at 5:03 AM, "J?rn M. Horschig"
<jm.horschig at donders.ru.nl> wrote:
> Dear Qi,
>
> I guess this page might help:
> http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_i
> ndividual_head_space_that_are_all_aligned_in_mni_space?s[]=warp
>
> Best,
> J?rn
>
>
> On 10/25/2012 6:00 PM, qi li wrote:
>>
>> Hi,
>>
>> Is there any function to co-register the individual cortical mesh
>> points(8196 in total) generate by fieldtrip to the standard brain.
>> Thanks!
>>
>> Qi
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> J?rn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour Centre for 
> Cognitive Neuroimaging Radboud University Nijmegen Neuronal 
> Oscillations Group FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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------------------------------

Message: 4
Date: Tue, 6 Nov 2012 17:31:54 +0100 (CET)
From: Eleanor Harding <harding at cbs.mpg.de>
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] 'rule of thumb' for defining how many independent
	components to analyze for EEG?
Message-ID: <1002956758.7127.1352219514263.JavaMail.root at zimbra>
Content-Type: text/plain; charset=utf-8

Dear Fieldtrip community,

I intend to run ICA on an EEG dataset with 64 channels (+ 2 eye channels), on epochs which are about 4 seconds long, and I am unsure as to how many independent components I should define (20,65,..?).

My question is, is there a 'rule of thumb' for defining how many independent components to analyze for EEG? In the archives I have found only references to MEG datasets with many channels, for example reducing over 200 channels to 80 components. Looking in the literature today I also wasn't able to interpret an answer.

If anyone has any information, references, or other input I would be much obliged.

Thanks,
Ellie



-- 
------------------------------------------------------------------ 
Eleanor Harding 
PhD Student 
Max Planck Institute for Human Cognitive and Brain Sciences 
Stephanstra?e 1A, 04103 Leipzig, Germany 
Phone: +49 341 9940-2268 
Fax: +49 341 9940 2260 
http://www.cbs.mpg.de/~harding 





------------------------------

Message: 5
Date: Tue, 6 Nov 2012 18:34:45 +0100
From: Nenad Polomac <polomacnenad at gmail.com>
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] opposite to the ft_appenddata
Message-ID:
	<CAEk4EpHgJ+Y5huoiEFnfcMaq_YoFUK02d5sB5qiYnRvhOmZ=Ng at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Thank you very much to both of you!

I will use Stephen's suggestion. It fits better with my situation!

All the best!
Nenad
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Eleanor Harding 
PhD Student 
Max Planck Institute for Human Cognitive and Brain Sciences 
Stephanstraße 1A, 04103 Leipzig, Germany 
Phone: +49 341 9940-2268 
Fax: +49 341 9940 2260 
http://www.cbs.mpg.de/~harding

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