JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for SPM Archives


SPM Archives

SPM Archives


SPM@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

SPM Home

SPM Home

SPM  February 2011

SPM February 2011

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Question about lead field matrix

From:

Vladimir Litvak <[log in to unmask]>

Reply-To:

Vladimir Litvak <[log in to unmask]>

Date:

Tue, 15 Feb 2011 11:29:30 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (164 lines)

Dear Carsten,

I actually see now that the option to use OpenMEEG is already in the
code of the present version 4010. If you look in spm_eeg_inv_forward
around line 88, you'll find it there. It's just not in the GUI, which
is easy to fix by adding 'OpenMEEG BEM' to the list in
spm_eeg_inv_forward_ui. I'm sure Alexandre will be glad to help you
with installation. I suspect on LINUX it's more straightforward than
on Windows.

Best,

Vladimir

On Mon, Feb 14, 2011 at 9:58 PM, Carsten Stahlhut
<[log in to unmask]> wrote:
> Dear Vladimir,
>
> Thanks for clarifying the issue with the physical units - that confirmed a
> little suspicion on my that it would probably be better for me to leave out
> the units in some plots that I did of reconstructed sources.
>
> Yes, indeed the platform is also one my concerns - however, I think it
> should work with Linux.
> Regarding the computation time - my impression is that it is very fast
> compared to other FEM implementations and almost just as fast as computing
> BEM solutions. I guess the reason why I suddenly found the SimBio's FEM head
> model very appealing was that in one of their recent papers (see e.g. the
> attached paper page 1926), they claim that with a grid of 2 * 2 * 2 mm^3
> they can build a FEM with 71 electrodes in less than 22 min and less than 38
> min for a sensor configuration of 258 electrodes! That's quite an
> improvement.
> All of this is performed just on a Linux-workstation - Intel Core 2 Duo
> E6600 processor (2.4 GHz) with 4 GB memory.
>
> Thanks for bringing the OpenMEEG software to my attention. I think that's a
> really good alternative. Yes, that would be really great if I would send me
> your code for using the OpenMEEG BEM implementation.
>
> Best,
> Carsten
>
>
>
>
> 2011/2/14 Vladimir Litvak <[log in to unmask]>
>>
>> Dear Carsten
>>
>> On Fri, Feb 11, 2011 at 11:56 PM, Carsten Stahlhut <[log in to unmask]> wrote:
>> > Dear Vladimir,
>> >
>> > I have approx three questions (or issues) that I hope you can help me
>> > out
>> > with.
>> >
>> > Do you know what the units are for the lead field matrix and the source
>> > estimates in SPM8?
>>
>> These are two different questions.
>>
>> > If you apply one of the EEG imaging methods (as I understood it) then
>> > the
>> > source estimates should be current density i.e. the unit should be
>> > something
>> > like A/m^2  or uA/mm^2 depending on the scaling of the EEG data and lead
>> > field matrix.
>> > And then the units of the lead field should be something like m^2 * Ohm
>> > ( =
>> > m^2 / S ).
>>
>> In theory the forward computation done by the 'forward' toolbox should
>> be unit-blind so the units of the lead field should depend on units of
>> the head model (mm in SPM). In practice this might not be the case. We
>> recently found a difference in scaling between 'single shell' and
>> other MEG models. This will be fixed in the next update. There might
>> be something similar also for EEG. SPM is not sensitive to it but it's
>> still something worth looking into.
>>
>> > Does this also holds for SPM8 or do there exist any type of scaling of
>> > the
>> > lead field matrix such as a normalization of the columns or something
>> > like
>> > that?
>> >
>>
>> Yes, there are several scaling and normalization steps so the units of
>> the output images are not related to original physical units but are
>> normalize to the total power across sources and conditions.
>>
>> > The second question is related to the lead field matrix as well. If I
>> > compare two different head models a BEM and 3-spheres model then they
>> > seem
>> > to be on two very different scales - is that really the case? Or am I
>> > missing an important step? Of course it is two very different head model
>> > assumptions so they should be quite different but I'm a bit surprised
>> > that
>> > there exists a scaling factor of 100 between the largest element in the
>> > BEM
>> > gain matrix and the 3-spheres gain matrix.
>>
>> See above.
>>
>> > What I just did was to load the mat-files with the gain-matrices and
>> > used
>> > the imagesc-function to show the amplitudes of the two lead field
>> > matrices.
>> >
>> > The 28th Jul 2010 you sent an answer to a post regarding head models and
>> > you
>> > here mentioned that FEM head models from SimBio might be an option in
>> > the
>> > very nice MEEGTool. I was wondering what the status is on integrating
>> > the
>> > SimBio FEM implementation with SPM, as I'm very interested to try out
>> > the
>> > FEM head models. I guess there is no reason that I will try to write the
>> > code my self if the option is almost done and will be part of the
>> > MEEGTool.
>> >
>>
>> I am aware of some efforts to integrate SimBio support in the forward
>> toolbox. Even if this is done I don't expect it to become one of the
>> standard options in SPM because SimBio runs only on a particular Unix
>> platform (I'm not even sure it's LINUX) and I suspect has very lengthy
>> computing time. But if you compute a gain matrix for the canonical
>> mesh in SimBio you can just replace the mat file generated by SPM with
>> your file and it will be used by spm_eeg_invert. If there is
>> inconsistency in units, it shouldn't be a problem.
>>
>> There is also a possibility to use another BEM implementation OpenMEEG
>> (http://www-sop.inria.fr/athena/software/OpenMEEG/). That's something
>> that works and I tested it last year, but found it impractical for
>> most users again because of difficulties with installation and long
>> computation time (about 24 h for normal mesh). The differences in the
>> lead fields with our BEM were only for a small number of vertices
>> close to the surface. But I can give you the glue code for this if you
>> want.
>>
>> Best,
>>
>> Vladimir
>>
>>
>>
>>
>> > Best,
>> > Carsten
>> >
>> >
>> >
>
>
>
> --
> Carsten Stahlhut
> Section for Cognitive Systems
> Department of Informatics and Mathematical Modelling
>
> Richard Petersens Plads, Building 321
> Technical University of Denmark
> DK-2800 Kongens Lyngby, Denmark
>

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001
2000
1999
1998


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager