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SPM  November 2011

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Subject:

Re: EEG BEM inaccuracy

From:

Vladimir Litvak <[log in to unmask]>

Reply-To:

Vladimir Litvak <[log in to unmask]>

Date:

Thu, 17 Nov 2011 15:42:18 +0000

Content-Type:

text/plain

Parts/Attachments:

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text/plain (187 lines)

Dear Tom,

I have some experience with BESA and Curry but I haven't compared the
forward solutions in those packages. I think the BESA head model is a
4-sphere model whereas in Curry they also have BEM and FEM. In
Fieldtrip there is now an effort to support a range of forward
solutions some of which would be hard to make standard in SPM due to
difficulties with installation on all the platforms that SPM should
run on and long computation times. But you can find something to suit
any taste there from a basic 3-sphere model to Simbio FEM that can
take into account individual conductivity and DTI data. In terms of
BEMs with isotropic conductivity my understanding is that OpenMEEG is
more or less as good as it gets. Christiano Micheli from the Donders
is responsible for interfacing with all those tools in Fieldtrip and
he can give you more specific advice based on what you need. I CC him
on this message.

Best,

Vladimir

On Wed, Nov 16, 2011 at 9:31 PM, tom h <[log in to unmask]> wrote:
> Vladimir, Rik,
> Thanks so much for your replies. It's helpful that you confirm this BEM
> issue is a limitation of the current implementation, which makes it less
> likely it stems from my inexperience with the software. I will stick to the
> spherical methods for now and spend some time exploring openMEEG as you
> suggest.
> Vladimir -- thanks for pointing out that single_subj_T1 is the correct
> template to use (wasn't aware of that). I tried it and the correspondence
> has indeed improved. This template is also much sharper and creates more
> beautiful pictures, which is great.
> BTW, if I may bother you with one more question -- just in case you have
> experience with commercial software for lead field computation, such as
> CURRY, BESA, or EMSE, might you be willing to share your assessment of which
> package(s) provide the most accurate EEG lead fields?
> Thanks!
> Best,
>    Tom
>
> On Mon, Nov 14, 2011 at 4:33 AM, Vladimir Litvak <[log in to unmask]>
> wrote:
>>
>> Dear Tom,
>>
>> The problem you found with EEG BEM is a known limitation of the method
>> used by the BEM code of Christophe Phillips. Vertices which are closer
>> to the inner skull surface than the edge length of that surface cannot
>> be handled correctly. There are just a few such vertices in the
>> standard template mesh and it doesn't seem to affect the SPM source
>> reconstruction methods (although may well affect other methods using
>> the same BEM). Also when transforming the meshes to fit individual
>> MRIs the problem might be aggravated but I haven't seen any examples
>> of that.
>>
>> There is a more precise method implemented in the OpenMEEG library
>> (http://www-sop.inria.fr/athena/software/OpenMEEG/). This library is
>> supported by spm_eeg_inv_forward (as 'OpenMEEG BEM') but the option is
>> not in the GUI. The reason for this is that OpenMEEG is not trivial to
>> install and rather slow to run (e.g. it might take more than a day to
>> compute one set of leadfields). Therefore it is not practical for most
>> SPM users. However if you are very worried about EEG leadfield quality
>> this might be a good method for you. Also note that you can replace
>> the gain matrix file generated by SPM with your own file computed with
>> external software as long as the leadfields match.
>>
>> For SPM12 we are planning to add the possibility to use pre-computed
>> leadfields stored as images. Then the pre-computing can be done with
>> OpenMEEG but the installation and slow running problems will be
>> circumvented. This will only work, however, for the standard EEG
>> template head and users who want to warp the meshes will have to run
>> OpenMEEG themselves.
>>
>> Regarding your second issue, note that the mesh was computed from the
>> individual image stored in canonica/single_subj_T1.nii so you should
>> check for the correspondence with that image and not with the average
>> template which might be slightly different.
>>
>> Best,
>>
>> Vladimir
>>
>> On Sun, Nov 13, 2011 at 10:24 PM, Rik Henson
>> <[log in to unmask]> wrote:
>>
>> > ________________________________
>> > From: tom h [[log in to unmask]]
>> > Sent: 11 November 2011 21:43
>> > To: [log in to unmask]
>> > Cc: Rik Henson; [log in to unmask]
>> > Subject: Re: M+EEG+fMRI Face Dataset
>> >
>> > Hello Rik, SPM methods group,
>> > I'm interested in creating EEG lead fields, and have been trying SPM8
>> > for
>> > this purpose. I noticed two curious features, perhaps you can comment on
>> > them -- I might have done some things incorrectly.
>> > 1. In this
>> >
>> > paper http://related.springerprotocols.com/lp/pubmed-central/eeg-and-meg-data-analysis-in-spm8-HDecQN27Jc
>> > you recommend using BEM. However, my BEM lead fields (and those created
>> > by
>> > some others in SPM8) all have the following property: some voxels have
>> > an
>> > order of magnitude higher norm than the rest. By norm I mean
>> > mean(G.^2,1),
>> > where G is the sensors X voxels lead field matrix. On the other hand, my
>> > 3-sphere lead fields created with SPM don't show this property.
>> > I'm attaching a figure (lead_field_norm) showing the norm of a BEM and a
>> > 3-sphere lead field created for the same 60-sensor system. I'm also
>> > attaching a mat file with the 2 lead field matrices and the sensor
>> > labels,
>> > in case you'd like to take a look.
>> > My question is, is the BEM result incorrect, and if so, what would you
>> > suggest doing to create an accurate BEM lead field?
>> > 2. I overlaid the voxels of my 3-sphere lead fields on the T1 MRI
>> > template.
>> > However, there seems to be some mismatch. I'm attaching 2 figures
>> > (spm_5124voxels_1,2) that show the voxels closest to each of the 91
>> > surfaces
>> > along the x-axis (except the extreme ones that don't contain voxels).
>> > There
>> > seem to be some voxels in places you wouldn't expect, and the coverage
>> > is
>> > not quite uniform.
>> > For comparison, I'm attaching the same figures for a non-SPM lead field
>> > (nonspm_2400voxels_1,2). These voxels (admittedly there are about 1/2 as
>> > many as in the SPM case) seems to line up better.
>> > My question here is, am I correct in assuming that the voxel locations
>> > in
>> > SPM-created lead fields are given in MNI coordinates, and do these
>> > overlays
>> > indicate to you there was an error made using the software?
>> > I realize this is a long email, and will truly appreciate any advice
>> > you'd
>> > be able to offer. Overall I find SPM very helpful and enjoy using it.
>> > Have a good weekend!
>> > Best,
>> >    Tom
>> >
>> >
>> > On Thu, Mar 10, 2011 at 11:23 AM, tom h <[log in to unmask]> wrote:
>> >>
>> >> Indeed I was using Chrome (doesn't everyone? :-)
>> >> Your solution works, thank you!
>> >> On Thu, Mar 10, 2011 at 3:12 AM, Guillaume Flandin
>> >> <[log in to unmask]> wrote:
>> >>>
>> >>> Hi Tom,
>> >>>
>> >>> I assume you are using Google Chrome, which seems to have trouble
>> >>> accessing some FTP servers. Try again with any other web browser or
>> >>> use
>> >>> this HTTP link:
>> >>> http://www.fil.ion.ucl.ac.uk/spm/ftp/data/mmfaces/
>> >>>
>> >>> Best regards,
>> >>> Guillaume.
>> >>>
>> >>>
>> >>> On 09/03/11 22:03, tom h wrote:
>> >>> > Hello, Rik, SPM Methods Group,
>> >>> >
>> >>> > I'm interested in the multimodal face
>> >>> > dataset http://www.fil.ion.ucl.ac.uk/spm/data/mmfaces/
>> >>> >
>> >>> > However, the data links don't work. Any advice?
>> >>> >
>> >>> > Thanks for your help!
>> >>> >
>> >>> > Best,
>> >>> >    Tom Holdman
>> >>> >
>> >>>
>> >>>
>> >>> --
>> >>> Guillaume Flandin, PhD
>> >>> Wellcome Trust Centre for Neuroimaging
>> >>> University College London
>> >>> 12 Queen Square
>> >>> London WC1N 3BG
>> >>
>> >
>> >
>
>

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