[FieldTrip] BEMCP

Mon Mar 14 11:46:36 CET 2016

Dear Vladimir,
thanks for your explanation. I tryed to use the option cfg.moveinward in
ft_prepare_sourcemodel ( I set it to 6 mm,, with inwardshift = 0), but this
did not solve the issue. As you can see from the attachment the cortex is
now partially uncovered. I am not sure I am using this option properly,
maybe there is a combination of values for cfg.moveinward and
cfg.inwardshift that works fine. I tryed several, but none of them gave me
the source localization that I expect.
I don't know whether the fact that some dipoles fall outside the brain
matters. For the attached figures I had no dipoles outside the brain,
whilst for some of the others attempts I had.

I actually found this post on the mailinglist where both you and John
already pointed out this issue using BEM:

http://mailman.science.ru.nl/pipermail/fieldtrip/2015-November/009783.html

Also I don't know whether this link (still under construction/discussion)
may be of interest in this contex:

http://www.fieldtriptoolbox.org/faq/is_it_good_or_bad_to_have_dipole_locations_outside_of_the_brain_for_which_the_source_reconstruction_is_computed

Furthermore, this other page (also under construction), uses the option
cfg.inwardshift for the template grid to be used in the creation of the
individual subject's grid, but without an explanation of why the option
is/should be used:

http://www.fieldtriptoolbox.org/tutorial/sourcemodel#subject-specific_grids_that_are_equivalent_across_subjects_in_normalized_space

In ft_prepare_sourcemodel I am using the standard grid (6 mm resolution)
provided by Fiedltrip, I don't know whether craeting my own template_grid
using the cfg.inwardshift option would actually fix the problem. I would
like to perform some further attempts, as soon as I have some time to go
through the function and understand how this options actually interplay.

Meanwhile, I am still working on producing the results using the FEM head
model. It is much more time-consuming than the BEM, and maybe that's one of
the reasons to choose BEM models. As soon as they are ready I will post
them as well :)

Anyway, thanks so much for your help. It was actually quite useful and
instructive!

All the best wishes,
Debora

On Sat, Mar 12, 2016 at 5:14 PM, Vladimir Litvak <litvak.vladimir at gmail.com>
wrote:

> Dear Debora,
>
> The critical thing with BEMCP is that your sources are not too close to
> the inner skull boundary. When they are closer than the safe distance the
> solution you get is completely wrong. When they are not too close, the
> solution is OK and comparable at least to concentric spheres. The safe
> distance is is more or less the average edge length in your  skull mesh. In
> SPM meshes this is 6 mm. In ft_prepare_sourcemodel there is an option
> cfg.moveinward that corrects the mesh to ensure that it is not too close.
> It would be interesting if you use this option and report whether this
> resolves your problem.
>
> This issue should occur in any BEM but depending on the implementation the
> critical distance might be shorter.
>
> Best,
>
> Vladimir
>
> On Sat, Mar 12, 2016 at 3:30 PM, Debora Desideri <deb.desideri at gmail.com>
> wrote:
>
>> Dear John,
>> thanks a lot for your promt reply and your suggestion. I guess that I was
>> sticking to the BEM head model just because I read the tutorial for EEG BEM
>> head model first, but going quickly through the studies you have mentioned
>> and considering the tests you have performed, I may also consider to switch
>> to the FEM head model or to simply use the concentric spheres (which
>> appeared to work similar to BEMCP in your comparisons). I am relatively new
>> to source localization and had no crash/errors in my pipeline, and this
>> combination makes always difficult to find possible pitfalls.
>>
>> As soon as I have them ready, I will post the results obtained with the
>> FEM head model as well, maybe they will be useful for some other users :)
>>
>> Thanks again for your support!
>> All the best,
>> Debora
>>
>> On Sat, Mar 12, 2016 at 3:42 PM, RICHARDS, JOHN <RICHARDS at mailbox.sc.edu>
>> wrote:
>>
>>> Deb:
>>>
>>> I have had problems with BEMCP.
>>>
>>>  1—one of the practical / technical problems is that if the compartments
>>> overlap, or even come close, then the procedure would not work—the
>>> ft_sourceanlaysis crashed.
>>>
>>>  2—There are a couple of studies comparing BEMCP and dipoli, among other
>>> methods.  The BEMCP method does not fare well, the dipoli fares better,
>>>
>>> E. g., among three or four studies I have seen.
>>> Gramfort, A., et al. (2010). "OpenMEEG: opensource software for
>>> quasistatic bioelectromagnetics." Biomed Eng Online *9*: 45.
>>>
>>> Gramfort, A., et al. (2011). "Forward field computation with OpenMEEG." Comput
>>> Intell Neurosci *2011*: 923703.
>>>
>>> 3—I have directly compared BEMCP, a 4-shell concentric spheres, dipoli,
>>> and the Simbio FEM model, by correlating results from each model (e.g.,
>>> correlations of all the dipole CDR estimates; or correlations across
>>> anatomical ROIs).  The BEMCP and concentric spheres work similarly, and the
>>> dipoli and Simbio-FEM work similarly.   This was with infants using
>>> participant-computed realistic models for the compartments and the FEM.
>>>
>>> I am not claiming from this and superiority of the dipoli (or FEM)
>>> models over the BEMCP, but I suggest looking at the research literature
>>> formally comparing these methods before going much further with BEMCP.
>>>
>>> John
>>>
>>> ***********************************************
>>> John E. Richards Carolina Distinguished Professor
>>> Department of Psychology
>>> University of South Carolina
>>> Columbia, SC  29208
>>> Dept Phone: 803 777 2079
>>> Fax: 803 777 9558
>>> Email: richards-john at sc.edu
>>> HTTP: jerlab.psych.sc.edu
>>> ***********************************************
>>>
>>>
>>
>>
>> --
>>
>> Debora Desideri, PhD Student
>> BNP Lab - Neurology Department
>> University Hospital Tübingen
>> Eberhard Karls University Tübingen
>> Hoppe-Seyler Str. 3
>> D-72076 Tübingen
>> Tel: +49 7071/29 80478
>>
>>
>> _______________________________________________
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>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
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-- 

Debora Desideri, PhD Student
BNP Lab - Neurology Department
University Hospital Tübingen
Eberhard Karls University Tübingen
Hoppe-Seyler Str. 3
D-72076 Tübingen
Tel: +49 7071/29 80478
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