[FieldTrip] BEMCP

Thu Mar 17 15:46:46 CET 2016

Dear Vladimir,
The correlation between concentric spheres and FEM (attached) it is not so
bad I think. There are quite "low" (ca. 0.4-0.5) correlaiton values  closer
to the surface, but it is close enough to our expectations. I used
concentric spheres because I am working with EEG data, isn't the local
spheres method only for MEG?
I am also surprised that the correlaiton between BEM and concentric spheres
lead fields is so bad. It almost looks random...
Best,
Debora

On Thu, Mar 17, 2016 at 3:21 PM, Vladimir Litvak <litvak.vladimir at gmail.com>
wrote:

> What about correlations between local spheres and the FEM? If it's only
> the BEM that's broken I'd expect that you should get decent values for
> those. Your plots don't look so good. I did something similar a couple of
> years ago and got much better results. Perhaps it'd be a good idea to
> re-check the BEM again.
>
> Vladimir
>
> On Thu, Mar 17, 2016 at 2:08 PM, Debora Desideri <deb.desideri at gmail.com>
> wrote:
>
>> Dear Vladimir and John,
>> attached you can find the results of the source localizaiton with the FEM
>> head model. Moreover, I also report the correlation of the lead fields for
>> the FEM and concentric spheres models and BEM and concentric spheres model
>> (the latter one using an inwardshift of 6 mm). Unfortunately, I could not
>> produce the correlation trend we expected (I tryed several values of
>> inwardshifts, ranging form 1mm to 10 mm and the plot is of course not
>> identical to the one I posted, but it is qualitatively similar).
>> There must still be something I don't fully get probably, since the
>> correlation between the concentric spheres lead fields and the BEM lead
>> fields is always so low, even close to the center of the head, regardless
>> of the inwardshift value.
>>
>> All considered, I would rather go for a FEM model at least for the moment
>> being.
>> Thanks a lot for your support!
>>
>> Best,
>> Debora
>>
>>
>>
>>
>> On Mon, Mar 14, 2016 at 12:11 PM, Vladimir Litvak <
>> litvak.vladimir at gmail.com> wrote:
>>
>>> Dear Debora,
>>>
>>> cfg.moveinward option is useful when your source space is a mesh as it
>>> actually deforms the mesh to push it inwards. When your source space is a
>>> grid you should use cfg.inwardshift to just exclude the points that are
>>> closer than 6 mm to the boundary.  It might be a useful exercise for you to
>>> compute the lead fields with concentric spheres and with a BEM for the same
>>> grid and then look at correlations between these lead fields. You should
>>> see that the correlations should be high at depth but might be low for some
>>> points close to the surface. Once you hit the right value of inwardshift
>>> the low correlations should disappear.
>>>
>>> Best,
>>>
>>> Vladimir
>>>
>>> On Mon, Mar 14, 2016 at 10:46 AM, Debora Desideri <
>>> deb.desideri at gmail.com> wrote:
>>>
>>>> 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
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> fieldtrip mailing list
>>>>>> fieldtrip at donders.ru.nl
>>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>> fieldtrip at donders.ru.nl
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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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>>>> fieldtrip mailing list
>>>> 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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>> fieldtrip mailing list
>> 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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