[FieldTrip] EEG Source reconstruction: sourcespace and the volume conductor misaligned

[Lilla.Magyari at mpi.nl]

Hello Leo and Stephen,

yes, it is unfortunate, that there is still a problem with the MNE
tutorial. I think the main problem is the integration of the pipeline with
Freesurfer which requires a more careful look on the script.
I could not find the attached image from Leo. If the sourcespace and the
volume conduction models are not well-aligned because one of them is too
small compared to the other, then it will probably help if you convert the
units.
In Fieldtrip, the handling of the units of the volume conduction model has
changed, which means that they are not automatically converted to 'cm'
anymore.
Lilla


> Hello Leo,
>
> This looks like the same problem I was having a few months ago, and there
> should be some messages on the list about it. I am not able to look at my
> data and scripts right now, but if I remember correctly (you can check the
> lists for more) the problem had to do with the transformation matrix, and
> ft_convert_units. In my case, during the "volume conduction model" step of
> the tutorial (the last step before you can plot the vol and sourcespace
> together), I had to add an extra
>
> vol = ft_convert_units(vol, 'cm')
>
> before ft_transform_geometry. I don't remember if this alone will solve
> the
> problem (unfortunately the the situation is kind of complicated right now,
> there is also a different version of the minimum norms tutorial that is
> still in development--see the previous messages for links--and I think my
> processing pipeline ended up being a mixture of the two to get things
> working. Which means that it's hard to track where exactly I solved the
> problem.)
>
> Best,
> Steve
>
>
>>
>> Message: 1
>> Date: Sat, 28 Sep 2013 15:25:32 +0200
>> From: Zizlsperger Leopold <zizlsperger at gmail.com>
>> To: <fieldtrip at science.ru.nl>
>> Subject: [FieldTrip] EEG Source reconstruction: sourcespace and the
>>         volume  conductor misaligned
>> Message-ID: <06D14B0C-655A-4EF2-A69A-B735DBDBC504 at gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi all,
>> I am following the instructions in the "Source reconstruction of
>> event-related fields using minimum-norm estimate" tutorial closely to do
>> a
>> source-analysis of EEG data using the example MRI. As I am following the
>> tutorial almost unchanged I am not including the script here.
>>
>> When I re-align the volume conduction model to the sourcespace they are
>> not aligned very well, see screenshot attached. I remember a similar
>> question in the mailing list a while ago but cannot find it...
>>
>> Is there a way to interactively realign volume conduction model and
>> sourcespace? Re-doing the fiducials did not change the aligment
>> considerably. Also, my volume conduction model looks weird...
>> I used ft_determine_coordsys on both the vol and the sourcespace, see
>> screenshots attached, too.
>> Would be nice if you could point me in the right direction.
>> Thanks in advance.
>> Leo
>>
>> ----
>>
>>
>>
>>
>> Dr. med. Leopold Zizlsperger
>> Klinik f?r Neurologie
>> Uniklinik RWTH Aachen
>> Pauwelsstrasse 30
>> 52074 Aachen
>> Tel: +49 241 80 35465
>> lzizlsperger at ukaachen.de
>>
>> Leopold Zizlsperger, MD
>> Department of Neurology
>> RWTH Aachen University
>> Pauwelsstrasse 30
>> 52074 Aachen, Germany
>> Tel: +49 241 80 35465
>> lzizlsperger at ukaachen.de
>>
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <
>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130928/aff715c6/attachment.html
>> >
>> -------------- next part --------------
>> A non-text attachment was scrubbed...
>> Name: align 2.png
>> Type: image/png
>> Size: 200601 bytes
>> Desc: not available
>> URL: <
>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130928/aff715c6/attachment.png
>> >
>> -------------- next part --------------
>> A non-text attachment was scrubbed...
>> Name: align.png
>> Type: image/png
>> Size: 208103 bytes
>> Desc: not available
>> URL: <
>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130928/aff715c6/attachment-0001.png
>> >
>> -------------- next part --------------
>> A non-text attachment was scrubbed...
>> Name: vol.png
>> Type: image/png
>> Size: 148045 bytes
>> Desc: not available
>> URL: <
>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130928/aff715c6/attachment-0002.png
>> >
>> -------------- next part --------------
>> A non-text attachment was scrubbed...
>> Name: sourcespace.png
>> Type: image/png
>> Size: 122200 bytes
>> Desc: not available
>> URL: <
>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130928/aff715c6/attachment-0003.png
>> >
>>
>> ------------------------------
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> End of fieldtrip Digest, Vol 34, Issue 28
>> *****************************************
>>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip