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

Mon Sep 30 12:53:06 CEST 2013

Hello
thanks for your answers, in combination with the tutorial they were a big
help.
I think I got closer but have a last issue:
@ Jan-Mathijs: I redid the headmodel and it looks better now as shown on
the screenshots attached, thanks
@ Lilla and Stephen: the scaling in general should not be the problem I
think, the sizes seem to match, thank you
While both the volume conduction and the headmodel are expressed in CTF
coordinates, see second screenshot vol vs sourcespace, they don't align
very well > first screenshot
Is there a way to align them manually? Or would it be legitimate to "cheat"
with the fiducials of the sourcemodel ? By changing the preauricular points
I think I could align them, but I am not sure if that would cuase problems
later on...
Thanks in advance
Leo

On Mon, Sep 30, 2013 at 12:43 PM, Leopold Zizlsperger <zizlsperger at gmail.com
> wrote:

> Hello
> thanks for your answers, in combination with the tutorial they were a big
> help.
> I think I got closer but have a last issue:
> @ Jan-Mathijs: I redid the headmodel and it looks better now as shown on
> the screenshots attached, thanks
> @ Lilla and Stephen: the scaling in general should not be the problem I
> think, the sizes seem to match, thank you
> While both the volume conduction and the headmodel are expressed in CTF
> coordinates, see third screenshot vol vs sourcespace, they don't align very
> well > first two screenshots
> Is there a way to align them manually? Or would it be legitimate to
> "cheat" with the fiducials of the sourcemodel ? By changing the
> preauricular points I think I could align them, but I am not sure if that
> would cuase problems later on...
> Thanks in advance
> Leo
>
>
>
> On Mon, Sep 30, 2013 at 10:29 AM, jan-mathijs schoffelen <
> jan.schoffelen at donders.ru.nl> wrote:
>
>> Hi Leo,
>>
>> May I add to Lilla's comments that the reconstructed headmodel looks
>> quite bad to me. This suggests that the automatic anatomical segmentation
>> did not work well. The most likely cause is that the coordinate system
>> which you specified for the anatomical image in the input was incorrect
>> (e.g. specifying 'spm', while it should have been 'ctf' or so), or that the
>> transformation matrix mapping from voxels to head coordinates was not
>> correct.
>>
>> Best,
>> Jan-Mathijs
>>
>>
>> On Sep 30, 2013, at 9:53 AM, lilla.magyari at mpi.nl wrote:
>>
>> 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
>>
>>
>>
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>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>     Jan-Mathijs Schoffelen, MD PhD
>>
>> Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>>
>> Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>>
>> J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>>
>> http://www.hettaligebrein.nl
>>
>>
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