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

[Stephen Politzer-Ahles]

Hi Leo,

If I am remembering correctly, I think the problem could still be related
to ft_convert_units even if the volume conductor and head model look like
they're similar in size. For example, in the images I sent out when I was
having this problem earlier, the volume conductor and hte sourcespace are
the same size but one is tilted more, and the solution was nevertheless
related to ft_convert_units (I think). In my case, this was because the
conversion had to happen at a different time than it does in the tutorial.
(I had to insert ft_convert_units somewhere earlier in the pipeline than
where it was happening in the tutorial.) I'm sorry I can't be more
specific, but if it will help I could try to look through my old code and
re-figure out what I changed at the time.

Best,
Steve



Stephen Politzer-Ahles
New York University, Abu Dhabi
Neuroscience of Language Lab
http://www.nyu.edu/projects/politzer-ahles/



>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 30 Sep 2013 12:53:06 +0200
> From: Leopold Zizlsperger <zizlsperger at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] EEG Source reconstruction: sourcespace and
>         the volume conductor misaligned
> Message-ID:
>         <CAAk5s=
> WTe+T1PZO0jMb6KUvpHFyi-c0tFuG8Mc0m9um6vVdacA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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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> >>
> >> ------------------------------
> >>
> >>
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> >>
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> >>
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> >>
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> >>
> >>
> >> End of fieldtrip Digest, Vol 34, Issue 28
> >>
> >> *****************************************
> >>
> >>
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> >>
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> >>
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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
> >>
> >>
> >> _______________________________________________
> >> fieldtrip mailing list
> >> fieldtrip at donders.ru.nl
> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >>
> >
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