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

Lilla.Magyari at mpi.nl Lilla.Magyari at mpi.nl
Wed Oct 2 15:12:45 CEST 2013 

Dear all,

I just would like to mention that I also went through again on the MNE
tutorial and I managed to reproduce the results. I also had to convert the
units of the volume conductor. However, it was not possible to convert the
units of the volume conductor directly. I converted the units of the
segmentation, and then I created the vol which got the same units as the
segmentation.  I do not if this is due to a difference between the
FieldTrip versions. I was using the latest one.

Best,
Lilla




> Hey Steve,
> thanks, you are great, I tried that again and it basically fixed my
> problem
> (see picture).
> For documentation and maybe others to profit from:
> Going through the
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
> tutorial I had problems building the volume conduction model which I
> solved
> by going through the additional tutorial
> http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg
>
> But after the combination of the matrices and aligning them I got a
> considerable sizing problem, see 2nd picture
> [[[ mri_nom_ctf = ft_convert_units(mri_nom_ctf, 'cm');
>
>
> T   = mri_nom_ctf.transform*inv(mri_nom_ctf.transformorig);
> % go to the Subject01/bem directory
> bnd  = ft_read_headshape('Subject01-oct-6-src.fif', 'format',
> 'mne_source');
> sourcespace = ft_convert_units(bnd, 'cm');
> sourcespace = ft_transform_geometry(T, sourcespace);
> save sourcespace sourcespace;
> save T T; %we will need the transformation matrix in the next step
>
>
> ...
>
> figure;hold on;
> ft_plot_vol(vol, 'facecolor', 'none');alpha 0.5;
> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight]]]
>
> So I included Steve's suggestion
>
> vol = ft_convert_units(vol, 'cm')
>
> and specified the location of the fiducials again
>
> [[[ cfg = [];
>
>
> cfg.method = 'interactive';
> mri_nom_ctf = ft_volumerealign(cfg, mri_nom);
>
>
> with the preauricular points this time in front of the auditory canals
> and it worked out well.
>
>
> Thanks all
>
>
> Leo
>
>
>
>
>
>
> On Mon, Sep 30, 2013 at 1:12 PM, Stephen Politzer-Ahles <
> politzerahless at gmail.com> wrote:
>
>> 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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>>> >>
>>> >> fieldtrip at donders.ru.nl
>>> >>
>>> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> >>
>>> >>
>>> >> End of fieldtrip Digest, Vol 34, Issue 28
>>> >>
>>> >> *****************************************
>>> >>
>>> >>
>>> >> _______________________________________________
>>> >>
>>> >> fieldtrip mailing list
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>>> >>
>>> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> >>
>>> >>
>>> >>
>>> >> _______________________________________________
>>> >> 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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>>> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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>>> >
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>>
>>
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