[Mne_analysis] Calculate forward model using digitization from eximia system

[Eric Larson]

>
> I know it has been a while, but I finally went back to this project and
> managed to create the DigMontage using the mne.channels.read_dig_montage.
> ..
> It works, but I'm not sure if this is the correct way to do it.
>

Given that your alignments look approximately correct (other than the
scaling issue!) I suspect these steps are correct. Can you open an
MNE-Python issue with this procedure? It would be good if we could turn it
into a tutorial or improve the docs to describe it.


> *Is it ok to use electrodes as head points?*
>

If you don't have "extra" points directly on the scalp, I would say that
electrodes can be used, yes. But keep in mind how your digitization was
actually done during the experiment; some electrodes (e.g., BrainVision
actiCap <http://www.brainproducts.com/productdetails.php?id=4>) are
actually a bit thick, say half a centimeter, so if they were digitized on
the center of those electrodes, you'd expect them to be that far off of the
MRI during coregistration.

*Is it not enough to use the fiducials alone?*
>

You can use just the fiducials, but fitting a the rotation + translation
using three points manually placed on an MRI surface is might be less
robust than fitting extra dig points. So it depends on how much you trust
your fiducial digitization and your ability to pinpoint those equivalent
locations no an MRI.

Perhaps I should open a new thread less specific about eximia, since my
> question is more generic:* how can I align electrodes to individual MRIs
> just having the fiducials from the digitization process in a text file?*
>

We have an eXimia data-reading pull request open
<https://github.com/mne-tools/mne-python/pull/3523>, and support is a
work-in-progress. So I suggest we discuss eXimia things there to converge
on something usable.

The digitization issues are more generic, and hopefully someone else can
comment more meaningfully. I don't have much experience with it. But in
theory once you have your info['dig'] populated properly via DigMontage,
using the coreg gui in MNE-Python, or even saving the data to FIF and using
mne_analyze should be possible. But it sounds like you have already gone
that route...

However, for some reason all the electrodes are quite far from the scalp,
> even though the fiducials were aligned:
>
> https://drive.google.com/open?id=0B0p7WZ2wlTFSNklmcTlPakJERXc
> https://drive.google.com/open?id=0B0p7WZ2wlTFScXF4NGMtNXBiZ2M
>
> since it happened with 5 subjects, and the error is always similar, I
> think it is unlikely to be a simple switch between subjects digitization (I
> double checked the origin of the files in any case)
> it could be, however, a systematic error in the acquisition... But this
> system was successfully used with brainstorm, so I would not start with
> this hypothesis.
>

I assume by this you mean the plots looked okay in BrainStorm, so we need
to dig into it a bit.

It's possible that BrainStorm projects the electrodes onto the scalp for
visualization. Do you have data from one subject you could share? If so,
feel free to open an MNE-Python issue and we can work through it. For
example, as a first pass you could look at the distribution histogram of
the dig points in X and Y, and do the same thing for the MRI head surface
coordinates. You can also look at the transformation matrix and ensure that
it's a pure rotation + translation matrix, with no scaling (but it really
should be!).

Eric
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20161026/9c9d3478/attachment.html