[Mne_analysis] How to get -trans from .spf

[Eric Larson]

        External Email - Use Caution        

If your sfp is already in the Freesurfer MRI surface RAS coordinate frame
("mri" coordinate frame in MNE), then you can import it using the montage
functions without transforming it to the head, then use the lpa/nasion/rpa
to get the transformation to Neuromag head coordinates with something like:

mri_head_t = mne.transforms.get_ras_to_neuromag_trans(nasion, lpa, rpa)
trans = mne.transforms.Transform('mri', 'head', mri_head_t)

Then I'd read and apply the montage the normal way (with the conversion to
head coordinate frame included), and make sure everything is correct by
plotting this using `plot_alignment` and the `show_axes=True` and
`dig=True` arguments.

Eric


On Thu, Jul 18, 2019 at 11:20 AM <ugobruzadin at gmail.com> wrote:

>         External Email - Use Caution
>
> Hi,
>
> I can’t find if this question has already been answered before. I’m 98%
> sure we already co-registered the electrodes in EEGLAB in a 3D field, and I
> wanted to batch the dataset and get the spectral activation from brain
> areas using sLORETA. How do I get the -trans for a forward computation
> (later for the inverse computation)? I’ve managed to import the .sfp to MNE
> via montage, and it asks if I want to do the transform of it to a Neuromag
> space, and I’m saying True. How can I export this transformed matrix to a
> -trans file? Is this the -trans file it’s looking for? The website mentions
> that I need to use the co-register using the browser gui coreg function. Is
> this the only way to save the -transformed matrix? Can’t it be done in code
> via some function? We have hundreds if not thousands of files to run, we
> would like to batch it (I’m using MNE to avoid the manual work in the
> LORETA-key software).
>
> Thanks in advance,
>
> Ugo Bruzadin Nunes,* M.A.*
> *PSYC 312 Instructor - Sensation and Perception*
> *Brain and Cognitive Sciences Ph.D Program || Department of Psyschology
> || Southern Illinois University - Carbondale*
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