[Mne_analysis] How to obtain MNI coords using mne.vertex_to_mni (newbie)

[Eric Larson]

        External Email - Use Caution        

If you already have a STC, doing:

left_mni = mne.vertex_to_mni(stc.vertices[0], 0)
right_mni = mne.vertex_to_mni(stc.vertices[1], 1)

​
might do it.

Eric


On Thu, May 10, 2018 at 4:05 AM, Adela Glez. <adelaglezcom at gmail.com> wrote:

>         External Email - Use Caution
>
> Thanks, Alex.
>
> Since I don't know how to write python code (I work with Matlab), I want
> to do my statistical analysis in Matlab. But first I need to have the data
> in MNI coordinates. I need a piece of Python code that gives me the MNI
> coordinates for the source locations for each subject. The only code I
> could find is this, which calculates MNI coordinates of center of mass. How
> to modify this to give me instead the stc locations?
>
> # calculate center of mass and transform to mni coordinatesvtx, _, t_lh = stc_lh.center_of_mass('sample')mni_lh = mne.vertex_to_mni <https://martinos.org/mne/stable/generated/mne.vertex_to_mni.html#mne.vertex_to_mni>(vtx, 0, 'sample')[0]vtx, _, t_rh = stc_rh.center_of_mass('sample')mni_rh = mne.vertex_to_mni <https://martinos.org/mne/stable/generated/mne.vertex_to_mni.html#mne.vertex_to_mni>(vtx, 1, 'sample')[0]
>
>
> Thanks again,
> Adela
>
> On 10 May 2018 at 08:37, <mne_analysis-request at nmr.mgh.harvard.edu> wrote:
>
>>
>>    1. Re: How to obtain MNI coords using mne.vertex_to_mni      (newbie)
>>       (Alexandre Gramfort)
>
>  ----------
>> From: Alexandre Gramfort <alexandre.gramfort at inria.fr>
>> Subject: Re: [Mne_analysis] How to obtain MNI coords using
>>         mne.vertex_to_mni       (newbie)
>> To: Discussion and support forum for the users of MNE Software
>>         <mne_analysis at nmr.mgh.harvard.edu>
>> Message-ID:
>>         <CADeotZr4Z0oa7QWVitPPGRCzaKBe-ju7ngOckTUSL=N0fOqxhw at mail.gm
>> ail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>>         External Email - Use Caution
>>
>> hi,
>>
>> what do you mean your MEG data?
>>
>> vertices here are SourceEstimate (aka stc) vertices.
>>
>>
>> HTH
>> Alex
>>
>>
>> On Thu, May 10, 2018 at 2:14 AM, Adela Glez. <adelaglezcom at gmail.com>
>> wrote:
>>
>> >         External Email - Use Caution
>> >
>> > Hi,
>> >
>> > In order to obtain the MNI coordinates of my MEG data, I have to use
>> mne.vertex_to_mni.
>> > Could someone give me an example of its usage?
>> >
>> > As for the first argument, how to obtain the vertex numbers of my data?
>> > I'm new in Python. Then, second argument, I can't find what code is
>> right
>> > or left hemisphere. Is there a way to get in one output both hemispheres
>> > (=the whole brain)?
>> >
>> > Thank you,
>> > Adela
>> >
>> > This is the help of the function:
>> >
>> > mne.vertex_to_mni(*vertices*, *hemis*, *subject*, *subjects_dir=None*,
>> > *mode=None*, *verbose=None*)
>> > [source]
>> > <http://github.com/mne-tools/mne-python/blob/master/doc/%3Cs
>> tring%3E#L1129-L1187>
>> > <https://martinos.org/mne/dev/generated/mne.vertex_to_mni.ht
>> ml#mne.vertex_to_mni>
>> >
>> > Convert the array of vertices for a hemisphere to MNI coordinates.
>> > Parameters: *vertices* : int, or list of int
>> >
>> > Vertex number(s) to convert
>> > *hemis* : int, or list of int
>> >
>> > Hemisphere(s) the vertices belong to
>> > *subject* : string
>> >
>> > Name of the subject to load surfaces from.
>> > *subjects_dir* : string, or None
>> >
>> > Path to SUBJECTS_DIR if it is not set in the environment.
>>
>>
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