[Mne_analysis] source space vertices locations

Tue Mar 29 10:06:10 EDT 2016

look at that! There is a manual!

Thanks for your help!
Keith

----------------------------------
Keith Doelling
Dept of Psychology
Center for Neural Science
NYU

science.keithdoelling.com

On Tue, Mar 29, 2016 at 9:44 AM, dgw <dgwakeman at gmail.com> wrote:

> rr is what you want.
>
> In the pdf manual you would find the description in the matlab toolbox
> chapter (there is a description of all the fields). I haven't been
> able to find these things after the C-manual was removed from the wiki
> (it is probably there, but I don't know the new layout).
>
> hth
> d
>
> On Tue, Mar 29, 2016 at 9:33 AM, Keith Doelling <kd889 at nyu.edu> wrote:
> > Thanks for bearing with me.
> >
> > Based on shape, It seems as though they are in either the 'nn' or 'rr'
> keys
> > of the source space dict. Maybe this is obvious, but what is the
> difference
> > between these?
> >
> > After that I can use vertno to select the correct vertices?
> >
> > Keith
> >
> > ----------------------------------
> > Keith Doelling
> > Dept of Psychology
> > Center for Neural Science
> > NYU
> >
> > science.keithdoelling.com
> >
> > On Tue, Mar 29, 2016 at 9:17 AM, dgw <dgwakeman at gmail.com> wrote:
> >>
> >> Hi Keith,
> >>
> >> The xyz coordinate for each vertex is in the source space. you can
> >> just calculate anterior vs. posterior using the locations there.
> >>
> >> hth
> >> d
> >>
> >> On Tue, Mar 29, 2016 at 9:13 AM, Keith Doelling <kd889 at nyu.edu> wrote:
> >> >
> >> > I have been working off of that example that you linked in. The
> >> > mne.stc_to_label is very useful and gets me part of the way there but
> I
> >> > still can't say which is anterior and which is posterior until I plot
> >> > them.
> >> > Which is fine with two labels but could get complicated with more (or
> to
> >> > iterate across many subjects). If I can avoid the manual option,
> that'd
> >> > be
> >> > great.
> >> >
> >> > Really all I'm looking for is access to the spatial location of each
> >> > vertex
> >> > in some kind of xyz coordinate space. With that, the rest is, as you
> >> > mentioned, a bit of simple self-written code but I haven't been able
> to
> >> > find
> >> > any documentation on how the vertices are sorted or structured.
> >> >
> >> > Thanks!
> >> >
> >> > Keith
> >> >
> >> > ----------------------------------
> >> > Keith Doelling
> >> > Dept of Psychology
> >> > Center for Neural Science
> >> > NYU
> >> >
> >> > science.keithdoelling.com
> >> >
> >> > On Tue, Mar 29, 2016 at 8:20 AM, dgw <dgwakeman at gmail.com> wrote:
> >> >>
> >> >> You can do this in mne_analyze by simply drawing around the ROI, and
> >> >> selecting (the procedure is described in the manual). You can also do
> >> >> this programmatically in the mne-python code (this is a good starting
> >> >> point:
> >> >>
> >> >>
> http://martinos.org/mne/stable/auto_examples/inverse/plot_label_from_stc.html?highlight=label
> >> >> ). or with a simple bit of self-written matlab/python code depending
> >> >> on your needs.
> >> >>
> >> >> hth
> >> >> d
> >> >>
> >> >> On Tue, Mar 29, 2016 at 7:59 AM, Keith Doelling <kd889 at nyu.edu>
> wrote:
> >> >> > Hi all,
> >> >> >
> >> >> > I'm curious about how to select vertices based on their overall
> >> >> > location.
> >> >> > For example, say I have found two peaks in my source estimates. I
> >> >> > want
> >> >> > to
> >> >> > build two functional labels for each. One blob is in the anterior
> >> >> > half
> >> >> > and
> >> >> > the other is in the posterior half of the left hemisphere. Are the
> >> >> > vertices
> >> >> > organized in such away that I can select each blob on the basis of
> >> >> > its
> >> >> > overall location in the brain?
> >> >> >
> >> >> > Thanks in advance!
> >> >> > ----------------------------------
> >> >> > Keith Doelling
> >> >> > Dept of Psychology
> >> >> > Center for Neural Science
> >> >> > NYU
> >> >> >
> >> >> > science.keithdoelling.com
> >> >> >
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