[Mne_analysis] Plotting multiple individual's dipole locations on standard brain

[Eric Larson]

There is currently no way to constrain the location of estimates other than
ensuring they are inside the inner skull surface, which is done
automatically.

Eric


On Mon, Aug 15, 2016 at 9:13 PM, Talitha Ford <tcford at swin.edu.au> wrote:

> Hi again,
>
> Is it possible to specify a ROI for dipole fitting? Or a range of
> coordinates? I’m particularly interested in auditory cortices, but
> selecting gravimeters over the cortex sometimes results in the max dipole
> located well away from this region.
>
> I have looked at mne.DipoleFixed, but this function is not suitable as I
> also want to see the difference in dipole locations within the ROI for
> different groups of subjects.
>
> Talitha
>
> On 16 Aug 2016, at 09:15, Talitha Ford <tcford at swin.edu.au> wrote:
>
> Thank you Alex,
>
> Unfortunately, dip_1[idx_1+1].pos = dip_2[idx_2].pos.copy() did not copy
> (I had tried a number of variations using the .copy() function before
> emailing).
>
> I have opened an issue in git.
>
> Is there a way to get the vertex of the dipole coordinates from dip.pos?
> So that I can use the mne.vertex_to_mni function?
>
> Cheers,
> Talitha
>
> On 15 Aug 2016, at 19:04, Alexandre Gramfort <alexandre.gramfort at telecom-
> paristech.fr> wrote:
>
> hi,
>
> > dip_1[idx_1+1].pos = dip_2[idx_2].pos
>
> does not copy indeed. This:
>
> dip_1[idx_1+1].pos = dip_2[idx_2].pos.copy()
>
> will copy.
>
> now what you need is a way to "morph" dipoles from each subjects to
> fsaverage or MNI space. AFAIK there is no such function in mne-python yet
> although you can find some hints:
>
> http://martinos.org/mne/stable/generated/mne.vertex_
> to_mni.html#mne.vertex_to_mni
>
> please open an issue on github:
>
> https://github.com/mne-tools/mne-python/issues
>
> so we can follow up on this.
>
> Best,
> Alex
>
> On Sun, Aug 14, 2016 at 4:46 AM, Talitha Ford <tcford at swin.edu.au> wrote:
> > Hello,
> >
> > I was wondering whether anyone has used Dipole.plot_locations to plot
> the maximal dipole for a each subject/participant on the same brain
> structure (a standardised T1, for example)? I am interested in relative
> dipole location and strengths between two groups, for each hemisphere. So
> ideally would like to plot each participants left and right auditory
> dipole, on the same brain, with the groups differentiated by colour (e.g.
> blue for group1 and red for group2).
> >
> > I have tried copying the pos of each individuals maximal dipole into
> sequential indices of the 1st individual Dipole object, however the pos
> won’t copy in.
> >
> >
> > evoked = mne.read_evokeds(fname_ave, baseline=(None, 0))[0]
> > # crop at individual maximum peak latency and 1ms later
> > evoked.crop(.15, .20 )
> >
> > # this plots each individual on a separate brain for the max dipole
> across the cortex
> > for pid in [‘1’,’2’,’3’]:
> >       # Fit a dipole
> >       dip = mne.fit_dipole(evoked, fname_cov, fname_bem, fname_trans)[0]
> >
> >       m = dip.amplitude.max()
> >       t = np.where(dip.amplitude == m)
> >       idx = t[0][0]
> >       dip[idx:idx+1].plot_locations(fname_trans, 'app'+pid,
> subjects_dir)
> >
> >
> > # I tried something like this, to hack the position of the second
> participant into the index+1 of the max for participant 1 (if that makes
> sense)
> > evoked_1 = mne.read_evokeds(fname_1, baseline=(None, 0))[0]
> > dip_1 = mne.fit_dipole(evoked_1, fname_cov, fname_bem, fname_trans)[0]
> > m = dip_1.amplitude.max()
> > t = np.where(dip_1.amplitude == m)
> > idx_1 = t[0][0]
> >
> > evoked_2 = mne.read_evokeds(fname_2, baseline=(None, 0))[0]
> > dip_2 = mne.fit_dipole(evoked_2, fname_cov, fname_bem, fname_trans)[0]
> > m = dip_2.amplitude.max()
> > t = np.where(dip_2.amplitude == m)
> > idx_2 = t[0][0]
> >
> > dip_1[idx_1+1].pos = dip_2[idx_2].pos # this doesnt copy
> >
> > I tried several variations of copy
> > dip_1[idx_1+1][:].pos = dip_2[idx_2][:].pos
> > dip_1[idx_1+1][:].pos[:] = dip_2[idx_2][:].pos[:]
> > dip_1[idx_1+1][:].pos = copy(dip_2[idx_2][:].pos)
> > etc.
> >
> > Any help would be greatly appreciated.
> >
> > Cheers,
> > Talitha
> >
> >
> >
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