[Mne_analysis] Plotting topographies for MEG sensors

Diana Omigie d.omigie at gmail.com
Sun Nov 4 09:02:04 EST 2012
Search archives: 
Thanks Sheraz

On Sun, Nov 4, 2012 at 8:55 AM, <sheraz at nmr.mgh.harvard.edu> wrote:

> Hi Diana and Alex,
>
> One thing I like to clear there is difference between new electronics and
> old electronics of Elekta system, New system do not have space between MEG
> and the channel identifier, but old system have space.
>
> Alex, after MEG upgrade Martinos center MEG do not have space anymore.
>
> Sheraz
>
> > Hi Alex
> >
> > I seemed to have a version of the layout function that generated names
> > which didn't have the white space between MEG and the sensor number e.e.
> > MEG0113 instead of  MEG 0113
> > It works fine when, as advised, I change the layout channel names to be
> > the
> > same as my evoked/ raw file
> > layout.names = raw.ch_names[:len(layout.names)]
> >
> > Diana
> >
> > On Fri, Nov 2, 2012 at 5:53 AM, Alexandre Gramfort <
> > gramfort at nmr.mgh.harvard.edu> wrote:
> >
> >> hi Diana,
> >>
> >> can you confirm that this example renders properly on your machine?
> >>
> >>
> >>
> http://martinos.org/mne/auto_examples/plot_topography.html#example-plot-topography-py
> >>
> >> if yes, please send me the evoked fif file so I can investigate.
> >>
> >> Best,
> >> Alex
> >>
> >> On Fri, Nov 2, 2012 at 1:25 AM, Diana Omigie <d.omigie at gmail.com>
> wrote:
> >> > Thanks,
> >> > I'm using neuromag. Comparing the evoked/raw channel names with layout
> >> > names, I notice there is a space in the latter that isn't there in the
> >> > former
> >> >
> >> > MEG 0113
> >> > vs
> >> > MEG0113
> >> >
> >> > Diana
> >> >
> >> >
> >> > p.s.
> >> > my script below
> >> >
> >> > #mne
> >> > #export
> >> PATH=/home/do232950/MyPython/epd_free-7.2-2-rh5-x86_64/bin:$PATH
> >> > #export PYTHONPATH=/home/do232950/MyPython/mne-python:$PYTHONPATH
> >> > print __doc__
> >> > #ipython
> >> > import os
> >> >
> >> > import mne
> >> > import pylab as pl
> >> > import numpy as np
> >> > from mne import fiff
> >> > from mne.layouts import Layout
> >> > from mne.viz import plot_evoked,plot_topo
> >> > #conditions = ['Pa_Ac','Vav','A']
> >> > conditions = ['A']
> >> >
> >> >
> >> > #evoked=dict()
> >> > #subj_id = ['s02']
> >> > subj_id =
> >> >
> >>
> ['s01','s02','s04','s05','s06','s07','s09','s10','s11','s12','s13','s14','s16','s17']
> >> >
> >> >
> >> > for s, subj in enumerate(subj_id):
> >> >  data_ave_path =  'Desktop/ave/'
> >> >  for i, cond in enumerate(conditions):
> >> >   fname= data_ave_path + subj + '/'+subj +'_'+ cond +'_ave.fif'
> >> >   evoked= fiff.read_evoked(fname, setno=0, baseline=(None, 0))
> >> >   layout=Layout('Vectorview-all',path='Desktop')
> >> >  plot_topo(evoked, layout)
> >> >  title="mne"
> >> >  pl.figtext(0.03,0.93,title,color='w',fontsize=18)
> >> >  pl.show()
> >> >
> >> >
> >> >
> >> >
> >> > On Thu, Nov 1, 2012 at 6:55 PM, Denis-Alexander Engemann
> >> > <d.engemann at fz-juelich.de> wrote:
> >> >>
> >> >> Hi Diana,
> >> >>
> >> >> could you share the script you were using?
> >> >> Did you make sure that you were using the correct layout. In case
> >> your
> >> >> MEG-system isn't a Neuromag 'vectorview-all' will not work. The
> >> plotting
> >> >> function assumes that channel names of raw match the layout names.
> >> >> So you could compare raw.ch_names with layout.names.
> >> >>
> >> >> Hope this helps.
> >> >>
> >> >> Denis
> >> >>
> >> >>
> >> >>
> >> >> On Thu, Nov 1, 2012 at 11:20 PM, Diana Omigie <d.omigie at gmail.com>
> >> wrote:
> >> >>>
> >> >>> Thanks both, unfortunately Im now getting the black image box with
> >> my
> >> >>> title but no actual plots when I use the plot_topo function even
> >> though I
> >> >>> can see the evoked object when I use plot_evoked.
> >> >>>
> >> >>> Diana
> >> >>>
> >> >>>
> >> >>> On Thu, Nov 1, 2012 at 5:33 PM, Denis A. Engemann
> >> >>> <denis.engemann at gmail.com> wrote:
> >> >>>>
> >> >>>> Hi Diana,
> >> >>>>
> >> >>>> this looks like the mne-python interface. Which version do you
> >> currently
> >> >>>> use?
> >> >>>> Recently there was an API change recently. Here is a script that
> >> >>>> demonstrates how to do it with the current developmental version.
> >> >>>>
> >> >>>>
> >> >>>>
> >>
> https://github.com/mne-tools/mne-python/blob/master/examples/time_frequency/plot_tfr_topography.py
> >> >>>>
> >> >>>>
> >> >>>> Denis
> >> >>>>
> >> >>>>
> >> >>>> On 01.11.2012, at 22:11, Diana Omigie <d.omigie at gmail.com> wrote:
> >> >>>>
> >> >>>> I am trying to plot meg evoked data using vector-view layouts but
> >> keep
> >> >>>> getting the error message that the .lout files cannot be found when
> >> I
> >> call
> >> >>>> this line
> >> >>>>
> >> >>>> layout = Layout('Vectorview-all')
> >> >>>>
> >> >>>> Any obvious reasons why I might be having trouble?
> >> >>>>
> >> >>>> Many thanks
> >> >>>>
> >> >>>> _______________________________________________
> >> >>>> Mne_analysis mailing list
> >> >>>> Mne_analysis at nmr.mgh.harvard.edu
> >> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >> >>>>
> >> >>>>
> >> >>>>
> >> >>>> The information in this e-mail is intended only for the person to
> >> whom
> >> >>>> it is
> >> >>>> addressed. If you believe this e-mail was sent to you in error and
> >> the
> >> >>>> e-mail
> >> >>>> contains patient information, please contact the Partners
> >> Compliance
> >> >>>> HelpLine at
> >> >>>> http://www.partners.org/complianceline . If the e-mail was sent to
> >> you
> >> >>>> in error
> >> >>>> but does not contain patient information, please contact the sender
> >> and
> >> >>>> properly
> >> >>>> dispose of the e-mail.
> >> >>>
> >> >>>
> >> >>>
> >> >>> _______________________________________________
> >> >>> Mne_analysis mailing list
> >> >>> Mne_analysis at nmr.mgh.harvard.edu
> >> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >> >>>
> >> >>>
> >> >>> The information in this e-mail is intended only for the person to
> >> whom
> >> it
> >> >>> is
> >> >>> addressed. If you believe this e-mail was sent to you in error and
> >> the
> >> >>> e-mail
> >> >>> contains patient information, please contact the Partners Compliance
> >> >>> HelpLine at
> >> >>> http://www.partners.org/complianceline . If the e-mail was sent to
> >> you in
> >> >>> error
> >> >>> but does not contain patient information, please contact the sender
> >> and
> >> >>> properly
> >> >>> dispose of the e-mail.
> >> >>>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >>
> ------------------------------------------------------------------------------------------------
> >> >>
> >> >>
> >>
> ------------------------------------------------------------------------------------------------
> >> >> Forschungszentrum Juelich GmbH
> >> >> 52425 Juelich
> >> >> Sitz der Gesellschaft: Juelich
> >> >> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> >> >> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> >> >> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
> >> >> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> >> >> Prof. Dr. Sebastian M. Schmidt
> >> >>
> >> >>
> >>
> ------------------------------------------------------------------------------------------------
> >> >>
> >> >>
> >>
> ------------------------------------------------------------------------------------------------
> >> >>
> >> >> Kennen Sie schon unsere app? http://www.fz-juelich.de/app
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > Mne_analysis mailing list
> >> > Mne_analysis at nmr.mgh.harvard.edu
> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >> >
> >> >
> >> > The information in this e-mail is intended only for the person to whom
> >> it is
> >> > addressed. If you believe this e-mail was sent to you in error and the
> >> > e-mail
> >> > contains patient information, please contact the Partners Compliance
> >> > HelpLine at
> >> > http://www.partners.org/complianceline . If the e-mail was sent to
> you
> >> in
> >> > error
> >> > but does not contain patient information, please contact the sender
> >> and
> >> > properly
> >> > dispose of the e-mail.
> >> >
> >>
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20121104/581c10d3/attachment.html

More information about the Mne_analysis mailing list