[Mne_analysis] Plotting topographies for MEG sensors

Sun Nov 4 08:55:05 EST 2012

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
>> >>>>
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