[Mne_analysis] Plotting topographies for MEG sensors

Fri Nov 2 12:22:21 EDT 2012

Hi Diana,

this is rather a hack for short-term satisfaction.
On the long, run you will save trouble if you make sure the versions you
installed aren't mutually interfering.
(It's kind of weird that you need the new layout syntax but get wrong /
outdated names)
Would be good to see whether the example Alex pointed out runs on your
machine with your setup.
You might want to consider making a new clean installation (current release
0.40 OR the dev branch).

Best,
Denis

On Fri, Nov 2, 2012 at 5:11 PM, Diana Omigie <d.omigie at gmail.com> wrote:

> 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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