[Mne_analysis] Plotting topographies for MEG sensors

[Diana Omigie]

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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