[Mne_analysis] Grand average over subjects when bad channels are excluded?

[Maria Hakonen]

Hi all,

Many thanks for all help!
I will try mne.evoked.grand_average.
Can I find it if I first get the latest code as: git clone git://
github.com/mne-tools/mne-python.git
and then simply type mne.evoked.grand_average ? in python?

Regards,
Maria

2014-11-17 11:28 GMT+02:00 Mads Jensen <mje.mads at gmail.com>:

> Hi all,
>
> I can give the  mne.evoked.grand_average function a try.
>
> best regards,
> mads
>
> On 17/11/14 09:21, Alexandre Gramfort wrote:
> > hi Maria,
> >
> > your best option is to do a first for loop to get the list of all
> > channels to drop,
> > then drop them with evoked.drop_channels and then average.
> >
> > also pay attention to the number of epochs if it varies, as the +
> operator
> > uses it.
> >
> > any volunteer to add a mne.evoked.grand_average function?
> >
> > HTH
> > Alex
> >
> >
> > On Mon, Nov 17, 2014 at 8:59 AM, Maria Hakonen <maria.hakonen at gmail.com>
> wrote:
> >> Hi all,
> >>
> >> I have computed grand average over subjects as follows:
> >>
> >> for subject in subjects:
> >>                  evoked = mne.read_evokeds(filename, baseline=(None, 0),
> >> proj=True,verbose=False)
> >>                  if flag == 1:
> >>                          evoked_all = evoked[0]
> >>                          flag = 0
> >>                  else:
> >>                          evoked_all = evoked_all+evoked[0]
> >>          evoked_all = evoked_all / len(subjects)
> >>
> >> However, a problem arises when the evoked files don't contain the same
> >> channels (this is because I have excluded bad channels and they are not
> same
> >> in all files):
> >>
> >> AssertionError: <Evoked  |  comment : 'Unknown', time : [-0.099994,
> >> 2.999808], n_epochs : 147, n_channels x n_times : 305 x 3721> and
> <Evoked  |
> >> comment : 'Unknown', time : [-0.099994, 2.999808], n_epochs : 154,
> >> n_channels x n_times : 306 x 3721> do not contain the same channels
> >>
> >> I wonder if there is any way to get the grand average over subjects if
> bad
> >> channels are excluded?
> >>
> >> Many thanks already in advance!
> >>
> >> Regards,
> >> Maria
> >>
> >>
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