[Mne_analysis] averaging in MNE

Gustavo Sudre gsudre at gmail.com
Tue Apr 14 12:04:31 EDT 2009
Search archives:

Matti,

That worked great. Thanks!

Best,

Gus


On Tue, Apr 14, 2009 at 6:44 AM, Matti Hamalainen
<msh at nmr.mgh.harvard.edu>wrote:

>
> HI Gustavo,
> On Apr 13, 2009, at 10:39 AM, Gustavo Sudre wrote:
>
> Hello,
>
> I have a couple questions regarding averaging MEG data with MNE and I was
> wondering if you could help me.
>
> 1) Is it possible to average a certain event only if something else
> happened after it? For example, let's say I have conditions 1 and 2. I want
> to average each condition, but only when the trigger happened and I received
> a response from the subject, which is coded as a 3 in the trigger line. In
> other words, average all the occurrences of 1 or 2 only when there's a 3
> after them. I wrote a script to do that in Matlab using the MNE toolbox, but
> since then lots of people have joined the lab and they are not very familiar
> with matlab, so I was wondering if there was a way to do such average within
> MNE, either by using the GUI or a combination of .ave and .eve files.
>
>
> Unfortunately, there is no direct way to do conditional averaging in
> mne_process_raw/mne_browse_raw (yet). However, the easiest way around this
> is to output a text format event file a and manipulate this file so that new
> event numbers are assigned to the events meeting the requested combinations.
> I guess such a script could be even written in Excel.
>
> 2) Something else my script does is to average conditions across different
> fif files. In the example above, I could have several fif files with such
> events, and the final .fif averaged file would represent the averages across
> all files. I imagine this is possible to do with the MNE software by using
> the global average parameter. Is that correct? Is there a different way to
> do it besides specifying a different .ave file for each of my raw .fif
> files? It's usually not a problem to do that for only a couple .fif files,
> but when there're about 10 different .fif files to be averaged, it starts to
> get a little cumbersome to keep track of all the .ave files, which look very
> similar except for the output parameter.
>
>
> You can, indeed, make a grand average file using mne_process_raw. You can
> use the --saveavetag option to create the output file names automatically.
> Also, if mne_process_raw runs out of ave file name names when processing the
> raw files, the last one available will be used. If you use custom event
> files, you can specify them on the command line (in version 2.6).
>
> Let's assume
>
> my.ave is your averaging file
> my1_raw.fif and my2_raw.fif are your raw data files
> my1.eve and my2.eve  are your event files
>
> You can do
>
> mne_process_raw <other options>  --raw my1_raw.fif --raw my2_raw.fif --eve
> my1.eve --eve my2.eve --ave my.ave --saveavetag -ave --gave my-gave.fif
>
> This will produce the averages in my1-ave.fif and my2-ave.fif and log files
> my1-ave.log and my2-ave.log independent of what is specifie in my.ave. Also,
> the my1.eve and my2.eve override the event file specification (if any) in
> my.ave.
>
> Similarly, the --savecovtag option can be used to generate the
> noise-covariance calculation output file names.
>
> I hope this helps.
>
> - Matti
>
>
>
>
>
>
> -------------
>
>
> Matti Hamalainen, Ph.D.
>
> Athinoula A. Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> Building 149, 13th Street, Mailcode 149-2301
>
> Charlestown, MA 02129-2060
>
> USA
>
>
> e-mail          msh at nmr.mgh.harvard.edu
>
>
>
>
>
>


-- 
Gustavo Sudre
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20090414/2385700c/attachment.html 


More information about the Mne_analysis mailing list