[Mne_analysis] averaging in MNE

LABYT Etienne INSERM etienne.labyt at cea.fr
Wed Apr 15 12:51:00 EDT 2009
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Dear all,

I have a question about conversion of fif file into mat file;. I would like to convert my raw data (fif file) into matlab file. For this, I tried to use the function mne_convert_mne_data but I have a message "no evoked data here". I have the same message if I try this with averaged data (fif file) directly obtained by on-line averaging. 

I exactly wrote this command line:

 

mne_convert_mne_data -meas my filename.fif -mat -out my filename.mat

 

Something is wrong ?

Thanks for your help !

Bye

 

Etienne LABYT

________________________________

De : mne_analysis-bounces at nmr.mgh.harvard.edu [mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] De la part de Gustavo Sudre
Envoyé : mardi 14 avril 2009 18:05
À : Matti Hamalainen
Cc : Mne_analysis at nmr.mgh.harvard.edu
Objet : Re: [Mne_analysis] averaging in MNE

 

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

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