# averaging in MNE **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [April 13, 2009, 2:39pm UTC](https://mne.discourse.group/t/averaging-in-mne/112 "2009-04-13T14:39:39Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 13, 2009, 2:39pm UTC](https://mne.discourse.group/t/averaging-in-mne/112/1 "2009-04-13T14:39:39Z")
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. 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. Thanks, Gustavo ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 14, 2009, 10:44am UTC](https://mne.discourse.group/t/averaging-in-mne/112/2 "2009-04-14T10:44:45Z")
HI Gustavo, > 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 \ --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 ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 14, 2009, 4:04pm UTC](https://mne.discourse.group/t/averaging-in-mne/112/3 "2009-04-14T16:04:31Z")
Matti, That worked great. Thanks! Best, Gus ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 15, 2009, 4:51pm UTC](https://mne.discourse.group/t/averaging-in-mne/112/4 "2009-04-15T16:51:00Z")
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 ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 15, 2009, 6:34pm UTC](https://mne.discourse.group/t/averaging-in-mne/112/5 "2009-04-15T18:34:24Z")
Dear Etienne, Here are some relevant points: 1. mne\_convert\_mne\_data does not convert raw data files (mne\_raw2mat does this). 2. Were your data collected with MaxShield on? If so, I think even the averages need to be passed through maxfilter before they can be processed further (not absolutely sure about this). 3. The MNE Matlab toolbox pretty much makes mne\_convert\_mne\_data and mne\_raw2mat obsolete. The fif files can be now read directly from Matlab without having to waste disk space for the converted data. - Matti