[Mne_analysis] Combine epoched ave fif files?

[Linda Moya]

Dear Don,

Thank you very much. This was exactly what I was looking for. I had tried
all of this, but somehow missed the --gave option (didn't read the manual
closely enough)...

Thank you.

Linda Moya

| Hi Linda,
|
| mne_process_raw can handle this directly.
| It can accept specification of multiple input raw files, an event file for
| each, and even an average file for each if needed.  I have used it for
| this.
| You can find the documentation in the version 2.7.3.pdf manual on page 48
| in the section 4.2.3 Batch-mode options and in the preceding section for
| the options which are common with mne_browse_raw.  Here are the key
| switches:
|
| --raw <name>
| Specifies the raw data file to be opened. This option is required for
| batch version, mne_process_raw. If a raw data file is not specified for
| the interactive version, mne_browse_raw, and empty interactive browser
| will open.
| --events <name>
| Specifies the name of a fif or text format event file (see Section 4.10.5)
| to be associated with a raw data file to be processed. If multiple raw
| data files are specified, the number of --eventsoptions can be smaller or
| equal to the number of raw data files. If it is equal, the event filenames
| will be associated with the raw data files in the order given. If it is
| smaller, the remaining raw data files for which an event file is not
| specified will not have an event file associated with them. The event file
| format is recognized from the file name: if it ends with .fif, the file is
| assumed to be in fif format, otherwise a text file is expected.
| --ave <name>
| Specifies the name of an off-line averaging description file. For details
| of the format of this file, please consult Section 4.13. If multiple raw
| data files are specified, the number of --ave options can be smaller or
| equal to the number of raw data files. If it is equal, the averaging
| description file names will be associated with the raw data files in the
| order given. If it is smaller, the last description file will be used for
| the remaining raw data files.
| --gave <name>
| If multiple raw data files are specified as input and averaging is
| requested, the grand average over all data files will be saved to <name>.
|
| You can double check its grand averaging operation including your setup by
| handing it 2 or more copies of the same raw data file and events file.  In
| that case, the grand average will be the same as the average of the one
| set of raw trials.
|
| Don
|
| Don Krieger, Ph.D.
| Department of Neurological Surgery
| University of Pittsburgh
| (412)648-9654 Office
| (412)521-4431 Cell/Text
|
| ________________________________________
| From: mne_analysis-bounces at nmr.mgh.harvard.edu
| [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Linda Moya
| [lhmoya at cmu.edu]
| Sent: Thursday, November 07, 2013 4:57 PM
| To: mne_analysis at nmr.mgh.harvard.edu
| Subject: [Mne_analysis] Combine epoched ave fif files?
|
| Dear MNE community,
|
| I've collected data for a given subject across 6 runs, which after
| pre-processing, result in 6 separate *.fif files. I can extract the events
| of interest, epoched and averaged separate conditions using
| mne_process_raw and the offline averaging mechanism. This results in 6
| separate epoched data .fif files. I can view these atop of each other in
| mne_browse_raw.
|
| A) What I really want to do is to epoch and average the 6 input *.fif
| files into ONE output *.fif file for each condition. So that instead of
| say 6 epoched fif files with N=20 averages for a condition, I have one
| epoched fif file with N=6*20 averages for that condition.
|
| B) Alternatively I can read the 6 averaged epoch files into matlab, and
| combine them there, so that I have this information in one structure in
| matlab. But then I would like to convert that structure back into a fif
| file that contains the average of all trials for a given condition for a
| given subject.
|
| Can I do either A) or B) above. Thank you very much for any help you can
| provide.
|
| Best Regards,
|
| Linda Moya
|
|
|
|
| --
| Linda Moya, Ph.D.
| Electrical and Computer Engineering
| Center for the Neural Basis of Cognition
| Carnegie Mellon University and University of Pittsburgh
| http://www.andrew.cmu.edu/user/lhmoya/
|
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-- 
Linda Moya, Ph.D.
Electrical and Computer Engineering
Center for the Neural Basis of Cognition
Carnegie Mellon University and University of Pittsburgh
http://www.andrew.cmu.edu/user/lhmoya/