[Mne_analysis] Event file old vs. new format

Linda Moya lhmoya at cmu.edu
Thu Sep 29 09:57:43 EDT 2011
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Hi Alex,

Great, I will take a look at this. Thank you.

Re: MNE discarding trials on the fly during averaging, this is reflected in the log files created, right? I am then using the log files to create the new event files to use when I average the epochs myself. Could you confirm or correct my assumption here?

Again, thank you.


-- Linda Moya

Sent from my iPad

On Sep 29, 2011, at 9:32 AM, Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu> wrote:

> Hello Linda,
> I can send you the mne C code but let me try to suggest something.
> It seems to me that your choice is binary either offset the time sample
> in the eve file with raw.first_samp or not. The output of this experiment
> should tell you easily if you do the right thing. Regarding the comparison
> with the MNE C code, be careful that MNE discards bad epochs on the
> fly so you'll need to pass only good events to have a real comparison.
> if you feel like it, I think this example:
> http://martinos.org/mne/auto_examples/time_frequency/plot_time_frequency.html
> is doing pretty much what you want to do.
> let me know if you need help to give it a try.
> Alex
> On Wed, Sep 28, 2011 at 11:53 PM, Linda Moya <lhmoya at cmu.edu> wrote:
>> Hello Alex,
>> Thank you for your very quick response. I think my question can be
>> answered by looking at the code for mne_process_raw (which I gather is
>> written in C, since I see no associated Matlab code, and it is an
>> executable).
>> The mne_process_raw program while executing at some point puts out:
>> ...
>> Data skip of 18000 samples in the beginning
>> ...
>> Event file is in the old format. Taking into account offset of 18000 samples
>> Read 118 events from valid_lh_target_run1_inp.eve
>> ...
>> where valid_lh_target_run1_inp.eve is one of the event files I created
>> (for the valid condition, left hemfield targets for the first run). So
>> yes, I do think I mean the raw.first_samp field.
>> The reason I want to know the exact answer to this question, is that I
>> both use mne_process_raw to average the MEG time-series data, AND I use
>> fiff_read_setup_read_raw and fiff_read_raw_segment to average the file
>> myself for the following reason:
>> 1) I re-reference the EEG data and then average it myself
>> 2) I conduct a wavelet analysis on each trial before averaging for both
>> the MEG and EEG data.
>> I want to be sure that I am averaging it the same way (taking the initial
>> skip into account) as mne_process_raw after I do these manipulations of
>> the data for EEG, and for the wavelet analysis for both MEG and EEG, when
>> I am doing the averaging myself. In all cases I use the same event files.
>> I have read the MNE manual for fiff_read_setup_read_raw and
>> fiff_read_raw_segment, but the info on these routines is cryptic and it is
>> unfortunately not clear to me exactly how to use these routines to
>> correctly account for the initial skip, in the same way as mne_browse_raw.
>> Again in both cases I use the same event files.
>> The answer to my question could probably be answered by looking at the C
>> code for mne_process_raw around the place where it outputs the statement
>> "Event file is in the old format. Taking into account offset ..." etc.
>> Somewhere in the vicinity would exist the code to take that into account.
>> If you don't want to read the code, would it be possible to send the C
>> code text file to me? I don't plan to do anything with it other than read
>> the code in the vicinity of that statement.
>> Please let me know how I can make my question more clear so that I can get
>> the answer that I need.
>> Thank you for your consideration.
>> Best Regards,
>> -- Linda Moya
>> On Wed, September 28, 2011 9:30 pm, Alexandre Gramfort wrote:
>> | Hello Linda,
>> |
>> | I've never had to deal with old event file format but I'll try to answer.
>> |
>> |> In using mne_process_raw to epoch and average across trials in a given
>> |> condition (output is a *.fif file for the given condition), the log output
>> |> states that my event file is in the the old format. So it says it is
>> |> taking into account the offset.
>> |
>> | by offset do you mean the raw.first_samp field?
>> |
>> |> First, how exactly does it take into account the offset? In other words
>> |> how does the sample start time ultimately used to index the raw fif file
>> |> differ from the sample start time specified in the event file?
>> |
>> | I guess in one case the first time point is 0 in the other it
>> corresponds to
>> | offset.
>> |
>> |> Second, how does the new format differ from the old format? The format I
>> |> am using is:
>> |> <sample>  <time>  <from> <to>
>> |>
>> |> where <sample> is a number, <time> turns out to always be sample/1000
>> |> <from> is 0 and <to> is the specific condition number.
>> |
>> | no clue.
>> |
>> |> I am creating my own event files, so that I can cut the data many
>> |> different ways not necessarily specified by the triggers in the raw fif
>> |> file, and want to make sure that the format is accurate.
>> |
>> | I would try with a simple dataset to see if the approach produces a
>> | nice evoked response.
>> |
>> | sorry for not being able to help more
>> |
>> | Alex
>> |
>> |
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>> --
>> Linda Moya, Ph.D.
>> Electrical and Computer Engineering
>> Center for the Neural Basis of Cognition
>> Carnegie Mellon University
>> http://www.andrew.cmu.edu/user/lhmoya/

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