[Mne_analysis] event file and noise covariance matrix

Matti Hamalainen msh at nmr.mgh.harvard.edu
Wed Apr 3 07:11:13 EDT 2013
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Jungpeng et al.

Just to clarify:

mne_browse_raw works well with other digitital trigger channels as well.
It is not necessary to enclose the channel name in quotes.
An event in mne_browse_raw/mne_process_raw is defined as a transition from value zero to something else. Such transitions do not exist in this measurement.
From the list, it looks like there is always 'offset' 192 present. This equals 128 + 64 = 192, which means that trigger lines 7 and 8 have been permanently up in your setup. 
Adding --digtrigmask 63 option should help to get the actual events out.

Best,
Matti

On Apr 3, 2013, at 5:04 AM, "Junpeng.zhang at gmail.com" <junpeng.zhang at gmail.com> wrote:

> Hi  Eric,
> 
> Thank you for your response!
> In fact, I input two command
> --digtrig 'STI101'  and --digtrig STI101
> and the results have no difference.
> mne_browse_raw recognized the modification since it responded,
> 
> Scanning STI101 for triggers...[done]
> 674 events found in /mnt/share/Huang_zhaoyang_MEG/Yang_Yingxue_MEG_data/MEG/MYB/mi_yu_bi_SEF_R_20120106_raw_tsss.fif
> 674 events written to /mnt/share/Huang_zhaoyang_MEG/Yang_Yingxue_MEG_data/MEG/MYB/mi_yu_bi_SEF_R_20120106_raw_tsss-eve.fif
> Trigger channel : STI101 max_event : 0
> 
> When I click the average button,  the response is,
> 
> single category :
> 	stim ignore : off
> 	grad reject : 2000.0 fT/cm
> 	mag  reject : off
> 	EEG  reject : off
> 	EOG  reject : off
> 	ECG  reject : off
> 	grad flat : off
> 	mag  flat : off
> 	EEG  flat : off
> 	EOG  flat : off
> 	ECG  flat : off
> 	Do not fix trigger skew
> 	Average to trigger # 1 :
> 		t = -200.0 ... 500.0 ms
> 		event = 1
> 		ignore = 0
> 		nave  = 0
> 
> Obviously, nothing is averaged.
> 
> I load the data into matlab using the following function (in which, the stim channel was changed to 'STI101' ),
> 
> [ data, times] =mne_ex_read_raw_01('mi_yu_bi_SEF_R_20120106_raw_tsss.fif',10,20);
> 
> Then,
> >> plot(data(307,1:1000))
> got the following pictures (307 th channels in data  is STI101).
> 
> <DD5C975E at 18BBDE65.A0F05B51.jpg>
> 
> The results confirm me that STI101 is the stim channels.
> 
> I also read the *-eve.fif created auto by mne_browse_raw,
> the result as following,
> 
> >> event=mne_read_events('mi_yu_bi_SEF_R_20120106_raw_tsss-eve.fif')
> 
> event =
> 
>        12128         192         193
>        12139         193         192
>        12726         192         194
>        12737         194         192
>        13273         192         194
>        13284         194         192
>        13925         192         193
>        13936         193         192
>        14478         192         193
>        14489         193         192
>        15050         192         193
>        15061         193         192
>        15651         192         194
>        15662         194         192
>        16163         192         193
>        16174         193         192
>        16747         192         194
>        16758         194         192
>        17395         192         194
>        17406         194         192
>        17956         192         193
>        17967         193         192
>        18460         192         193
>        18471         193         192
>        19094         192         193
>        19105         193         192
>        19763         192         193
>        19774         193         192
>        20397         192         194
>        20408         194         192
>        20934         192         193
>        20945         193         192
>        21435         192         193
>        21446         193         192
>        22119         192         194
>        22130         194         192
>        22738         192         194
>        22749         194         192
>        23385         192         194
>        23396         194         192
>        23923         192         194
>        23934         194         192
>        24613         192         194
>         ...               ...           ...
> 
> I guess that my raw data and --digtrig option are right.
> mne_browse_raw works well with stim channel = STI 014 and  may be not ready for a difference stim channels.
> 
> I also tried to change the Channel name 'STI101' to 'STI 014', but failed.
> 
> Anyone encountered the similar questions? How to correct the event recognizing problem?
> 
> Best wishes,
> Junpeng
> 
> ps,  the link to download the raw file, 
> http://share.kupan.me/download/index/?key=yLBcOrzZ42CSstiAvYHxJgTU3tL5dblMWXYKpyKtBmm3PFDkDlSmCLhGf2Ltd7fa4eUtNFXo1jsRY6cC&checkSum=6504a3f9d74441dfe848f804d72b91f0&type=1
> 
> 
> 
> ------------------ Original ------------------
> From:  "Eric Larson"<larson.eric.d at gmail.com>;
> Date:  Wed, Apr 3, 2013 11:51 AM
> To:  "Junpeng.zhang at gmail.com"<junpeng.zhang at gmail.com>;
> Cc:  "Alexandre Gramfort"<gramfort at nmr.mgh.harvard.edu>; "mne_analysis at nmr.mgh.harvard.edu"<mne_analysis at nmr.mgh.harvard.edu>;
> Subject:  Re: [Mne_analysis] event file and noise covariance matrix
> 
> Hey Junpeng,
> 
> I think I had to be careful with my use of quotation marks to get mne_process_raw to recognize the "STI101" stim channel. I /think/ it was:
> 
> --digtrig 'STI101'
> 
> that eventually worked. You can also try loading the raw data file in MATLAB or mne-python. There, all channel names are easily accessible, so you can then use them to get indices for the raw data to double-check that you have the correct channel name.
> 
> Eric
> 
> 
> 
> On Tue, Apr 2, 2013 at 8:14 PM, Junpeng.zhang at gmail..com <junpeng.zhang at gmail.com> wrote:
> Hi Alex,
> 
> As you guess, the engineer told me that the stim channel is STI101.
> I start using the command
> mne_browse_raw --digtrig STI101
> and then load the *sss.fif
> 
> The response is,
> 
> 674 events found in /mnt/share/Huang_zhaoyang_MEG/Yang_Yingxue_MEG_data/MEG/MYB/mi_yu_bi_SEF_R_20120106_raw_tsss-eve.fif
> Trigger channel : STI101 max_event : 0
> 
> in fact, the data is collected from an experiment: stimulus to the left and right median nerve and there should be two kinds of events.
> But when I click "show event list", the event list is blank!
> 
> The engineer told me that
> 
> The left wrist stimulus in STI101 is 192, and right is 194. But why the response is max_event =0?
> 
> I also tried to click the average button to average the data over event 1 or 2,
> and the response as,
> 
> Single category :
> 	stim ignore : off
> 	grad reject : 2000.0 fT/cm
> 	mag reject : off
> 	EEG reject : off
> 	EOG reject : off
> 	ECG reject : off
> 	grad flat : off
> 	mag flat : off
> 	EEG flat : off
> 	EOG flat : off
> 	ECG flat : off
> 	Do not fix trigger skew
> 	Average to trigger # 1 :
> 		t = -200.0 .... 500.0 ms
> 		event = 1
> 		ignore = 0
> 		nave = 0
> 
> 
> Would you like to help me figure out it?
> 
> Best wishes,
> Junpeng
> 
> 
> 
> 
> 
> 
> ------------------ Original ------------------
> From: "Alexandre Gramfort"<gramfort at nmr.mgh.harvard.edu>;
> Date: Tue, Apr 2, 2013 03:00 PM
> To: "Junpeng.zhang at gmail.com"<junpeng.zhang at gmail.com>;
> Cc: "mne_analysis at nmr.mgh.harvard.edu"<mne_analysis at nmr.mgh.harvard.edu>;
> Subject: Re: [Mne_analysis] event file and noise covariance matrix
> 
> hi Junpeng,
> 
> what you need to average in an event file (-eve.fif file) or a stim channel..
> 
> You can start mne_browse_raw with the --digtrig option to set a specific channel
> if different from STI014.
> 
> HTH
> Alex
> 
> On Tue, Apr 2, 2013 at 6:31 AM, Junpeng.zhang at gmail.com
> <junpeng.zhang at gmail.com> wrote:
> > Hi Experts,
> >
> > My coauthor sent to me a *sss.fif.
> > I would use it to do research.
> > My questions are,
> >
> > I only loaded the file into mne_browse_raw,
> > but I found I can not do average operations.
> > Anyone know what additional file is needed to conduct average?
> > The engineer who operates the MEG device may not use MNE toolbox, but he
> > used maxfilter.
> > So should I tell him which additional files I need to conduct average or
> > calculation of noise covariance matrix?
> > assume that he could use all the software associated with eketa MEG device
> > and never use mne toolbox and that I need the files he created to conduct
> > average and calculation of noise covariance matrix.
> >
> > Please laugh at my so simple questions :).
> >
> > Thank you all in advance.
> > Junpeng
> >
> >
> >
> >
> >
> >
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---------

Matti Hamalainen, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital

msh at nmr.mgh.harvard.edu
mhamalainen at partners.org






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