[Mne_analysis] event file and noise covariance matrix

Junpeng.zhang@gmail.com junpeng.zhang at gmail.com
Wed Apr 3 05:04:32 EDT 2013
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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). 





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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