[Mne_analysis] averaging result: "nothing accepted"
Jeff Eriksen
eriksenj at ohsu.edu
Tue Apr 24 20:56:50 EDT 2012
Eric,
No, I have never got a log file produced.
I have to go home now and pack for a trip, but will try your suggestion
soon. Now I recall I tried something like it last week, but was not
successful then.
I will also look into the bmin/max issue.
Thanks,
-Jeff
On 4/24/12 5:30 PM, "Eric Larson" <larson.eric.d at gmail.com> wrote:
>I think you might have mentioned this in a previous email, but does it
>actually produce the "A1_ave_log.txt" log file? That file should
>record any trials that were rejected, but I'd be surprised if
>rejections were the issue.
>
>You could try running something like this (assuming the syntax is
>adjusted):
>
>mne_process_raw --raw
>/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_b
>cm_epc1.fif
>--ave /$WHATEVER_THE_CORRECT_PATH_IS/A1_ec1_bcm_epc1.ave --projon
>
>With the events (with and then without the dummy line I mentioned
>before) in a text file named A1_ec1_bcm_epc1.eve, in the directory
>where you're calling mne_process_raw. I believe this will cause MNE to
>ignore the events in the actual FIF while doing the averaging and
>instead use the text events read from the text file.
>
>Also, it just occurred to me that I've always used a "bmin" and "bmax"
>to set the baseline when doing averaging---it's possible MNE defaults
>to -200ms to 0ms for the baseline if you don't tell it otherwise, in
>which case I think your first epoch wouldn't be used because there is
>no data for the baseline time span.
>
>Eric
>
>
>On Tue, Apr 24, 2012 at 4:44 PM, Jeff Eriksen <eriksenj at ohsu.edu> wrote:
>> Eric et al.,
>>
>> I am using v2.7.3 on a Macintosh.
>> I verified that it does read the events in properly - if I use your
>> suggestion I get two events.
>> I left the single event in, and saved events in a -eve.fif file. Below
>>is
>> the result of the last mne_browse_raw session. I tried to average using
>> Process:Average, and all indications seem to confirm the event is in
>> there, but in the end is says "nave = 0".
>>
>> I wonder if there are some default rejection settings that are still in
>> effect and for some reason it is rejecting the epoch based on some
>> artifact criteria?
>>
>> Thanks,
>> -Jeff
>>
>> ********** Begin console output
>>
>>*************************************************************************
>>**
>> **
>> kje-macbook:MNE jefferiksen$ mne_browse_raw &
>> [1] 767
>> kje-macbook:MNE jefferiksen$ Using a 4096-point FFT in filtering of raw
>> data with 2048-sample tapers
>> bandpass = 0.0 ( 0.0) ... 40.0 ( 5.0) Hz
>> filter is on
>> 32-bit architecture. Using 1000.00 Mbytes for ring buffers
>> 9 selections loaded from /Users/jefferiksen/.mne/mne_browse_raw.sel
>> Current selection is GSN 1-16
>> Initial settings data created.
>>
>> --- Opening
>>
>>/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_
>>bc
>> m_epc1.fif ---
>>
>> No compensation data in
>>
>>/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_
>>bc
>> m_epc1.fif
>> Compensation in file : uncompensated
>> Setting up compensation data...
>> No compensation set. Nothing more to do.
>> No compensation was requested.
>> A new compensation value (uncompensated) was assigned to 0 MEG channels.
>> No SSS data in
>>
>>/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_
>>bc
>> m_epc1.fif
>> 0 bad channels read from
>>
>>/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_
>>bc
>> m_epc1.fif
>> filter : 0.000 ... 40.0 Hz bins : 0 ... 327 of 4097 hpw : 3 lpw :
>>20
>> Highpass filter will work as specified.
>> filter : 0.000 ... 40.0 Hz bins : 0 ... 327 of 4097 hpw : 3 lpw :
>>20
>> Highpass filter will work as specified.
>> Initial dc offsets determined
>> Raw data file
>>
>>/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_
>>bc
>> m_epc1.fif:
>> nchan = 257
>> nsamp = 900
>> sfreq = 1000.000 Hz
>> length = 0.900 sec
>> 1 events found in
>>
>>/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_
>>bc
>> m_epc1-eve.fif
>> Trigger channel : STI 014 max_event : 1
>> Annotation file
>>
>>/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_
>>bc
>> m_epc1-annot.fif containing 1 events read
>> No projection operator found in
>>
>>/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_
>>bc
>> m_epc1.fif
>> Average EEG reference projection added.
>>
>> --- Projection status ---
>>
>> # 1 : Average EEG reference : 1 vecs : 257 chs EEG active
>>
>> --- Complete ---
>>
>> Warning:
>> Name: scroll
>> Class: XmScrollBar
>> Specified slider size is greater than the maximum scrollbar
>> value minus the minimum scrollbar value.
>>
>> Average :
>> stim ignore : off
>> grad reject : off
>> 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
>> output file : A1_ec1_bcm_epc1-ave.fif
>> log file : A1_ave_log.txt
>> event file : A1_ec1_bcm_epc1.eve
>> ave1epoch :
>> t = 0.0 ... 900.0 ms
>> event = 1
>> ignore = 0
>>
>> Event file is in the new format
>> Read 1 events from A1_ec1_bcm_epc1.eve
>> ave1epoch : nave = 0
>> Saved 1 user-defined events to annotation file
>>
>>/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_
>>bc
>> m_epc1-annot.fif
>>
>> ******************* end console output
>>
>>*************************************************************************
>>**
>> ***
>>
>>
>> On 4/24/12 4:12 PM, "Eric Larson" <larson.eric.d at gmail.com> wrote:
>>
>>>Which version of MNE are you running? I think that one of the older
>>>versions of MNE didn't recognize the last event in a text file, which
>>>you could overcome by adding a dummy event line like this:
>>>
>>>changing the event file from:
>>>
>>>0 0 0 0 psuedo_event
>>>10 0.009 0 1 trigger1
>>>
>>>to:
>>>
>>>0 0 0 0 psuedo_event
>>>10 0.009 0 1 trigger1
>>>10 0.009 0 111 trigger1
>>>
>>>The choice of 111 as the trigger number here is arbitrary, it's just
>>>putting something there so the second-to-last line (important one)
>>>actually gets picked up.
>>>
>>>Eric
>>>
>>>On Tue, Apr 24, 2012 at 4:04 PM, Jeff Eriksen <eriksenj at ohsu.edu> wrote:
>>>> I have managed to insert one event into my EEG FIF file, which I want
>>>>to
>>>> average (yes, Nave = 1). I did this by importing a text file list of
>>>>events
>>>> using mne-browse-raw. I can see this event when I list them within
>>>> mne-browse-raw. When I try to average inside the GUI, I get a brief
>>>>display
>>>> of a window that goes by too fast to read, then the message "nothing
>>>> accepted"
>>>>
>>>> Any suggestions on debugging this? Some of my files are included
>>>>below.
>>>> Thanks,
>>>> -Jeff
>>>>
>>>> Here is the event file I created:
>>>>
>>>> # sample time from to text
>>>> 0 0 0 0 psuedo_event
>>>> 10 0.009 0 1 trigger1
>>>>
>>>> Here is the ave file I created:
>>>>
>>>> average {
>>>> outfile A1_ec1_bcm_epc1-ave.fif
>>>> eventfile A1_ec1_bcm_epc1.eve
>>>> logfile A1_ave_log.txt
>>>> category {
>>>> name ave1epoch
>>>> event 1
>>>> tmin 0.0
>>>> tmax 0.9
>>>> }
>>>> }
>>>>
>>>> Here is the console output of trying to average:
>>>>
>>>> Event file is in the new format
>>>> Read 1 events from A1_ec1_bcm_epc1.eve
>>>> test : nave = 0
>>>> Average :
>>>> stim ignore : off
>>>> grad reject : off
>>>> 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
>>>> output file : A1_ec1_bcm_epc1-ave.fif
>>>> log file : A1_ave_log.txt
>>>> event file : A1_ec1_bcm_epc1.eve
>>>> test :
>>>> t = 0.0 ... 900.0 ms
>>>> event = 1
>>>> ignore = 0
>>>>
>>>> Event file is in the new format
>>>> Read 1 events from A1_ec1_bcm_epc1.eve
>>>> test : nave = 0
>>>>
>>>>
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